Contacts of the strand formed by residues 1548 - 1551 (chain G) in PDB entry 6C3P
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 VAL1548 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1375G GLY 3.2 3.1 - - - -
1377G CYS* 4.2 5.8 - - - -
1542G ILE* 4.0 34.3 - - + +
1545G ALA 5.1 0.2 - - - +
1547G LEU* 1.3 77.1 - - - +
1549G ILE* 1.3 63.7 + - - +
1550G VAL* 4.1 19.6 + - + -
1559G PHE* 3.0 7.1 - - - +
1560G ASP 2.6 36.9 + - - +
1562G PRO* 3.6 36.6 - - + -
1565G LEU* 3.9 13.6 - - + +
1573G PHE* 4.6 12.6 - - + -
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Residues in contact with ILE1549 (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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1366G ALA* 5.4 5.2 - - + -
1368G ILE* 4.9 12.3 - - + -
1374G ILE* 3.8 22.2 - - + -
1375G GLY 2.4 17.1 + - - +
1376G ILE* 3.2 36.2 - - + +
1377G CYS* 2.8 33.6 + - - +
1387G PHE* 6.1 0.7 - - + -
1547G LEU* 5.1 5.2 - - + -
1548G VAL* 1.3 78.3 - - - +
1550G VAL* 1.3 61.3 + - - +
1551G LEU* 4.7 2.7 - - + -
1556G ILE* 3.7 34.1 - - + -
1559G PHE* 3.7 21.5 - - + -
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Residues in contact with VAL1550 (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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1377G CYS* 3.8 15.3 - - - +
1548G VAL* 4.1 11.8 + - + +
1549G ILE* 1.3 77.6 - - - +
1551G LEU* 1.3 69.0 + - - +
1552G LYS* 4.9 2.9 - - + +
1556G ILE* 3.0 9.8 - - - +
1557G LEU* 2.8 50.6 + - + +
1558G GLU 5.4 0.4 - - - +
1559G PHE* 4.8 1.0 - - - +
1565G LEU* 5.0 4.3 - - + -
1571G SER* 4.4 10.5 - - - +
1572G VAL* 5.5 4.7 - - + +
1573G PHE* 4.0 26.2 - - + +
1576G PHE* 4.6 19.5 - - + -
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Residues in contact with LEU1551 (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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1361G LEU* 4.4 12.3 - - + -
1364G VAL* 5.5 0.9 - - + -
1376G ILE* 4.1 17.5 - - + -
1377G CYS 3.4 8.7 + - - +
1378G GLY* 4.1 8.3 - - - -
1379G ARG* 3.9 6.1 + - - -
1382G SER* 2.9 33.0 + - - +
1383G GLY 4.2 5.4 - - - +
1384G LYS* 3.7 39.3 - - + +
1387G PHE* 5.0 8.5 - - + -
1549G ILE* 4.7 1.8 - - + -
1550G VAL* 1.3 78.4 - - - +
1552G LYS* 1.3 60.4 + - - +
1555G ALA* 3.3 28.9 - - - +
1556G ILE* 3.6 19.7 - - + -
1576G PHE* 6.0 0.2 - - - -
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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
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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