Contacts of the strand formed by residues 1502 - 1506 (chain E) 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 ILE1502 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1343E GLY* 6.0 1.1 - - - -
1392E PHE* 3.8 26.9 - - + -
1405E ILE* 5.7 3.8 - - + -
1406E ASP* 5.7 7.0 - - + +
1422E LEU* 5.5 6.6 - - + +
1423E SER 2.9 20.3 + - - +
1500E THR* 3.3 9.0 - - - -
1501E SER* 1.3 86.7 + - - +
1503E PHE* 1.3 60.0 + - - +
1531E ARG* 5.9 0.2 - - - -
1532E THR* 3.2 20.4 - - - -
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Residues in contact with PHE1503 (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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1392E PHE* 4.6 5.6 - - - -
1423E SER 4.2 4.7 - - - +
1424E ILE* 4.9 2.2 - - - +
1425E ILE 5.6 4.5 - - - +
1500E THR* 5.9 0.7 - - - -
1502E ILE* 1.3 72.2 - - - +
1504E ILE* 1.3 56.5 + - - +
1505E MET* 5.9 3.4 - - + -
1527E ALA* 6.4 2.7 - - + -
1531E ARG* 6.5 0.2 - - + -
1532E THR 2.4 25.8 + - - +
1533E VAL* 3.5 11.6 - - + -
1534E VAL* 2.6 34.7 + - - +
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Residues in contact with ILE1504 (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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1389E SER* 5.9 2.5 - - - -
1392E PHE* 3.6 29.8 - - + -
1393E PHE* 3.7 26.9 - - + -
1424E ILE* 3.4 23.2 - - + +
1425E ILE 3.7 12.8 + - - +
1426E LEU* 4.4 2.1 + - - +
1503E PHE* 1.3 73.8 - - - +
1505E MET* 1.3 61.2 - - - +
1506E ASP 4.3 0.2 + - - -
1534E VAL* 3.3 8.1 - - + +
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Residues in contact with MET1505 (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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1425E ILE 4.1 13.2 - - - +
1426E LEU* 5.0 1.3 - - - -
1427E GLN 5.5 0.9 - - - +
1503E PHE* 5.6 3.6 - - + -
1504E ILE* 1.3 74.7 - - - +
1506E ASP* 1.3 60.4 + - - +
1507E GLU* 3.8 0.6 + - - -
1534E VAL 2.6 15.2 + - - +
1535E THR* 3.5 10.9 - - - -
1536E ILE* 2.5 36.8 + - - +
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Residues in contact with ASP1506 (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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1426E LEU* 3.8 20.5 - - + +
1427E GLN* 3.2 23.7 + - - +
1428E ASP 4.9 0.8 + - - +
1504E ILE 4.3 0.4 - - - -
1505E MET* 1.3 72.3 - - - +
1507E GLU* 1.3 66.7 + - - +
1536E ILE* 4.1 8.1 - - + -
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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