Contacts of the strand formed by residues 1262 - 1268 (chain A) in PDB entry 4YOC
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 PHE1262 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1139A LEU* 3.8 18.4 - - + -
1218A GLU 3.5 2.4 + - - -
1219A MET* 3.6 23.2 - - + -
1220A LEU 3.0 24.8 + - - -
1260A PRO* 3.4 9.7 - - - +
1261A ARG* 1.3 97.5 - - + +
1263A PHE* 1.3 60.9 + - - +
1292A TYR* 5.7 0.2 - - - -
1317A ALA 3.4 5.8 - - - -
1318A ALA* 4.0 12.8 - - + -
1322A GLU* 3.7 24.0 - - - -
1323A LYS 3.8 19.3 - - - -
1325A PRO* 3.8 23.8 - - + -
1592A ILE* 4.2 14.4 - - + -
1595A CYS* 4.0 17.3 - - + -
1596A MET* 4.1 22.4 - - + -
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Residues in contact with PHE1263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1219A MET* 5.0 1.1 - - - +
1220A LEU* 3.2 21.3 - - + -
1251A PHE* 3.4 41.1 - + - -
1252A LEU* 4.1 12.3 - - + -
1255A CYS* 3.5 35.4 - - + -
1260A PRO* 4.7 2.9 - - + -
1262A PHE* 1.3 78.4 - - - +
1264A LEU* 1.3 61.6 + - - +
1265A LEU* 4.0 23.1 - - + -
1283A THR* 5.6 0.2 - - + -
1287A LEU* 4.0 20.9 - - + -
1292A TYR* 5.1 2.5 - - + -
1315A ILE* 4.4 5.8 - - + -
1316A LEU* 3.5 7.0 - - - +
1317A ALA* 2.9 58.0 + - + +
1592A ILE* 6.6 0.2 - - - -
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Residues in contact with LEU1264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1151A LEU* 4.8 11.9 - - + -
1155A PHE* 3.5 31.2 - - + -
1219A MET* 5.5 4.0 - - + -
1220A LEU 2.9 9.7 + - - +
1221A CYS* 3.3 13.7 - - + -
1222A GLY 2.9 27.7 + - - +
1251A PHE* 3.6 6.0 - - - -
1263A PHE* 1.3 74.8 - - - +
1265A LEU* 1.3 64.4 + - - +
1266A GLU* 3.5 31.0 - - + +
1314A ILE* 4.4 9.2 - - + -
1315A ILE 3.4 3.1 - - - +
1316A LEU* 4.1 14.8 - - + -
1588A ILE* 3.6 31.9 - - + -
1592A ILE* 4.9 2.0 - - + -
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Residues in contact with LEU1265 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1222A GLY 3.4 2.9 - - - -
1224A PRO* 3.8 29.2 - - + -
1248A VAL* 4.4 11.4 - - + -
1251A PHE* 3.6 24.9 - - + -
1252A LEU* 4.9 2.7 - - + -
1263A PHE* 4.0 14.7 - - + -
1264A LEU* 1.3 75.3 - - - +
1266A GLU* 1.3 66.0 + - - +
1267A ASN* 4.5 2.7 - - + -
1271A PHE* 3.9 28.3 - - + -
1283A THR* 4.4 20.2 - - + -
1313A ALA 3.6 2.8 - - - +
1315A ILE* 2.9 47.1 + - + +
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Residues in contact with GLU1266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1151A LEU* 4.6 7.0 - - + -
1222A GLY 2.9 17.5 + - - +
1223A GLY* 3.2 29.8 - - - +
1224A PRO* 3.9 1.6 - - - +
1264A LEU* 3.5 17.2 - - + +
1265A LEU* 1.3 73.8 - - - +
1267A ASN* 1.3 67.4 + - - +
1312A ARG* 3.3 35.5 + - - +
1313A ALA 3.4 4.7 - - - -
1314A ILE* 3.8 14.4 - - + -
1578A ASN 5.0 5.0 - - - +
1580A VAL* 3.4 35.0 - - + +
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Residues in contact with ASN1267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1223A GLY 4.5 1.0 - - - -
1224A PRO* 2.4 38.2 + - - +
1226A CYS* 3.9 13.3 + - - +
1265A LEU* 4.5 2.9 - - + -
1266A GLU* 1.3 81.2 + - - +
1268A VAL* 1.3 88.9 + - - +
1271A PHE* 3.7 34.1 - - + -
1312A ARG* 3.4 19.1 - - - +
1313A ALA 2.9 28.2 + - - +
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Residues in contact with VAL1268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702A ASP 6.0 1.6 - - - +
703A GLU* 5.9 1.6 - - - +
1226A CYS* 5.9 0.2 - - + -
1267A ASN* 1.3 97.1 + - - +
1269A ARG* 1.3 64.8 + - - +
1270A ASN* 4.2 5.6 - - + +
1271A PHE* 3.1 20.7 + - - +
1274A PHE* 3.9 26.2 - - + -
1311A ARG 4.6 0.4 - - - -
1312A ARG* 3.8 30.0 - - - +
1313A ALA* 3.2 2.1 - - - +
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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