Contacts of the helix formed by residues 134 - 152 (chain A) in PDB entry 5J13
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 THR 134 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLY 4.3 2.6 + - - -
133A THR* 1.3 78.2 - - - +
135A ASN* 1.3 58.8 + - - +
136A LYS* 3.4 9.6 + - - +
137A CYS* 2.9 33.7 + - - +
138A LEU* 2.9 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A THR* 1.3 73.8 - - - +
136A LYS* 1.3 58.9 + - - +
138A LEU* 3.6 14.9 + - + +
139A GLU* 3.1 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLY* 3.0 32.2 - - - +
90A CYS* 4.3 2.9 - - - +
134A THR* 3.1 6.3 + - - +
135A ASN* 1.3 78.5 - - - +
137A CYS* 1.3 60.3 + - - +
139A GLU* 3.9 7.9 + - - +
140A GLN* 3.4 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A TYR* 4.2 14.4 - - - +
90A CYS* 2.0 53.1 - - - -
91A ALA* 4.2 3.6 - - - -
93A LEU* 4.7 5.2 - - + -
133A THR* 5.0 1.3 - - - -
134A THR* 2.9 33.1 + - - +
136A LYS* 1.3 77.6 - - - +
138A LEU* 1.3 58.8 + - - +
139A GLU 3.2 0.2 - - - -
140A GLN* 3.2 3.0 + - - +
141A VAL* 3.0 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A TYR* 4.3 19.7 - - + +
55A MET* 3.6 31.1 - - + +
56A SER* 5.6 3.6 - - - +
133A THR* 4.4 16.2 - - - +
134A THR* 2.9 22.5 + - - +
135A ASN* 4.0 14.8 - - + +
137A CYS* 1.3 74.0 - - - +
139A GLU* 1.3 60.2 + - + +
142A SER* 3.0 29.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ASN* 3.1 19.4 + - + +
136A LYS* 3.9 9.0 - - - +
137A CYS 3.2 0.2 - - - -
138A LEU* 1.3 78.9 - - + +
140A GLN* 1.3 59.1 + - - +
142A SER* 2.6 22.8 + - - -
143A GLN* 3.2 17.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 2.9 49.6 + - + +
85A ASN 4.4 5.3 + - - -
87A THR* 3.0 35.7 + - - +
90A CYS* 3.3 20.8 - - - +
91A ALA 5.3 1.4 + - - -
93A LEU* 4.1 10.7 - - + +
136A LYS 3.4 10.4 + - - +
137A CYS* 3.2 10.6 + - - +
139A GLU* 1.3 80.2 - - - +
141A VAL* 1.3 57.8 + - - +
143A GLN* 3.2 11.0 + - - +
144A LEU* 3.1 23.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 3.4 29.2 - - + +
54A TYR* 3.7 25.6 - - + -
55A MET* 3.5 29.8 - - + -
93A LEU* 3.8 25.6 - - + -
98A PHE* 4.0 8.1 - - + -
137A CYS 3.0 18.6 + - - +
140A GLN* 1.3 73.5 - - - +
142A SER* 1.3 59.9 + - - +
144A LEU* 3.1 8.6 + - + +
145A GLN* 3.0 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A MET* 4.0 8.5 - - - -
60A SER* 3.4 24.7 + - - -
65A ASN* 5.6 0.3 - - - +
138A LEU 3.0 14.0 + - - -
139A GLU* 2.6 27.9 + - - -
141A VAL* 1.3 74.1 - - - +
143A GLN* 1.3 69.1 + - - +
144A LEU 3.1 0.2 - - - -
145A GLN* 3.3 12.2 + - - -
146A GLY* 3.2 15.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASN 3.2 24.6 + - - -
65A ASN* 3.8 13.6 - - - +
66A THR* 3.2 43.1 + - - +
67A VAL* 3.4 20.8 + - + +
82A LEU* 4.0 13.9 - - + -
139A GLU* 3.2 16.9 + - - +
140A GLN* 3.4 11.2 - - - +
142A SER* 1.3 85.2 + - - +
144A LEU* 1.3 56.7 + - - +
146A GLY* 3.1 3.4 + - - +
147A LEU* 3.0 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 4.6 3.6 - - + -
79A ILE* 3.8 31.2 - - + -
82A LEU* 3.8 19.0 - - + +
83A THR* 3.3 34.8 - - - +
93A LEU* 4.9 2.0 - - + -
98A PHE* 3.6 30.3 - - + -
140A GLN 3.1 12.2 + - - +
141A VAL* 3.1 19.5 - - + +
142A SER 3.1 0.4 - - - -
143A GLN* 1.3 75.1 - - - +
145A GLN* 1.3 63.3 + - - +
147A LEU* 3.3 7.5 + - + +
148A TRP* 3.1 38.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TYR* 4.5 7.4 + - - +
51A LEU* 4.1 23.3 - - + +
52A ILE* 3.7 24.4 - - - +
55A MET* 3.5 30.6 - - - +
58A THR 3.4 20.1 + - - +
59A LYS* 4.1 8.4 - - + +
60A SER* 3.5 28.1 + - - +
141A VAL 3.0 12.9 + - - +
142A SER* 3.3 9.3 + - - +
144A LEU* 1.3 76.5 - - - +
146A GLY* 1.3 57.0 + - - +
148A TRP* 3.4 6.9 + - - +
149A ARG* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A SER* 4.4 8.5 - - - -
65A ASN* 5.1 9.6 - - - -
142A SER 3.2 7.3 + - - -
143A GLN* 3.1 8.9 + - - -
145A GLN* 1.3 77.7 - - - +
147A LEU* 1.3 64.3 + - - +
149A ARG* 3.4 10.3 + - - +
150A ARG* 3.2 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 4.2 7.9 - - + +
68A SER* 3.5 42.6 - - - +
69A CYS* 3.8 18.5 - - + -
75A CYS* 4.1 1.0 - - - +
78A GLU* 3.8 28.7 - - + -
79A ILE* 3.8 18.4 - - + +
82A LEU* 3.8 29.4 - - + -
143A GLN 3.0 15.6 + - - +
144A LEU* 3.3 9.6 + - + +
146A GLY* 1.3 77.3 - - - +
148A TRP* 1.3 56.2 + - - +
150A ARG* 3.2 5.6 + - - +
151A PHE* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 3.8 24.9 - - + -
43A TYR* 3.5 47.3 - + + +
47A ILE* 4.1 26.8 - - + +
51A LEU* 3.7 23.1 - - + +
76A LEU* 4.5 4.9 - - + -
79A ILE* 3.8 39.0 - - + +
83A THR* 5.4 0.4 + - - -
98A PHE* 6.1 1.2 - - - -
102A THR* 4.2 14.7 + - + -
105A ALA* 5.9 0.7 - - + -
106A LEU* 5.9 1.3 - - + -
144A LEU* 3.1 33.7 + - + +
145A GLN* 3.7 4.3 - - - +
146A GLY 3.3 0.2 - - - -
147A LEU* 1.3 75.4 - - - +
149A ARG* 1.3 58.1 + - - +
151A PHE* 3.2 31.9 + + - +
152A ASN* 2.9 37.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TYR* 4.9 4.0 + - - +
59A LYS* 6.2 3.4 - - - -
60A SER 5.3 8.7 - - - -
145A GLN 3.0 15.8 + - - +
146A GLY* 3.5 13.9 - - - +
148A TRP* 1.3 75.9 - - - +
150A ARG* 1.3 64.2 + - + +
152A ASN* 3.3 15.1 + - - +
153A ARG* 3.5 14.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A SER* 3.5 20.5 + - - +
69A CYS* 2.9 38.2 + - - +
75A CYS* 4.3 0.2 - - - -
146A GLY 3.2 16.4 + - - +
147A LEU* 3.2 7.2 + - - +
149A ARG* 1.3 74.1 - - + +
151A PHE* 1.3 65.0 + - - +
153A ARG* 3.1 57.6 + - - +
103C PRO* 3.9 8.1 - - - +
104C GLN 2.6 31.3 + - - -
105C TRP* 3.2 20.0 - - + -
110C GLU* 2.9 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE* 3.9 25.4 - + + -
39A ILE* 3.7 31.0 - - + -
40A LYS* 4.0 17.4 - - + +
72A ARG* 3.3 60.1 + - + +
75A CYS* 4.1 13.2 - - + -
76A LEU* 3.7 26.2 - - + -
79A ILE* 4.6 1.1 - - + -
147A LEU 2.9 14.1 + - - +
148A TRP* 3.2 30.9 + + + +
150A ARG* 1.3 76.7 - - - +
152A ASN* 1.3 62.5 + - - +
153A ARG 3.2 0.4 - - - -
105C TRP* 4.3 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LYS* 3.3 45.4 + - - +
43A TYR* 3.2 35.0 - - + +
44A LEU* 3.4 27.4 - - - +
148A TRP* 2.9 20.9 + - - +
149A ARG* 3.7 9.6 - - - +
150A ARG 3.1 0.4 - - - -
151A PHE* 1.3 87.9 - - - +
153A ARG* 1.3 66.5 + - - +
154A PRO* 3.5 2.8 - - - +
----------------------------------------------------------
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