Contacts of the strand formed by residues 1502 - 1506 (chain F) in PDB entry 5YWB
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1339F TRP* 5.5 4.7 - - - +
1343F GLY* 3.7 32.5 - - - +
1345F ILE* 4.9 15.5 - - + -
1392F PHE* 4.6 10.3 - - + -
1405F ILE* 5.6 4.7 - - + -
1421F ARG 4.2 4.7 + - - +
1422F LEU* 3.6 31.4 - - + -
1423F SER 2.9 25.5 + - - -
1500F THR* 3.1 7.5 + - - -
1501F SER* 1.3 95.7 - - - +
1503F PHE* 1.3 71.2 + - - +
1504F ILE* 4.3 11.2 - - + -
1532F THR* 3.5 18.2 - - + +
1534F VAL* 5.3 2.2 - - + -
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Residues in contact with PHE1503 (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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1423F SER* 3.6 11.0 - - - -
1425F ILE* 5.4 5.8 - - + -
1495F ALA* 3.6 37.7 - - + -
1496F PHE* 5.7 0.2 - + - -
1499F LYS 5.3 0.4 - - - -
1500F THR* 4.0 22.0 - - - -
1502F ILE* 1.3 79.2 - - - +
1504F ILE* 1.3 72.2 + - - +
1505F MET* 4.3 4.0 - - + -
1528F PHE* 3.4 37.0 - + - -
1531F ARG* 3.5 33.2 - - + -
1532F THR 2.9 10.9 + - - +
1533F VAL* 3.6 30.2 - - + -
1534F VAL* 2.9 25.4 + - - +
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Residues in contact with ILE1504 (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 PHE* 6.3 2.9 - - + -
1389F SER* 3.3 34.1 - - - +
1392F PHE* 4.5 24.9 - - + -
1393F PHE* 4.8 10.3 - - + -
1422F LEU* 5.0 3.1 - - + -
1423F SER 2.8 18.2 + - - +
1424F ILE* 3.4 14.5 - - + -
1425F ILE* 2.9 29.2 + - - +
1502F ILE* 4.3 15.0 - - + -
1503F PHE* 1.3 88.0 - - - +
1505F MET* 1.3 66.0 - - - +
1506F ASP 4.0 1.1 - - - +
1534F VAL* 3.4 21.1 - - + +
1536F ILE* 5.2 5.6 - - + -
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Residues in contact with MET1505 (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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1425F ILE* 4.0 19.5 - - + -
1492F LEU* 5.9 2.9 - - + -
1503F PHE* 6.0 4.7 - - + -
1504F ILE* 1.3 75.0 - - - +
1506F ASP* 1.3 56.8 + - - +
1507F GLU 3.2 2.9 + - - -
1508F ALA* 3.5 31.2 - - + +
1509F THR* 6.1 0.4 - - - -
1521F GLN* 3.0 34.8 - - - +
1524F VAL* 4.7 17.7 - - + -
1525F MET* 5.8 0.7 - - + -
1533F VAL* 4.4 13.5 - - + -
1534F VAL 2.9 13.3 + - - +
1535F THR* 4.0 23.1 - - + -
1536F ILE* 2.9 27.8 + - - -
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Residues in contact with ASP1506 (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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1385F LYS* 4.4 8.1 - - - -
1386F SER* 3.4 33.6 - - - -
1389F SER* 4.8 4.6 - - - +
1424F ILE* 4.8 7.6 - - + -
1425F ILE* 2.9 19.2 + - - +
1426F LEU* 3.4 9.3 - - + +
1427F GLN* 3.2 32.3 + - - +
1504F ILE* 4.0 0.8 - - + -
1505F MET* 1.3 68.2 - - - +
1507F GLU* 1.3 83.6 + - - +
1508F ALA 3.6 0.2 - - - -
1536F ILE* 3.6 23.3 - - + +
2504F MG 4.3 0.3 - - - -
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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