Contacts of the strand formed by residues 1469 - 1476 (chain A) in PDB entry 5M5X
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 TRP1469 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1293A HIS* 4.2 7.9 - - - +
1294A MET 3.4 10.3 - - - +
1295A ARG* 3.6 33.2 - - - +
1296A PHE* 3.4 11.8 - - - -
1459A LYS* 5.8 0.2 - - - -
1461A ASN* 3.2 38.1 - - - -
1463A ASP* 2.8 65.5 + - + +
1465A GLU* 4.9 6.3 + - - -
1468A LYS* 1.3 83.7 - - + +
1470A CYS* 1.3 81.3 + - - +
1471A GLU* 3.7 27.6 - - + -
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Residues in contact with CYS1470 (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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1292A ILE 4.0 0.2 - - - +
1293A HIS* 3.6 3.2 - - - -
1294A MET* 2.9 46.1 + - + +
1296A PHE* 3.6 20.0 - - + -
1317A ILE* 5.0 3.4 - - - -
1460A TYR* 4.0 21.5 - - - -
1461A ASN 3.5 17.0 - - - -
1462A PHE* 3.5 20.2 - - + +
1469A TRP* 1.3 82.0 - - - +
1471A GLU* 1.3 60.8 + - - +
1472A PHE* 4.2 10.7 - - - -
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Residues in contact with GLU1471 (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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1291A VAL* 3.2 28.7 - - + +
1292A ILE 3.3 14.1 - - - +
1293A HIS* 4.6 13.0 - - + -
1459A LYS* 2.8 34.4 + - - +
1461A ASN* 2.9 32.6 + - - +
1469A TRP* 3.7 18.7 - - + -
1470A CYS* 1.3 75.0 - - - +
1472A PHE* 1.3 72.3 + - - +
1473A LYS* 4.3 5.4 + - - +
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Residues in contact with PHE1472 (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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1292A ILE* 3.2 66.5 + - + +
1294A MET* 4.1 18.6 - - + -
1317A ILE* 5.9 1.6 - - + -
1321A PHE* 4.5 19.1 - + - -
1322A ILE* 5.6 7.2 - - + -
1325A LEU* 4.7 11.4 - - + -
1456A PHE* 5.2 1.3 - + - -
1457A ILE* 4.5 12.3 - - + -
1459A LYS 3.2 14.1 - - - +
1460A TYR* 3.5 31.6 - + + -
1470A CYS* 4.2 10.5 - - - -
1471A GLU* 1.3 82.5 - - - +
1473A LYS* 1.3 69.6 - - - +
1474A LEU* 4.5 13.0 - - + -
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Residues in contact with LYS1473 (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* 4.8 2.0 - - - -
1289A SER* 3.0 20.8 - - - -
1290A TYR 4.0 1.9 - - - +
1291A VAL* 3.7 33.2 - - + +
1457A ILE* 3.8 11.8 - - - +
1458A THR* 3.3 35.4 + - - +
1459A LYS* 2.8 27.0 + - + +
1471A GLU* 4.3 4.8 + - - +
1472A PHE* 1.3 75.1 - - - +
1474A LEU* 1.3 67.6 + - - +
1475A GLU* 1.9 40.7 + - - +
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Residues in contact with LEU1474 (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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1289A SER* 3.3 4.0 - - - -
1290A TYR* 2.8 50.0 + - + +
1292A ILE* 4.6 10.5 - - + -
1325A LEU* 4.8 9.9 - - + -
1329A ILE* 4.9 14.1 - - + -
1456A PHE* 3.5 42.4 - - + -
1472A PHE* 4.5 13.7 - - + -
1473A LYS* 1.3 81.8 + - - +
1475A GLU* 1.3 77.0 + - - +
1476A LEU* 3.5 27.4 - - + -
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Residues in contact with GLU1475 (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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1287A ALA* 4.7 6.8 - - - +
1288A ARG 2.9 9.5 - - - +
1289A SER* 2.5 21.2 + - - -
1456A PHE* 3.6 22.8 + - - +
1458A THR* 3.9 26.0 - - + +
1473A LYS* 1.9 41.0 + - - +
1474A LEU* 1.3 79.7 - - - +
1476A LEU* 1.3 72.2 + - - +
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Residues in contact with LEU1476 (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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1287A ALA* 3.9 6.2 - - - +
1288A ARG* 2.9 33.3 + - + +
1290A TYR* 3.5 31.0 - - + -
1329A ILE* 4.8 8.5 - - + -
1333A ILE* 4.8 10.8 - - + -
1474A LEU* 3.5 26.7 - - + -
1475A GLU* 1.3 77.9 - - - +
1477A ALA* 1.3 63.0 + - - +
1480A THR* 3.3 32.1 - - + +
1483A LEU* 4.6 15.9 - - + -
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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