Contacts of the strand formed by residues 1501 - 1504 (chain F) 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 ILE1501 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1339F PRO* 4.3 27.4 - - + +
1340F ASP 5.7 0.2 - - - +
1341F GLN 4.1 4.9 - - - +
1342F GLY* 3.6 29.4 - - - +
1344F ILE* 5.5 10.8 - - + -
1404F ILE* 5.4 7.0 - - + -
1420F ARG 4.7 2.7 - - - +
1421F LEU* 3.6 35.7 - - + -
1422F SER 4.4 4.7 + - - -
1499F THR* 4.0 9.8 - - - -
1500F SER* 1.3 88.4 - - - +
1502F PHE* 1.3 67.3 + - - +
1531F THR* 3.0 27.6 - - + +
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Residues in contact with PHE1502 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1391F PHE* 6.0 1.6 - - - -
1421F LEU* 5.8 2.5 - - - -
1422F SER* 3.5 34.1 - - - +
1423F ILE* 5.1 0.7 - - - -
1424F ILE* 4.9 3.6 - - + -
1494F ALA* 5.6 4.5 - - + -
1495F PHE* 4.3 8.7 - + - -
1497F ARG 5.9 0.7 - - - -
1499F THR* 4.0 23.1 - - - -
1501F ILE* 1.3 79.3 - - - +
1503F ILE* 1.3 83.6 + - - +
1504F MET* 3.5 29.8 - - + -
1527F PHE* 3.5 35.4 - + - -
1530F ARG* 4.8 2.0 - - + -
1531F THR 3.1 4.8 + - - +
1532F VAL* 3.3 32.9 - - + -
1533F VAL* 2.9 26.2 + - - +
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Residues in contact with ILE1503 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1376F ILE* 5.5 0.7 - - + -
1387F PHE* 5.3 3.1 - - + -
1388F SER* 3.6 38.1 - - - +
1391F PHE* 3.8 24.9 - - + -
1392F PHE* 5.5 2.5 - - + -
1422F SER 3.8 7.9 - - - +
1423F ILE* 3.2 30.3 - - + -
1424F ILE 3.1 19.1 + - - -
1502F PHE* 1.3 83.7 - - - +
1504F MET* 1.3 81.6 + - - +
1533F VAL* 3.2 38.1 - - + +
1535F ILE* 5.1 4.7 - - + -
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Residues in contact with MET1504 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1388F SER* 5.2 1.1 - - - -
1424F ILE* 3.6 25.1 - - + +
1491F LEU* 5.6 2.7 - - + -
1495F PHE* 3.6 28.5 - - + -
1502F PHE* 3.5 27.8 - - + -
1503F ILE* 1.3 83.5 - - - +
1505F ASP* 1.3 60.0 + - - +
1506F GLU 3.6 0.4 - - - +
1507F ALA* 4.4 15.0 - - + +
1519F LEU* 6.0 2.7 - - + -
1520F GLN* 5.4 7.4 - - - -
1523F VAL* 4.2 15.5 - - + -
1532F VAL* 4.2 11.9 - - + -
1533F VAL 3.0 8.8 + - - +
1534F THR* 4.9 9.9 - - - -
1535F ILE* 2.9 35.6 + - - +
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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