Contacts of the strand formed by residues 1322 - 1328 (chain B) in PDB entry 4Z4Q
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 GLN1322 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1220B GLN* 5.4 0.2 - - - -
1237B VAL* 3.8 25.6 - - + +
1238B VAL 3.2 17.5 - - - +
1239B ARG* 2.8 45.1 + - + +
1316B PHE* 3.5 36.1 + - + +
1317B LYS* 5.7 1.4 - - - +
1319B THR 3.2 16.7 + - - +
1320B ASP* 2.8 2.5 - - - +
1321B LEU* 1.3 81.0 - - - +
1323B ILE* 1.3 65.6 + - - +
1324B ASN* 5.3 2.8 + - - -
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Residues in contact with ILE1323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1237B VAL* 3.6 5.7 - - - +
1238B VAL* 2.8 44.6 + - + +
1260B PRO* 3.7 20.9 - - + -
1261B TYR* 4.0 15.0 - - + +
1263B ILE* 4.2 11.7 - - + -
1320B ASP* 3.4 39.3 - - + +
1322B GLN* 1.3 80.6 - - - +
1324B ASN* 1.3 79.9 + - - +
1325B TYR* 4.9 5.8 - - + +
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Residues in contact with ASN1324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1235B ARG* 3.4 44.4 - - + +
1236B VAL 3.4 8.5 - - - +
1237B VAL* 3.9 15.3 - - - +
1322B GLN* 5.3 3.1 + - - -
1323B ILE* 1.3 84.7 - - - +
1325B TYR* 1.3 60.9 + - - +
1326B ASN* 3.9 7.6 + - - +
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Residues in contact with TYR1325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1177B ASP* 3.4 21.6 + - - -
1178B ILE 3.2 9.4 + - - -
1179B PRO* 2.9 51.4 - - + +
1213B PHE* 4.2 18.6 - + - -
1235B ARG* 3.7 1.6 - - - -
1236B VAL* 3.0 46.6 + - + +
1238B VAL* 4.0 15.0 - - + +
1261B TYR* 4.5 17.2 - + + -
1262B GLU* 4.6 7.6 - - - -
1323B ILE* 4.0 9.7 + - + +
1324B ASN* 1.3 73.0 - - - +
1326B ASN* 1.3 81.0 + - - +
1327B PHE* 3.7 18.9 + + - -
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Residues in contact with ASN1326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1177B ASP* 3.7 13.7 - - - +
1234B GLY 3.5 4.3 - - - +
1235B ARG* 3.3 49.0 + - - +
1324B ASN* 3.9 9.7 + - - +
1325B TYR* 1.3 88.5 - - - +
1327B PHE* 1.3 66.3 + - - +
1328B ASN* 3.3 5.0 + - + +
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Residues in contact with PHE1327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1177B ASP 3.8 4.3 - - - -
1179B PRO* 3.2 34.3 - - + -
1211B PRO* 3.4 30.7 - - + -
1224B GLU 5.1 0.7 - - - -
1225B ILE* 4.6 12.3 - - + -
1228B ALA* 3.4 34.3 - - + -
1229B TYR* 4.3 17.9 - + - -
1232B GLY 3.5 6.7 - - - +
1233B LYS* 3.3 19.9 - - - +
1234B GLY 2.8 23.0 + - - +
1235B ARG 4.9 0.2 - - - -
1236B VAL* 4.3 22.2 - - + -
1325B TYR* 4.0 12.1 - + - -
1326B ASN* 1.3 73.3 - - - +
1328B ASN* 1.3 60.7 - - - +
1329B MET* 4.1 13.5 - - + -
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Residues in contact with ASN1328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1175B ALA* 3.3 32.1 + - - +
1176B THR* 3.3 2.5 - - - -
1177B ASP* 2.7 42.8 + - + +
1232B GLY 3.4 2.0 - - - -
1233B LYS* 3.3 34.3 - - + +
1326B ASN* 3.3 4.2 + - + +
1327B PHE* 1.3 75.6 - - - +
1329B MET* 1.3 55.9 + - - +
1330B VAL* 3.1 11.8 + - - +
1339B GLN* 3.5 10.2 - - - +
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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