Contacts of the strand formed by residues 1556 - 1561 (chain G) in PDB entry 6BAA
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 ALA1556 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1363G LYS* 3.6 22.0 - - + +
1364G HIS 5.3 1.3 - - - +
1365G VAL* 4.2 6.5 - - + -
1552G LEU* 3.3 6.8 - - - -
1553G LYS 2.5 44.1 + - - +
1554G ARG 3.2 2.9 - - - +
1555G GLY* 1.3 79.1 - - - +
1557G ILE* 1.3 64.9 + - - +
1558G LEU* 3.3 0.6 + - - -
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Residues in contact with ILE1557 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1365G VAL* 4.7 14.0 - - + +
1366G ASN 3.9 24.5 + - - +
1367G THR* 4.8 9.0 - - - -
1550G MET* 5.7 3.4 - - + -
1551G VAL 3.3 12.1 - - - +
1552G LEU* 3.8 14.2 - - + +
1556G ALA* 1.3 75.0 - - - +
1558G LEU* 1.3 61.0 + - - +
1559G GLU 4.5 7.0 - - - +
1560G PHE* 5.7 2.5 - - + -
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Residues in contact with LEU1558 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1551G VAL* 2.9 7.5 + - + +
1552G LEU 4.9 0.4 - - - -
1553G LYS* 3.7 26.7 - - + +
1556G ALA* 3.3 3.0 + - + -
1557G ILE* 1.3 73.7 - - - +
1559G GLU* 1.3 61.9 + - + +
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Residues in contact with GLU1559 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1550G MET* 4.1 0.2 - - - -
1551G VAL* 2.8 45.0 + - + +
1557G ILE* 3.6 4.7 - - - +
1558G LEU* 1.3 80.1 + - + +
1560G PHE* 1.3 65.3 + - - +
1561G ASP* 4.1 2.0 - - + +
1569G GLN* 5.0 17.7 - - + +
1571G ASP* 5.8 2.5 - - + -
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Residues in contact with PHE1560 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1367G THR* 4.2 23.1 - - - -
1368G LEU 3.2 30.7 - - - -
1369G ILE* 5.0 4.5 - - + -
1375G ILE* 5.2 8.1 - - + -
1548G LEU* 4.4 16.8 - - + -
1549G VAL 3.6 8.7 - - - -
1550G MET* 3.6 28.9 - - + -
1557G ILE* 5.7 2.7 - - + -
1559G GLU* 1.3 76.2 - - - +
1561G ASP* 1.3 59.1 + - - +
1562G LYS* 3.8 19.4 + - + -
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Residues in contact with ASP1561 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1549G VAL* 2.9 34.0 + - + +
1551G VAL* 6.0 0.6 - - - +
1559G GLU* 4.1 2.0 - - + +
1560G PHE* 1.3 72.8 - - - +
1562G LYS* 1.3 63.2 + - - +
1563G PRO* 5.0 1.1 - - + -
1564G GLU 4.9 0.7 + - - -
1565G THR* 4.0 22.5 + - - +
1566G LEU* 5.0 0.4 - - - +
1569G GLN* 3.9 29.8 - - + +
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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