Contacts of the strand formed by residues 165 - 173 (chain 4) 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 4).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1634 PRO* 3.7 2.2 - - - +
1644 ASP* 1.3 107.6 + - - +
1664 CYS* 1.3 63.7 + - - +
2244 GLU* 5.8 7.4 - - + -
2254 PHE 3.3 9.6 - - - +
2264 ASP* 3.1 28.2 + - + +
2274 LEU* 4.8 0.9 - - - -
2284 ASN* 5.1 0.8 + - - -
2604 ILE* 3.7 5.0 - - - +
2614 VAL* 2.9 52.5 + - + +
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Residues in contact with CYS 166 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1334 TRP* 3.8 27.1 - - + -
1384 LEU* 4.0 11.9 - - + -
1444 MET* 5.3 0.4 - - - -
1634 PRO* 6.0 0.2 - - + -
1654 LYS* 1.3 77.0 - - - +
1674 SER* 1.3 62.6 + - - +
2244 GLU* 3.5 3.7 - - - +
2254 PHE* 2.8 65.5 + - - +
2274 LEU* 4.2 6.7 - - - -
2594 ASP 3.2 9.2 - - - -
2604 ILE* 3.8 20.6 - - + -
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Residues in contact with SER 167 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1384 LEU* 4.8 4.1 - - - +
1664 CYS* 1.3 79.6 - - - +
1684 ILE* 1.3 62.1 + - - +
1694 HIS* 3.1 25.4 + - - -
2214 LYS* 4.5 4.7 - - - -
2234 ILE 3.5 15.3 - - - -
2244 GLU* 4.0 15.1 + - - +
2254 PHE* 4.6 0.9 - - - +
2584 PHE* 3.1 7.0 - - - +
2594 ASP* 3.0 40.7 + - - +
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Residues in contact with ILE 168 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1374 PHE* 4.0 25.6 - - + +
1384 LEU* 3.6 35.8 - - + +
1674 SER* 1.3 72.2 - - - +
1694 HIS* 1.3 65.5 + - - +
2214 LYS* 3.9 1.2 - - - -
2224 LEU* 3.0 41.4 + - + +
2234 ILE* 3.3 26.0 + - + +
2254 PHE* 5.8 0.4 - - + -
2374 PHE* 3.2 40.2 - - + -
2574 TRP 3.4 12.3 - - - +
2584 PHE* 3.8 3.4 - - + -
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Residues in contact with HIS 169 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1674 SER* 3.1 41.1 + - - -
1684 ILE* 1.3 76.5 - - - +
1704 LEU* 1.3 65.0 + - - +
2194 SER* 5.6 3.6 - - - -
2204 ASP 3.4 19.3 - - - +
2214 LYS* 4.5 13.8 - - + +
2224 LEU* 4.7 1.8 - - - +
2564 THR* 3.1 8.7 - - - +
2574 TRP* 2.8 62.9 + + + +
2594 ASP* 3.7 24.7 + - + -
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Residues in contact with LEU 170 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1694 HIS* 1.3 78.4 - - - +
1714 ALA* 1.3 62.6 + - - +
2194 SER* 3.2 4.2 - - - -
2204 ASP* 2.7 49.9 + - + +
2224 LEU* 4.0 20.4 - - + +
2414 PHE* 3.9 56.5 - - + -
2434 LEU* 3.6 4.6 - - + +
2544 ILE* 3.3 31.2 - - + -
2554 VAL 3.1 8.1 - - - +
2564 THR* 3.8 10.8 - - + -
2574 TRP* 3.7 4.5 - - - -
3074 LEU* 5.1 5.6 - - + -
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Residues in contact with ALA 171 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1704 LEU* 1.3 77.8 - - - +
1724 GLY* 1.3 60.5 + - - +
2154 VAL* 3.8 24.0 - - + -
2174 THR* 3.7 11.4 - - - +
2194 SER* 3.8 19.3 - - - -
2434 LEU* 3.9 11.7 - - - -
2544 ILE* 3.2 4.7 - - - +
2554 VAL* 2.9 31.8 + - + +
2574 TRP* 4.0 9.2 - - + -
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Residues in contact with GLY 172 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1714 ALA* 1.3 73.3 - - - +
1734 LEU* 1.3 61.7 + - - +
2154 VAL* 3.4 8.8 - - - +
2164 ASN* 2.9 34.6 + - - -
2174 THR* 2.8 22.3 + - - -
2434 LEU* 3.7 6.9 - - - +
2514 ILE* 3.9 7.9 - - - -
2534 GLY 3.6 7.2 - - - -
2544 ILE* 4.6 2.2 - - - -
2554 VAL* 4.8 1.1 - - - +
3034 ILE* 6.3 0.2 - - - -
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Residues in contact with LEU 173 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1724 GLY* 1.3 76.1 - - - -
1744 GLU* 1.3 74.3 - - - +
1754 ASP* 3.8 17.3 - - + +
2104 VAL* 3.4 34.1 - - + -
2144 ASN* 3.4 15.5 - - + +
2164 ASN* 3.4 7.0 - - - +
2504 MET 3.4 0.9 - - - +
2514 ILE* 3.4 1.5 - - - +
2524 ASN* 2.8 31.9 + - - +
2534 GLY 2.8 18.8 + - - +
2544 ILE 4.7 1.8 - - - +
2554 VAL* 4.4 13.9 - - + +
2884 ILE* 3.5 42.0 - - + -
2904 TYR* 4.9 2.2 - - + -
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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