Contacts of the strand formed by residues 167 - 171 (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 167 (chain 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1126 ILE* 3.2 6.5 + - - +
1136 VAL* 3.4 5.1 - - + +
1146 PHE* 3.0 27.3 + - - +
1436 LYS* 3.4 24.0 - - + +
1456 VAL* 4.5 11.9 - - + -
1606 ALA* 4.1 30.5 - - + +
1636 ASP* 4.1 24.9 - - + +
1656 ASN 3.2 16.2 - - - +
1666 PRO* 1.3 76.8 - - - +
1686 VAL* 1.3 73.5 + - - +
1696 VAL* 4.0 3.6 - - + -
1956 ILE* 4.6 4.3 - - + -
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Residues in contact with VAL 168 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836 PHE* 3.8 13.2 - - + -
936 VAL* 4.7 1.8 - - + -
1146 PHE* 3.5 22.2 - - + -
1366 TYR* 4.2 18.6 - - + -
1426 LEU* 4.0 26.0 - - + -
1436 LYS 2.9 11.2 + - - +
1446 VAL* 4.1 11.7 - - + -
1456 VAL 3.1 24.8 + - - +
1676 VAL* 1.3 74.0 - - - +
1696 VAL* 1.3 63.6 + - - +
1706 LEU* 3.7 31.2 - - + -
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Residues in contact with VAL 169 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836 PHE* 3.7 3.8 - - - -
1136 VAL* 4.1 14.4 - - + -
1146 PHE 2.7 12.8 + - - +
1156 ARG* 3.5 23.0 - - + -
1166 GLY 3.6 2.9 + - - +
1456 VAL* 3.8 23.8 - - + -
1476 PRO* 4.0 18.8 - - + -
1566 LEU* 5.5 0.7 - - + -
1576 ILE* 4.5 16.2 - - + +
1606 ALA* 4.0 24.7 - - + -
1676 VAL* 4.2 2.7 - - + -
1686 VAL* 1.3 78.3 - - - +
1706 LEU* 1.3 57.9 + - - +
1716 GLU* 3.3 23.7 + - + +
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Residues in contact with LEU 170 (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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836 PHE* 3.6 32.3 - - + -
1166 GLY 4.2 1.1 - - - -
1186 ASN* 3.5 28.4 - - + +
1326 PHE* 4.0 1.6 - - + +
1336 ALA* 3.5 38.4 - - + +
1366 TYR* 4.5 7.0 - - + -
1446 VAL* 4.2 12.6 - - + -
1456 VAL 3.1 11.9 + - - +
1466 SER* 3.4 22.0 + - - +
1476 PRO* 3.3 16.4 - - - +
1686 VAL* 3.7 17.7 - - + -
1696 VAL* 1.3 66.7 - - - +
1716 GLU* 1.3 66.1 + - - +
2126 HIS* 5.7 0.2 - - + -
2136 SER* 4.5 2.9 + - - -
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Residues in contact with GLU 171 (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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56 VAL* 6.3 0.9 - - + -
96 ILE* 3.4 21.9 - - + +
1156 ARG* 2.7 44.3 + - - +
1166 GLY 3.1 21.4 + - - +
1176 PRO* 3.8 0.2 - - - -
1186 ASN* 2.7 27.1 + - - +
1476 PRO* 4.3 12.7 - - + +
1576 ILE* 4.4 2.1 - - - +
1696 VAL* 3.5 22.0 - - + +
1706 LEU* 1.3 78.8 - - - +
1726 ASN* 1.3 61.8 + - - +
1766 TYR* 2.5 40.5 + - + +
2136 SER* 4.9 1.1 + - - -
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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
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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