Contacts of the strand formed by residues 165 - 173 (chain 2) in PDB entry 1G6Q
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 LYS 165 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1632 PRO* 3.8 2.0 - - - +
1642 ASP* 1.3 112.0 + - - +
1662 CYS* 1.3 65.7 + - - +
2242 GLU* 5.8 10.5 - - + +
2252 PHE 3.4 8.5 - - - +
2262 ASP* 4.1 24.1 + - + +
2272 LEU* 4.9 0.4 - - - -
2282 ASN* 5.6 0.2 - - - +
2602 ILE* 3.6 3.1 - - - +
2612 VAL* 2.8 60.1 + - + +
2622 PHE 4.8 2.6 + - - -
2632 PRO* 5.5 1.2 - - - +
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Residues in contact with CYS 166 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1332 TRP* 3.5 27.6 - - + -
1382 LEU* 3.6 20.9 - - + -
1442 MET* 4.9 0.2 - - - -
1652 LYS* 1.3 77.0 - - - +
1672 SER* 1.3 64.2 + - - +
2242 GLU* 3.3 4.2 - - - +
2252 PHE* 2.7 55.2 + - - +
2272 LEU* 4.0 7.6 - - - -
2592 ASP 3.2 12.3 - - - +
2602 ILE* 3.5 15.7 - - + -
2612 VAL* 5.9 0.9 - - - -
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Residues in contact with SER 167 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1382 LEU* 4.9 0.4 - - - -
1662 CYS* 1.3 79.5 - - - +
1682 ILE* 1.3 65.5 + - - +
1692 HIS* 3.0 25.7 + - - -
2212 LYS* 4.3 6.9 - - - +
2232 ILE 3.3 15.5 - - - -
2242 GLU* 4.1 15.2 + - - +
2252 PHE* 5.5 0.4 - - - -
2582 PHE* 3.0 7.0 - - - +
2592 ASP* 2.9 41.4 + - - +
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Residues in contact with ILE 168 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1372 PHE* 3.9 44.0 - - + +
1382 LEU* 3.6 33.2 - - + -
1392 LEU* 4.5 3.4 - - + -
1672 SER* 1.3 74.8 - - - +
1692 HIS* 1.3 72.5 + - - +
2212 LYS* 3.8 0.7 - - - -
2222 LEU* 2.9 35.6 + - + +
2232 ILE* 3.1 33.1 + - + +
2252 PHE* 4.1 2.9 - - + -
2372 PHE* 3.9 20.0 - - + -
2562 THR* 5.0 0.2 - - - -
2572 TRP 3.4 9.9 - - - +
2582 PHE* 4.6 1.1 - - + -
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Residues in contact with HIS 169 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1672 SER* 3.0 32.2 + - - -
1682 ILE* 1.3 78.6 - - - +
1702 LEU* 1.3 62.4 + - - +
2192 SER* 5.4 6.5 - - - -
2202 ASP 3.5 18.4 - - - +
2212 LYS* 3.5 28.5 - - + +
2222 LEU* 4.4 2.0 - - - +
2562 THR* 3.2 10.4 - - - +
2572 TRP* 2.8 63.9 + + + +
2592 ASP* 3.5 22.8 + - - -
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Residues in contact with LEU 170 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1692 HIS* 1.3 79.1 - - - +
1712 ALA* 1.3 65.0 + - - +
2192 SER* 3.3 3.3 - - - -
2202 ASP* 3.0 45.5 + - + +
2222 LEU* 4.0 20.6 - - + -
2412 PHE* 3.8 40.4 - - + -
2432 LEU* 3.4 22.2 - - + -
2542 ILE* 3.8 24.2 - - + -
2552 VAL 3.2 11.4 - - - +
2562 THR* 3.8 9.4 - - + -
2572 TRP* 3.7 5.2 - - - -
3072 LEU* 4.5 1.8 - - + -
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Residues in contact with ALA 171 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1702 LEU* 1.3 78.7 - - - +
1722 GLY* 1.3 62.1 + - - +
2152 VAL* 3.7 25.1 - - + -
2172 THR* 3.7 13.0 - - - +
2182 THR 3.8 6.5 - - - +
2192 SER* 4.1 6.7 - - - -
2432 LEU* 3.7 10.5 - - - -
2542 ILE* 3.2 4.1 - - - -
2552 VAL* 2.8 33.0 + - + +
2572 TRP* 4.1 10.5 - - + -
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Residues in contact with GLY 172 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1712 ALA* 1.3 74.5 - - - +
1732 LEU* 1.3 57.9 + - - -
2152 VAL* 3.5 9.4 - - - +
2162 ASN* 3.0 30.3 + - - -
2172 THR* 2.8 28.8 + - - -
2432 LEU* 3.3 8.2 - - - +
2512 ILE* 4.0 6.1 - - - -
2532 GLY 3.5 8.7 - - - -
2542 ILE* 4.4 0.4 - - - -
2552 VAL* 4.5 0.2 - - - -
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Residues in contact with LEU 173 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1722 GLY* 1.3 75.3 - - - -
1742 GLU* 1.3 77.3 + - - +
1752 ASP* 3.6 24.7 - - + +
2102 VAL* 3.4 36.6 - - + -
2142 ASN* 3.6 7.6 - - + +
2162 ASN* 3.6 5.4 - - - +
2512 ILE* 3.6 1.3 - - - +
2522 ASN* 2.8 27.7 + - - -
2532 GLY 2.9 18.7 + - - +
2542 ILE 4.9 0.7 - - - +
2552 VAL* 4.3 13.2 - - + +
2882 ILE* 3.4 36.8 - - + -
2902 TYR* 4.2 5.8 - - + -
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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