Contacts of the helix formed by residues 108 - 127 (chain B) in PDB entry 2BKU
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 GLU 108 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 3.6 45.1 - - + +
58B ARG* 5.6 0.2 - - - +
106B SER* 2.8 18.3 + - - +
107B ILE* 1.3 82.4 - - + +
109B PRO* 1.3 78.9 - - - +
110B ARG* 4.5 7.4 + - - +
111B ILE* 3.1 24.0 + - + +
112B ALA 3.3 8.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B SER 5.1 1.1 - - - +
107B ILE 3.3 10.5 - - - +
108B GLU* 1.3 94.5 - - - +
110B ARG* 1.3 63.9 + - + +
112B ALA* 3.2 3.4 + - + -
113B ASN* 2.8 38.6 + - - +
153B ARG* 3.4 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ILE* 4.8 3.4 - - - +
82A GLN* 2.8 49.0 - - - +
111A VAL* 4.4 18.6 + - - +
113A GLU* 6.0 7.6 - - - +
55B LEU* 3.8 24.6 - - + +
56B GLU* 5.3 0.8 - - - +
59B ILE* 3.5 51.3 - - + +
108B GLU* 3.4 9.0 + - - +
109B PRO* 1.3 82.4 - - + +
111B ILE* 1.3 59.3 + - - +
113B ASN* 3.8 13.1 - - - +
114B ALA* 3.4 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 4.1 19.4 - - + +
55B LEU* 3.6 28.0 - - + -
58B ARG* 3.1 52.3 - - + +
59B ILE* 4.5 9.9 - - + +
103B ALA* 3.8 19.1 - - + +
106B SER* 3.9 9.0 - - - +
108B GLU* 3.1 25.3 + - + +
110B ARG* 1.3 77.6 - - - +
112B ALA* 1.3 59.0 + - - +
114B ALA* 3.3 5.0 + - - +
115B ALA* 2.9 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ALA 3.4 12.8 - - - +
104B LEU* 3.2 29.5 - - - +
106B SER 4.4 8.1 - - - +
108B GLU 3.3 8.3 + - - +
109B PRO* 3.2 8.8 + - + +
111B ILE* 1.3 78.5 - - - +
113B ASN* 1.3 55.5 + - - +
115B ALA* 3.2 1.4 + - - +
116B ALA* 2.6 36.4 + - - +
150B ASN 5.8 0.2 - - - +
153B ARG* 4.0 4.9 - - - +
154B ALA* 3.6 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ARG 4.6 14.9 - - - +
113A GLU* 5.5 2.9 - - - +
109B PRO* 2.8 23.9 + - - +
110B ARG* 3.8 13.0 - - - +
112B ALA* 1.3 76.4 - - - +
114B ALA* 1.3 62.7 + - - +
116B ALA* 3.2 5.0 + - - +
117B GLN* 3.1 28.3 + - - +
153B ARG* 3.0 35.3 + - - +
154B ALA* 5.1 0.4 - - - +
157B LEU* 3.3 21.1 - - + +
161B TYR* 4.2 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 5.2 0.7 - - + -
59B ILE* 4.0 26.2 - - + +
62B ALA* 3.7 23.4 - - + +
63B LEU* 4.3 6.5 - - + +
110B ARG 3.4 11.4 + - - +
111B ILE* 3.3 8.8 + - - +
113B ASN* 1.3 78.7 - - - +
115B ALA* 1.3 62.7 + - - +
117B GLN* 3.1 17.5 + - - +
118B LEU* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 4.5 5.1 - - + +
62B ALA* 4.3 4.0 - - - +
100B ALA* 3.6 6.7 - - - +
103B ALA* 3.6 14.6 - - + -
104B LEU* 3.4 29.8 - - - +
111B ILE 2.9 17.5 + - - +
112B ALA 3.5 3.6 - - - +
114B ALA* 1.3 77.3 - - - +
116B ALA* 1.3 56.0 + - - +
118B LEU* 3.3 7.4 + - - +
119B ILE* 2.9 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU* 3.9 17.6 - - + +
112B ALA 2.6 17.7 + - - +
113B ASN 3.2 11.9 - - - +
115B ALA* 1.3 74.5 - - - +
117B GLN* 1.3 60.3 + - - +
119B ILE* 3.6 3.1 + - - +
120B ALA* 3.1 24.1 + - - +
154B ALA 3.9 11.9 - - - +
157B LEU* 4.1 5.6 - - + -
158B ALA* 3.9 19.3 - - + +
161B TYR* 4.0 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ASP* 4.0 4.5 - - - +
107A ASP 5.7 0.2 - - - +
110A ARG* 3.7 45.7 + - - +
111A VAL* 4.3 6.7 - - - +
63B LEU* 3.3 25.7 - - + +
66B LYS* 3.8 33.0 + - + +
113B ASN* 3.1 20.2 + - - +
114B ALA* 3.1 12.5 + - - +
116B ALA* 1.3 75.9 - - - +
118B LEU* 1.3 58.0 + - - +
120B ALA* 3.5 4.6 + - - +
121B ALA* 3.1 27.0 + - - +
161B TYR* 3.6 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B SER 6.3 0.4 - - - -
45B SER* 5.6 3.4 - - - -
48B LEU* 4.3 17.7 - - + -
62B ALA* 4.0 25.1 - - + +
65B LEU* 3.8 28.7 - - + -
66B LYS* 4.2 11.2 - - - +
69B LEU* 3.5 28.9 - - + -
96B ILE* 5.1 3.6 - - + -
100B ALA* 4.7 10.3 - - + -
114B ALA 3.0 16.1 + - - +
115B ALA* 3.8 4.9 - - - +
117B GLN* 1.3 74.3 - - - +
119B ILE* 1.3 65.4 + - - +
121B ALA* 3.2 4.6 + - - +
122B ILE* 2.9 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ALA* 3.8 22.4 - - + +
101B LEU* 3.9 14.6 - - + -
104B LEU* 3.6 42.4 - - + -
115B ALA 2.9 21.2 + - - +
116B ALA* 3.8 5.2 - - - +
118B LEU* 1.3 76.1 - - - +
120B ALA* 1.3 56.0 + - - +
122B ILE* 3.3 3.1 + - - -
123B ALA* 2.9 27.0 + - - +
132B TRP* 3.7 27.9 - - + -
135B LEU* 4.0 9.0 - - + -
139B MET* 4.8 1.8 - - + -
158B ALA* 5.0 0.7 - - + -
162B MET* 4.0 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ALA 3.1 18.9 + - - +
117B GLN* 3.6 5.8 - - - +
118B LEU 3.3 0.2 - - - -
119B ILE* 1.3 76.4 - - - +
121B ALA* 1.3 57.2 + - - +
123B ALA* 3.2 2.9 + - - +
124B ASP* 2.9 36.3 + - - +
158B ALA 4.6 1.6 - - - +
161B TYR* 3.7 28.0 - - + +
162B MET* 3.9 23.9 - - - +
165B SER* 4.9 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LYS* 3.6 23.8 - - + -
69B LEU* 4.2 15.7 - - + +
70B VAL* 4.2 15.5 - - + +
117B GLN 3.1 13.9 + - - +
118B LEU* 3.2 9.2 + - - +
120B ALA* 1.3 75.9 - - - +
122B ILE* 1.3 62.3 + - - +
124B ASP* 3.3 24.4 + - - +
125B ILE* 3.5 13.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 3.7 20.4 - - + -
84B TRP* 3.7 33.7 - - + +
96B ILE* 4.0 23.6 - - + -
97B LYS* 4.3 11.9 - - + -
100B ALA* 5.0 3.4 - - + -
118B LEU* 2.9 36.1 + - + +
119B ILE* 4.9 0.7 - - - -
121B ALA* 1.3 75.1 - - - +
123B ALA* 1.3 62.3 - - - +
125B ILE* 3.2 8.8 + - - +
126B GLU* 3.0 27.1 + - - +
132B TRP* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ILE 2.9 16.6 + - - +
120B ALA 3.2 5.8 + - - +
122B ILE* 1.3 74.5 - - - +
124B ASP* 1.3 65.5 - - - +
126B GLU* 4.5 0.7 - - - +
127B LEU* 3.0 42.7 + - + +
128B PRO* 3.7 0.3 - - - +
132B TRP* 4.1 6.9 - - - -
135B LEU* 3.8 18.8 - - + -
162B MET* 3.8 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B VAL* 3.9 20.1 - - + +
120B ALA 2.9 20.0 + - - +
121B ALA* 3.5 15.3 - - - +
122B ILE 3.3 0.4 - - - -
123B ALA* 1.3 75.9 - - - +
125B ILE* 1.3 60.5 + - + +
128B PRO* 3.1 26.2 - - - +
162B MET 4.1 5.9 - - - +
165B SER* 2.8 47.2 + - - +
166B ALA* 4.2 3.9 + - - +
167B ASP* 3.8 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 3.4 55.0 - - + +
70B VAL* 6.1 0.9 - - + -
77B THR* 6.6 0.4 - - + -
80B PHE 4.2 0.4 - - - +
81B ALA* 3.8 35.5 - - + +
84B TRP* 3.6 33.0 - - + -
85B ILE* 4.1 11.0 - - + +
121B ALA 3.5 9.4 + - - +
122B ILE* 3.2 9.3 + - - +
123B ALA 3.2 0.4 - - - -
124B ASP* 1.3 81.5 - - + +
126B GLU* 1.3 58.1 + - + +
128B PRO* 3.7 2.1 - - - +
129B HIS* 3.4 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B TRP* 2.8 34.7 + - + +
85B ILE* 5.6 3.4 - - + -
93B LYS* 3.4 21.4 - - - +
97B LYS* 2.5 38.4 + - - -
122B ILE* 3.0 16.9 + - - +
123B ALA* 5.0 0.7 - - - -
125B ILE* 1.3 77.3 - - + +
127B LEU* 1.3 63.3 + - - +
128B PRO* 3.4 2.9 - - - -
129B HIS* 3.1 10.3 + - - -
131B ALA* 3.0 42.7 + - + +
132B TRP* 3.4 15.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ALA* 3.0 37.2 + - + +
126B GLU* 1.3 74.5 - - - +
128B PRO* 1.3 68.6 - - + +
130B GLY* 2.9 14.6 + - - -
131B ALA 3.6 9.4 - - - +
132B TRP* 3.5 28.7 - - + +
133B PRO* 5.5 0.4 - - + -
135B LEU* 4.3 11.9 - - + -
136B MET* 4.1 19.1 - - + -
162B MET* 4.9 3.4 - - + -
172B ALA* 5.2 19.8 + - + +
173B LEU* 4.0 39.3 - - + +
----------------------------------------------------------
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