Contacts of the strand formed by residues 1501 - 1504 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1339E PRO* 4.3 27.1 - - + +
1340E ASP 5.7 0.2 - - - +
1341E GLN 4.1 4.3 - - - +
1342E GLY* 3.6 29.6 - - - +
1344E ILE* 5.5 10.1 - - + -
1404E ILE* 5.4 7.4 - - + -
1420E ARG 4.7 3.4 - - - +
1421E LEU* 3.6 36.2 - - + -
1422E SER 4.4 4.3 + - - -
1499E THR* 4.0 10.5 - - - -
1500E SER* 1.3 88.6 - - - +
1502E PHE* 1.3 66.6 + - - +
1531E THR* 3.0 26.9 - - + +
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Residues in contact with PHE1502 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1391E PHE* 6.0 1.6 - - - -
1421E LEU* 5.8 1.8 - - - -
1422E SER* 3.5 35.0 - - - +
1423E ILE 5.1 0.4 - - - -
1424E ILE* 4.9 4.0 - - + -
1494E ALA* 5.6 4.0 - - + -
1495E PHE* 4.3 9.6 - + - -
1497E ARG 5.9 0.4 - - - -
1499E THR* 4.0 22.9 - - - -
1501E ILE* 1.3 81.2 - - - +
1503E ILE* 1.3 84.8 + - - +
1504E MET* 3.5 29.4 - - + -
1527E PHE* 3.5 35.0 - + - -
1530E ARG* 4.8 2.2 - - + -
1531E THR 3.1 4.6 + - - +
1532E VAL* 3.3 31.9 - - + -
1533E VAL* 2.9 26.6 + - - +
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Residues in contact with ILE1503 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1376E ILE* 5.5 0.4 - - + -
1387E PHE* 5.3 3.1 - - + -
1388E SER* 3.6 37.7 - - - +
1391E PHE* 3.8 25.4 - - + -
1392E PHE* 5.5 2.5 - - + -
1422E SER 3.8 8.3 - - - +
1423E ILE* 3.2 29.9 - - + -
1424E ILE 3.1 19.4 + - - -
1502E PHE* 1.3 83.6 - - - +
1504E MET* 1.3 82.8 + - - +
1532E VAL* 4.5 0.2 - - - -
1533E VAL* 3.2 37.0 - - + +
1535E ILE* 5.1 4.0 - - + -
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Residues in contact with MET1504 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1388E SER* 5.2 0.9 - - - -
1424E ILE* 3.6 24.9 - - + +
1491E LEU* 5.6 2.7 - - - -
1495E PHE* 3.6 28.9 - - + -
1502E PHE* 3.5 27.6 - - + -
1503E ILE* 1.3 84.3 - - - +
1505E ASP* 1.3 60.1 + - - +
1506E GLU 3.6 0.9 - - - +
1507E ALA* 4.4 16.4 - - + +
1519E LEU* 6.0 2.5 - - + -
1520E GLN* 5.4 7.6 - - - -
1523E VAL* 4.2 15.7 - - + -
1532E VAL* 4.2 11.4 - - + -
1533E VAL 3.0 8.6 + - - +
1534E THR* 4.9 9.6 - - - -
1535E ILE* 2.9 35.5 + - - +
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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