Contacts of the helix formed by residues 5 - 20 (chain 6) in PDB entry 3EXG
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 VAL 5 (chain 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46 THR* 1.3 73.3 - - - +
66 ARG* 1.3 65.0 + - - +
86 ALA* 3.0 15.3 + - - +
96 ILE* 3.1 18.2 + - + +
1476 PRO* 6.3 0.7 - - + -
1486 TRP 3.9 16.6 - - - +
1496 ASN* 3.9 0.9 - - - -
1506 SER* 3.8 22.2 - - - +
1536 ALA* 4.1 17.7 - - + -
1716 GLU* 6.3 1.1 - - + -
1726 ASN 5.4 0.9 - - - +
1756 MET* 3.3 39.5 - - + +
1766 TYR* 3.5 17.4 + - + -
1786 VAL 3.2 9.9 + - - +
1806 PHE* 4.3 0.7 - - + -
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Residues in contact with ARG 6 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46 THR* 3.1 3.4 + - - +
56 VAL* 1.3 78.2 - - - +
76 ASP* 1.3 75.7 + - - +
96 ILE* 3.7 4.3 + - - +
106 ASN* 3.3 19.9 + - + +
376 TYR* 2.8 31.7 + - - +
386 LYS* 3.7 24.0 - - - +
396 VAL* 4.1 14.0 - - + +
416 ARG* 4.0 11.4 - - - +
1736 GLU* 6.3 0.2 - - - +
1766 TYR* 3.0 71.1 + - + +
1776 GLY* 3.8 9.5 - - - +
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Residues in contact with ASP 7 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36 VAL* 4.7 8.0 - - + +
46 THR* 3.1 28.2 + - - +
66 ARG* 1.3 92.3 - - - +
86 ALA* 1.3 67.7 + - - +
106 ASN* 3.1 8.2 + - - +
116 GLN* 3.0 28.2 + - + +
416 ARG* 4.8 5.7 + - - -
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Residues in contact with ALA 8 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36 VAL* 4.4 7.7 - - + +
46 THR 2.8 13.2 + - - +
56 VAL* 3.0 10.0 + - - +
76 ASP* 1.3 79.2 - - - +
96 ILE* 1.3 63.6 + - - +
116 GLN* 3.2 8.1 - - - +
126 GLY 3.0 18.0 + - - -
1506 SER* 3.6 38.1 - - - +
1536 ALA* 4.4 1.1 - - + -
1546 LYS* 3.6 17.6 - - + +
1826 PHE* 4.7 3.6 - - + -
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Residues in contact with ILE 9 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56 VAL* 3.1 16.9 + - + +
66 ARG 4.0 5.2 - - - +
86 ALA* 1.3 75.3 - - - +
106 ASN* 1.3 56.9 + - - +
126 GLY* 3.1 2.7 + - - +
136 MET* 2.8 38.5 + - + +
396 VAL* 4.0 18.6 - - + -
1156 ARG* 4.1 7.0 - - - +
1476 PRO* 6.0 1.1 - - + -
1536 ALA* 3.9 21.5 - - + +
1576 ILE* 4.3 18.8 - - + +
1716 GLU* 3.4 40.8 - - + +
1766 TYR* 3.7 21.1 - - + -
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Residues in contact with ASN 10 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66 ARG* 3.3 8.8 + - + +
76 ASP* 3.1 13.4 + - - +
96 ILE* 1.3 76.4 - - - +
116 GLN* 1.3 54.6 + - - +
136 MET* 2.9 9.7 + - - +
146 ASP* 2.8 39.7 + - - +
386 LYS 5.8 0.2 - - - +
396 VAL 3.1 28.1 + - - +
406 SER* 3.7 3.8 - - - +
416 ARG* 3.1 30.4 + - - +
436 LEU* 3.5 18.5 - - - +
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Residues in contact with GLN 11 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36 VAL* 4.7 9.5 - - - +
76 ASP* 3.0 13.7 + - + +
86 ALA* 3.2 11.2 - - - +
106 ASN* 1.3 78.1 + - - +
126 GLY* 1.3 62.0 - - - +
146 ASP* 3.4 7.8 + - - +
156 GLU* 3.0 36.8 + - + +
1546 LYS* 2.6 38.3 + - + +
1826 PHE* 3.6 24.8 - - - -
1876 GLN* 4.0 13.1 - - - +
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Residues in contact with GLY 12 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86 ALA 3.0 9.4 + - - -
96 ILE 3.1 3.8 + - - -
116 GLN* 1.3 80.6 - - - +
136 MET* 1.3 64.8 + - - +
156 GLU* 3.3 1.6 + - - +
166 GLU* 3.3 24.9 + - - +
1546 LYS* 4.1 3.2 - - - +
1576 ILE* 3.9 10.3 - - - -
1586 LYS* 3.7 31.7 - - - +
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Residues in contact with MET 13 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96 ILE* 2.8 20.3 + - + +
106 ASN* 3.5 5.4 - - - +
126 GLY* 1.3 73.5 - - - +
146 ASP* 1.3 64.2 + - - +
166 GLU* 3.4 2.1 + - - +
176 LEU* 3.1 32.5 + - + +
256 LEU* 4.1 18.8 - - + -
396 VAL* 3.8 38.4 - - + +
406 SER* 4.2 8.5 - - - -
436 LEU* 4.1 19.5 - - + -
776 ILE* 4.1 19.7 - - + -
1156 ARG* 4.0 25.1 - - - +
1576 ILE* 4.1 17.9 - - + +
1616 ILE* 4.6 8.0 - - + +
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Residues in contact with ASP 14 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106 ASN* 2.8 22.7 + - - +
116 GLN* 3.5 10.6 - - - +
136 MET* 1.3 78.0 - - - +
156 GLU* 1.3 64.9 + - + +
176 LEU* 3.2 8.7 + - - +
186 GLU* 3.1 9.4 + - - +
436 LEU* 4.4 16.9 - - + +
466 LYS* 3.0 23.9 + - - +
476 TYR* 2.8 49.6 + - - -
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Residues in contact with GLU 15 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116 GLN* 3.0 22.9 + - + +
126 GLY 3.3 1.5 + - - +
146 ASP* 1.3 79.8 - - + +
166 GLU* 1.3 58.4 + - - +
186 GLU* 3.3 12.1 + - - +
196 ARG* 3.0 27.8 + - - +
1546 LYS* 3.3 27.6 + - - -
1586 LYS* 3.2 27.2 + - - +
1876 GLN 4.0 4.7 - - - +
1896 LYS* 3.4 36.2 - - + +
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Residues in contact with GLU 16 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126 GLY 3.3 16.4 - - - +
136 MET 3.6 1.8 - - - +
156 GLU* 1.3 76.5 - - - +
176 LEU* 1.3 63.9 + - - +
186 GLU 3.2 0.2 - - - -
196 ARG* 3.2 24.2 + - - +
206 ASP* 3.2 16.8 + - - +
236 VAL* 4.5 4.6 - - - +
1586 LYS* 2.7 28.6 + - - +
1616 ILE* 3.5 45.0 - - + +
1626 ARG* 2.4 50.6 + - - -
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Residues in contact with LEU 17 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136 MET* 3.1 23.7 + - + +
146 ASP 3.4 6.1 - - - +
166 GLU* 1.3 78.6 - - - +
186 GLU* 1.3 61.5 + - - +
206 ASP 3.5 5.3 + - - +
236 VAL* 2.9 41.3 - - + +
246 PHE* 4.1 10.1 - - - -
256 LEU* 5.6 3.1 - - + -
436 LEU* 4.1 16.6 - - + -
476 TYR* 3.6 36.4 - - + -
516 ARG* 2.8 38.6 + - + +
526 ILE* 4.5 8.7 - - + -
776 ILE* 5.4 4.5 - - + -
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Residues in contact with GLU 18 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146 ASP* 3.1 8.4 + - - +
156 GLU* 3.4 13.3 - - - +
166 GLU 3.2 0.2 - - - -
176 LEU* 1.3 78.3 - - - +
196 ARG* 1.3 63.9 + - - +
206 ASP* 3.3 1.4 + - - -
466 LYS* 3.1 34.5 + - - -
476 TYR* 3.6 12.0 + - + +
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Residues in contact with ARG 19 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156 GLU 3.0 16.8 + - - +
166 GLU* 3.2 19.6 + - - +
186 GLU* 1.3 79.7 - - - +
206 ASP* 1.3 76.9 + - - +
756 ARG* 6.1 0.8 - - - +
1616 ILE* 6.1 1.0 - - - +
1626 ARG* 3.3 59.8 - - - +
1896 LYS 6.0 0.2 - - - -
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Residues in contact with ASP 20 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166 GLU 3.2 7.0 + - - +
176 LEU 3.5 4.9 - - - +
186 GLU 3.3 2.0 + - - -
196 ARG* 1.3 100.4 + - - +
216 GLU* 1.3 65.1 + - - +
226 LYS* 2.5 48.0 + - - +
236 VAL* 3.4 16.7 + - + +
516 ARG* 3.3 10.9 + - - -
756 ARG* 3.4 25.0 + - - -
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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
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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) + - + + + + + -
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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