Contacts of the strand formed by residues 1288 - 1296 (chain A) in PDB entry 5M64
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 ARG1288 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1274A GLU* 2.4 39.6 + - - +
1275A THR 4.4 2.7 + - - -
1276A THR* 2.6 41.8 + - - +
1287A ALA* 1.3 71.9 - - - +
1289A SER* 1.3 58.2 + - - +
1290A TYR* 3.4 26.5 + - + +
1475A GLU* 3.0 6.6 - - - +
1476A LEU* 2.9 42.0 + - + +
1477A ALA 3.3 18.3 + - - +
1478A ALA* 4.8 3.6 - - - +
1480A THR 3.6 14.4 - - - +
1481A GLU* 3.1 28.1 + - - +
1482A LYS* 4.8 7.5 - - - +
6I SER* 4.9 7.1 + - - -
19I ASN* 5.2 5.3 + - - +
21I ASN* 5.4 4.2 + - - -
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Residues in contact with SER1289 (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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1275A THR* 2.9 49.5 + - - +
1276A THR* 5.2 0.4 - - - -
1277A GLY 5.3 3.4 + - - -
1287A ALA* 3.5 9.7 + - - +
1288A ARG* 1.3 72.2 - - - +
1290A TYR* 1.3 68.4 + - - +
1473A LYS* 5.7 2.9 - - - -
1474A LEU 3.8 1.6 - - - -
1475A GLU* 2.5 33.9 + - - -
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Residues in contact with TYR1290 (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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1274A GLU* 3.2 36.3 + - + +
1275A THR* 5.0 1.8 - - - +
1288A ARG* 3.4 41.5 + - + +
1289A SER* 1.3 81.4 - - - +
1291A VAL* 1.3 59.3 + - - +
1292A ILE* 4.3 14.1 - - + -
1473A LYS* 3.3 6.1 - - - +
1474A LEU* 2.8 51.1 + - + +
1475A GLU 5.1 0.4 - - - -
1476A LEU* 4.0 18.6 - - + +
1483A LEU* 3.4 25.1 - - + +
1485A MET* 3.5 35.2 - - + -
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Residues in contact with VAL1291 (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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1272A VAL* 3.5 22.2 - - - +
1273A THR* 3.2 39.7 + - - +
1275A THR* 5.0 6.3 - - + +
1290A TYR* 1.3 74.9 - - - +
1292A ILE* 1.3 65.5 + - - +
1293A HIS* 4.2 2.9 + - + +
1471A GLU* 3.3 33.9 - - + +
1472A PHE 3.8 3.8 - - - +
1473A LYS* 4.3 10.3 - - + +
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Residues in contact with ILE1292 (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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1272A VAL* 3.6 17.5 - - + -
1290A TYR* 4.3 12.1 - - + -
1291A VAL* 1.3 84.1 - - - +
1293A HIS* 1.3 60.8 + - - +
1294A MET* 3.8 26.5 - - + +
1321A PHE* 6.0 0.2 - - + -
1470A CYS 3.4 1.6 - - - +
1471A GLU* 3.1 7.4 - - - -
1472A PHE* 2.9 79.4 + - + +
1474A LEU* 4.3 13.0 - - + -
1485A MET* 6.2 4.3 - - - -
1489A VAL* 5.3 13.5 - - + -
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Residues in contact with HIS1293 (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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1270A VAL* 4.6 0.5 - - - -
1271A ILE* 2.9 61.3 + - + +
1272A VAL* 4.9 0.4 - - - +
1291A VAL* 4.1 4.3 + - + -
1292A ILE* 1.3 73.2 - - - +
1294A MET* 1.3 64.4 + - - +
1295A ARG* 3.3 37.0 + - - -
1433A VAL 6.2 0.4 - - - -
1435A ALA* 4.8 13.7 - - + -
1469A TRP* 3.3 48.3 - + + +
1470A CYS 3.8 0.9 - - - -
1471A GLU* 4.2 14.1 - - + +
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Residues in contact with MET1294 (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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1267A ILE* 3.6 19.3 - - + -
1269A LYS 4.5 0.2 - - - -
1270A VAL* 3.6 44.4 - - + -
1292A ILE* 3.8 25.6 - - + -
1293A HIS* 1.3 71.1 - - - +
1295A ARG* 1.3 64.0 + - - +
1296A PHE* 3.5 28.7 + - + -
1317A ILE* 5.9 2.7 - - + -
1321A PHE* 4.8 11.0 - - + -
1469A TRP* 3.1 4.1 - - - -
1470A CYS* 2.9 39.0 + - + +
1472A PHE* 5.4 4.3 - - + -
1489A VAL* 4.1 15.7 - - + -
1493A CYS* 5.0 4.7 - - - -
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Residues in contact with ARG1295 (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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1267A ILE* 3.2 6.8 - - - +
1268A ASP* 3.1 37.2 + - + +
1269A LYS* 3.6 44.6 + - + +
1271A ILE* 5.1 3.5 - - + +
1293A HIS* 3.3 30.3 + - + +
1294A MET* 1.3 73.2 - - - +
1296A PHE* 1.3 66.9 + - - +
1433A VAL* 4.9 23.8 + - - +
1435A ALA* 6.2 1.2 - - - +
1468A LYS* 3.5 11.6 + - - +
1469A TRP* 3.5 34.0 - - - +
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Residues in contact with PHE1296 (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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1263A LEU* 6.5 0.7 - - + -
1266A VAL* 3.2 24.0 - - + +
1267A ILE* 3.6 13.0 - - + -
1268A ASP* 2.9 19.5 - - - +
1294A MET* 3.6 25.6 - - + -
1295A ARG* 1.3 82.2 - - - +
1297A PHE* 1.3 64.8 + - - +
1302A TYR* 5.2 3.4 - + + -
1313A LEU* 4.3 15.9 - - + -
1317A ILE* 4.0 17.9 - - + -
1462A PHE* 3.7 18.4 - + - -
1467A GLY 3.3 24.2 - - - +
1468A LYS* 2.5 27.6 + - - +
1469A TRP 3.8 11.7 - - - -
1470A CYS* 3.6 30.3 - - + -
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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