Contacts of the strand formed by residues 1284 - 1287 (chain P) in PDB entry 1YYL
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 ILE1284 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1272P ILE* 4.3 14.6 - - + -
1273P ARG 3.6 7.9 - - - +
1274P SER* 4.2 4.0 - - - +
1277P PHE* 3.6 39.7 - - + -
1282P LYS 3.9 8.5 - - - +
1283P THR* 1.3 74.2 - - - +
1285P ILE* 1.3 65.4 + - - +
1286P VAL* 3.7 7.6 + - + +
1349P LEU* 4.5 7.6 - - + -
1353P PHE* 4.8 2.9 - - + -
1452P LEU 3.7 0.7 - - - +
1453P LEU* 3.6 4.0 - - - -
1454P LEU* 2.8 44.4 + - + +
1455P THR* 5.3 0.7 - - - -
1456P ARG* 4.5 11.9 - - + +
1468P PHE* 3.8 33.2 - - + -
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Residues in contact with ILE1285 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095P MET* 5.5 2.9 - - - -
1096P TRP* 3.6 33.2 - - + -
1260P LEU* 4.2 12.8 - - + -
1271P VAL 4.0 0.9 - - - +
1272P ILE* 3.8 0.9 - - - -
1273P ARG* 2.8 41.6 + - + +
1283P THR* 4.6 3.6 - - + +
1284P ILE* 1.3 73.5 - - - +
1286P VAL* 1.3 65.3 + - - +
1287P GLN* 4.0 1.9 + - + +
1452P LEU 3.6 2.9 - - - -
1453P LEU* 4.0 13.2 - - + -
1477P ASP* 3.8 34.1 - - + +
1480P ARG* 4.3 8.7 - - + -
1481P SER* 3.8 27.6 - - - +
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Residues in contact with VAL1286 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1260P LEU* 4.2 5.9 - - - +
1270P ILE* 4.2 14.1 - - + -
1271P VAL 4.0 2.9 - - - -
1272P ILE* 4.1 17.0 - - + +
1284P ILE* 4.5 7.4 - - + +
1285P ILE* 1.3 76.1 - - - +
1287P GLN* 1.3 65.1 + - - +
1288P LEU* 4.4 2.0 - - + -
1345P ILE* 4.0 32.3 - - + -
1349P LEU* 5.8 0.2 - - + -
1451P GLY* 3.0 5.4 - - - -
1452P LEU* 2.7 50.7 + - + +
1454P LEU* 3.6 31.4 - - + -
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Residues in contact with GLN1287 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1264P SER* 3.1 31.3 + - - +
1265P LEU* 4.2 2.8 + - - -
1266P ALA* 2.9 29.6 - - - +
1270P ILE* 3.1 20.7 - - - +
1271P VAL* 3.1 23.2 + - - +
1273P ARG* 3.2 21.7 + - - +
1285P ILE* 4.0 2.6 + - + +
1286P VAL* 1.3 73.8 - - - +
1288P LEU* 1.3 68.2 + - - +
1450P THR 3.8 3.8 - - - +
1451P GLY* 4.4 0.4 - - - -
1481P SER* 4.2 10.2 + - - +
1484P TYR* 3.6 29.9 + - - -
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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