Contacts of the helix formed by residues 125 - 150 (chain Q) in PDB entry 2BKC
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 125 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Q THR* 3.5 21.5 - - - +
63Q ARG* 2.9 26.8 + - - -
67Q ILE* 4.1 8.8 - - - +
120Q THR* 3.2 18.5 + - - +
123Q GLU* 3.2 5.7 + - + +
124Q GLY* 1.3 73.3 - - - +
126Q ASP* 1.3 63.6 + - - +
127Q VAL 3.8 0.7 + - - -
128Q THR* 2.5 29.9 + - - -
129Q ASN* 3.2 22.7 + - - +
136U LYS* 5.4 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 126 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121Q ASP* 5.6 1.6 - - - +
124Q GLY* 3.2 11.9 + - - +
125Q ASP* 1.3 72.9 + - - +
127Q VAL* 1.3 58.6 + - + +
129Q ASN* 3.5 9.6 - - - +
130Q ASP* 3.1 27.5 + - - +
114U LYS* 2.8 33.1 + - - +
117U ILE* 3.5 21.2 - - + +
133U ILE* 3.6 31.8 - - + +
136U LYS* 5.7 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 127 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63Q ARG* 3.3 41.3 - - - +
125Q ASP* 3.3 0.8 + - - -
126Q ASP* 1.3 78.4 - - + +
128Q THR* 1.3 62.1 + - - +
130Q ASP* 3.3 3.8 + - - +
131Q MET* 3.2 23.4 + - + +
133U ILE* 3.7 30.1 - - + +
136U LYS* 3.8 30.5 - - + +
137U ALA* 3.7 24.5 - - + +
140U ASP* 4.0 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 128 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Q THR* 4.0 4.2 - - + +
13Q LEU* 3.6 37.3 - - + +
63Q ARG* 3.1 21.7 + - - +
67Q ILE* 4.7 0.2 - - - +
120Q THR* 3.7 14.4 - - - +
125Q ASP* 2.5 31.8 + - - -
127Q VAL* 1.3 73.7 - - - +
129Q ASN* 1.3 61.6 + - - +
131Q MET* 3.4 12.3 + - + +
132Q LEU* 3.0 34.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 129 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117Q ILE* 3.0 40.0 + - - +
120Q THR* 3.0 23.4 - - + +
121Q ASP* 3.7 17.8 + - - +
125Q ASP 3.2 11.8 + - - +
126Q ASP* 3.5 9.8 - - - +
128Q THR* 1.3 78.1 - - - +
130Q ASP* 1.3 63.6 + - - +
132Q LEU* 3.5 3.4 + - - +
133Q ILE* 3.2 42.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 130 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130M ASP* 3.4 23.0 - - - +
126Q ASP 3.1 17.2 + - - +
127Q VAL 3.7 4.9 - - - +
128Q THR 3.3 0.4 - - - -
129Q ASN* 1.3 78.8 + - - +
131Q MET* 1.3 65.5 + - - +
133Q ILE* 3.1 18.2 + - - +
134Q ALA* 3.1 14.4 + - - +
130U ASP* 3.9 10.1 - - - +
133U ILE* 4.1 17.9 - - + +
134U ALA* 5.6 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 131 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13Q LEU* 4.5 4.5 - - + -
59Q GLU* 3.8 22.9 - - + +
60Q VAL* 4.2 13.5 - - + -
63Q ARG* 4.0 27.4 - - + -
127Q VAL* 3.2 17.3 + - + +
128Q THR* 3.7 10.1 - - + +
130Q ASP* 1.3 79.0 + - - +
132Q LEU* 1.3 79.4 + - + +
134Q ALA* 3.4 6.5 + - - +
135Q PHE* 3.2 61.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Q PHE* 4.1 25.4 - - + -
13Q LEU* 4.4 5.8 - - + -
16Q GLN* 5.8 0.9 - - + -
60Q VAL* 5.4 2.9 - - + -
113Q TYR* 4.0 21.6 - - + +
116Q GLY 3.6 30.7 - - - +
117Q ILE* 3.6 17.6 - - + +
120Q THR* 4.3 4.9 - - + +
128Q THR* 3.0 30.3 + - + +
129Q ASN 3.9 2.2 - - - +
130Q ASP 3.3 0.2 - - - -
131Q MET* 1.3 97.2 - - + +
133Q ILE* 1.3 62.6 + - - +
135Q PHE* 3.4 15.1 + - + +
136Q LYS* 2.9 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 133 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126M ASP* 3.7 42.8 - - + +
127M VAL* 3.7 16.5 - - + +
130M ASP* 4.0 20.0 - - + +
117Q ILE* 3.8 24.2 - - + -
129Q ASN* 3.2 36.7 + - - +
130Q ASP* 3.1 12.2 + - - +
132Q LEU* 1.3 77.2 - - - +
134Q ALA* 1.3 57.4 + - - +
136Q LYS* 3.0 6.0 + - - +
137Q ALA* 2.9 24.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 134 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130M ASP* 5.7 4.9 - - - +
130Q ASP* 3.1 16.6 + - - +
131Q MET* 3.4 6.7 + - - +
133Q ILE* 1.3 78.8 - - - +
135Q PHE* 1.3 67.3 + - + +
137Q ALA* 3.3 16.3 + - - +
138Q SER* 3.3 13.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 135 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56Q GLN* 3.4 40.6 + - + +
59Q GLU* 3.2 37.5 - - + -
60Q VAL* 3.8 22.9 - - + -
113Q TYR* 3.4 26.5 - + + -
131Q MET* 3.2 43.5 + - + -
132Q LEU* 3.6 10.1 - - + +
133Q ILE 3.2 0.2 - - - -
134Q ALA* 1.3 78.5 - - + +
136Q LYS* 1.3 65.5 + - - +
138Q SER* 3.3 5.6 + - - -
139Q ILE* 3.1 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 136 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63M ARG* 4.3 6.7 - - - +
125M ASP* 5.3 2.0 + - - -
126M ASP* 5.9 3.0 - - + +
127M VAL* 4.0 15.7 - - + +
110Q ARG* 4.0 36.9 - - + +
113Q TYR* 4.3 9.2 - - + -
114Q LYS* 4.5 21.8 - - + +
117Q ILE* 4.0 22.2 - - + -
132Q LEU 2.9 14.7 + - - +
133Q ILE 3.4 9.0 - - - +
135Q PHE* 1.3 76.7 - - - +
137Q ALA* 1.3 62.4 + - - +
139Q ILE* 3.9 5.5 - - - +
140Q ASP* 2.9 50.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 137 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63M ARG* 5.2 1.0 + - - -
127M VAL* 3.2 34.5 - - + +
133Q ILE* 2.9 10.3 + - + +
134Q ALA* 3.5 13.2 - - - +
135Q PHE 3.1 0.6 - - - -
136Q LYS* 1.3 78.4 - - - +
138Q SER* 1.3 60.1 + - - +
140Q ASP* 3.6 4.6 + - - +
141Q LYS* 3.2 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 138 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52Q GLU* 2.4 30.9 + - - -
56Q GLN* 5.0 2.3 + - - -
134Q ALA 3.3 8.0 + - - -
135Q PHE* 3.3 9.0 + - - -
137Q ALA* 1.3 77.4 - - - +
139Q ILE* 1.3 66.2 + - - +
141Q LYS* 2.9 17.1 + - - +
142Q HIS* 3.0 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 139 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53Q PHE* 3.9 32.5 - - + -
56Q GLN* 4.3 2.7 - - - +
106Q LEU* 3.6 31.6 - - + +
109Q LEU* 4.3 16.4 - - + -
110Q ARG* 3.9 12.3 - - + +
113Q TYR* 3.8 31.2 - - + -
135Q PHE 3.1 18.1 + - - +
136Q LYS* 3.9 5.4 - - - +
138Q SER* 1.3 73.7 - - - +
140Q ASP* 1.3 63.2 + - - +
142Q HIS* 3.2 11.3 + - - +
143Q ILE* 3.0 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 140 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63M ARG* 3.0 27.6 + - - +
66M ALA* 3.9 20.8 - - + +
127M VAL* 4.0 1.6 - - - +
110Q ARG* 3.3 33.1 + - - +
136Q LYS* 2.9 46.2 + - - +
137Q ALA 3.6 6.1 - - - +
139Q ILE* 1.3 77.0 - - - +
141Q LYS* 1.3 60.3 + - - +
143Q ILE* 3.3 7.8 + - - +
144Q TRP* 3.2 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 141 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62M GLU* 2.8 34.8 + - + +
66M ALA* 4.6 7.8 - - + +
137Q ALA 3.2 10.3 + - - +
138Q SER* 2.9 13.2 + - - +
140Q ASP* 1.3 80.5 - - - +
142Q HIS* 1.3 62.3 - - + +
144Q TRP* 3.3 22.2 + - + +
145Q MET* 3.2 41.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 142 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45Q LYS* 4.3 4.7 + - - -
48Q ASP* 6.5 0.4 - - + -
49Q LEU* 3.6 29.5 - - + +
52Q GLU* 2.8 26.7 + - - -
53Q PHE* 4.3 11.4 - + - -
106Q LEU* 3.7 18.4 - - + -
138Q SER* 3.0 35.2 + - - -
139Q ILE* 3.7 9.4 - - - +
141Q LYS* 1.3 73.7 - - + +
143Q ILE* 1.3 60.7 + - - +
145Q MET* 3.2 26.4 + - + +
146Q PHE* 2.9 43.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 143 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103Q VAL* 4.6 9.6 - - + +
106Q LEU* 3.8 33.7 - - + +
107Q GLU* 4.1 14.4 - - + +
110Q ARG* 4.2 28.5 - - - +
139Q ILE* 3.0 38.5 + - + +
140Q ASP* 3.7 7.0 - - - +
141Q LYS 3.2 0.2 - - - -
142Q HIS* 1.3 74.7 - - - +
144Q TRP* 1.3 65.4 + - - +
146Q PHE* 5.1 1.1 - - - -
147Q LYS* 3.0 36.0 + - + +
154Q PRO* 3.7 27.1 - - + +
155Q LEU* 5.4 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 144 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62M GLU* 3.8 45.5 - - + -
65M LEU* 3.7 38.9 - - + +
66M ALA* 4.0 17.0 - - + -
31O HIS* 4.7 15.9 - + - -
32O TRP* 4.4 9.8 + - - -
34O MET 5.7 0.4 + - - -
39O PHE* 3.9 26.1 - + - -
140Q ASP 3.2 12.3 + - - +
141Q LYS* 3.3 20.2 + - + +
143Q ILE* 1.3 77.9 - - - +
145Q MET* 1.3 78.1 + - + +
147Q LYS* 3.8 1.7 - - - +
148Q ALA* 2.9 32.7 + - + +
152Q LYS 4.9 0.3 - - - +
154Q PRO* 4.2 27.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 145 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39O PHE* 3.5 35.9 - - + -
40O PHE* 4.0 10.7 - - + -
45Q LYS* 3.2 31.4 - - - +
141Q LYS* 3.2 25.5 + - + +
142Q HIS* 3.2 34.3 + - + +
144Q TRP* 1.3 97.5 - - + +
146Q PHE* 1.3 61.0 + - + +
148Q ALA* 3.3 2.8 + - - +
149Q PHE* 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 146 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40O PHE* 3.7 28.9 - + - -
42Q LEU* 4.6 2.9 - - + -
45Q LYS* 4.1 17.5 - - + -
46Q MET* 4.0 13.7 - - + -
49Q LEU* 4.0 29.8 - - + -
99Q MET* 4.0 22.2 - - + +
102Q LEU* 4.0 16.6 - - + -
103Q VAL* 3.5 22.2 - - + -
106Q LEU* 4.1 4.7 - - + -
142Q HIS* 2.9 51.6 + - + +
145Q MET* 1.3 70.1 - - + +
147Q LYS* 1.3 65.1 + - - +
149Q PHE* 3.2 8.3 + + + +
150Q LEU* 3.1 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 147 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103Q VAL* 3.9 21.1 - - + +
107Q GLU* 3.4 22.8 + - - -
143Q ILE* 3.0 23.1 + - + +
144Q TRP 3.9 2.2 - - - +
146Q PHE* 1.3 76.7 - - - +
148Q ALA* 1.3 61.3 + - - +
150Q LEU* 3.0 17.6 + - + +
152Q LYS* 2.9 46.5 + - + +
153Q ALA 3.3 14.6 - - - +
154Q PRO* 3.4 24.0 + - + +
155Q LEU 4.1 2.0 - - - -
156Q GLU 2.9 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34O MET 4.0 1.1 - - - +
35O ARG* 3.6 17.1 - - + +
36O GLY 3.1 18.1 + - - -
39O PHE* 3.6 28.0 - - + -
144Q TRP* 2.9 26.8 + - + +
145Q MET 3.6 5.4 - - - +
146Q PHE 3.3 0.2 - - - -
147Q LYS* 1.3 75.0 - - - +
149Q PHE* 1.3 56.9 + - - +
151Q GLY* 2.9 18.2 + - - -
152Q LYS 3.5 9.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 149 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36O GLY* 3.3 25.4 - - - -
37O HIS* 3.3 56.5 + + - -
39O PHE* 4.2 4.4 - - + +
40O PHE* 3.9 28.7 - + + -
38Q ASN* 4.2 11.9 - - + -
41Q THR* 5.9 0.7 - - - -
42Q LEU* 3.3 30.1 - - + -
95Q MET* 4.5 5.2 - - + -
96Q ASP* 3.9 17.9 - - - -
99Q MET* 3.9 25.8 - - + -
145Q MET 2.9 14.0 + - - +
146Q PHE* 3.4 10.5 - + - +
148Q ALA* 1.3 75.6 - - - +
150Q LEU* 1.3 69.1 + - + +
151Q GLY 3.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37O HIS* 5.5 0.4 - - - -
96Q ASP* 4.0 33.9 - - + +
99Q MET* 3.9 24.7 - - + +
100Q GLU* 4.2 21.8 - - + +
103Q VAL* 4.1 21.8 - - + -
146Q PHE 3.1 18.0 + - - +
147Q LYS* 3.0 18.2 + - + +
149Q PHE* 1.3 81.4 - - + +
151Q GLY* 1.3 59.8 + - - +
152Q LYS* 3.2 21.2 + - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il