Contacts of the strand formed by residues 1472 - 1477 (chain A) in PDB entry 4YKN
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 CYS1472 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1340A CYS 4.0 0.7 - - - +
1341A ALA* 3.3 4.1 - - - -
1342A THR* 3.0 49.9 + - + +
1442A ALA* 3.8 28.7 - - - -
1443A LEU 3.5 7.2 - - - -
1444A ASN* 3.5 28.0 - - - +
1468A LYS 5.8 0.4 - - - +
1470A THR 4.1 1.3 - - - +
1471A PRO* 1.3 72.9 - - - +
1473A LEU* 1.3 63.3 + - - +
1474A GLU* 4.0 6.4 + - - +
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Residues in contact with LEU1473 (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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1338A ILE* 3.9 21.1 - - + -
1340A CYS 3.3 21.1 - - - +
1341A ALA* 4.3 9.9 - - + +
1356A VAL* 4.0 25.4 - - + -
1383A TRP* 4.5 0.4 - - + -
1404A LEU* 3.7 29.8 - - + -
1406A ILE* 4.7 4.3 - - + -
1441A MET 3.9 0.5 - - - +
1442A ALA* 3.6 0.3 - - - -
1443A LEU* 2.8 44.7 + - + +
1445A LEU* 4.4 16.6 - - + +
1471A PRO 4.1 1.2 + - - -
1472A CYS* 1.3 72.7 - - - +
1474A GLU* 1.3 61.5 + - - +
1475A LEU* 3.6 26.4 + - + +
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Residues in contact with GLU1474 (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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1339A LEU* 3.0 46.1 + - + +
1340A CYS* 2.9 31.9 + - - +
1342A THR* 4.8 12.8 - - - +
1441A MET 3.3 4.9 - - - +
1442A ALA* 4.4 17.0 - - + +
1472A CYS* 4.9 7.3 - - - +
1473A LEU* 1.3 76.0 - - - +
1475A LEU* 1.3 64.7 + - - +
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Residues in contact with LEU1475 (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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1336A ILE* 4.9 2.9 - - + -
1337A LYS 3.5 4.0 - - - +
1338A ILE* 3.5 31.9 - - + -
1339A LEU* 4.1 5.5 - - - +
1402A LEU* 4.3 4.0 - - + -
1404A LEU* 3.9 15.9 - - + -
1427A ILE* 3.9 28.5 - - + -
1439A GLY 4.6 0.2 - - - -
1440A LYS* 3.2 6.4 - - - +
1441A MET* 2.6 41.6 + - + +
1443A LEU* 5.1 4.9 - - + -
1473A LEU* 3.6 28.0 - - + +
1474A GLU* 1.3 79.0 - - - +
1476A GLU* 1.3 60.2 + - - +
1477A PHE* 3.9 26.2 - - + -
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Residues in contact with GLU1476 (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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1336A ILE* 3.9 2.6 - - - +
1337A LYS* 2.9 67.2 + - + +
1339A LEU* 4.0 19.0 - - + +
1386A TRP* 4.3 11.9 - - + -
1439A GLY* 3.5 6.1 - - - +
1440A LYS* 4.1 22.1 - - + +
1475A LEU* 1.3 75.3 - - - +
1477A PHE* 1.3 71.7 - - - +
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Residues in contact with PHE1477 (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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1335A ARG 5.1 1.1 - - - -
1336A ILE* 3.6 44.0 - - + -
1386A TRP* 4.6 3.3 - - - -
1402A LEU* 4.3 9.0 - - + -
1427A ILE* 4.8 5.4 - - + -
1429A LEU* 4.6 2.7 - - + -
1437A VAL* 3.7 33.7 - - + +
1438A SER* 3.9 19.1 - - - -
1439A GLY* 2.7 35.6 + - - +
1441A MET* 3.7 39.7 - - + -
1475A LEU* 3.9 23.3 - - + -
1476A GLU* 1.3 82.1 - - - +
1478A ASP* 1.3 67.6 + - - +
1479A TRP* 3.5 3.5 + - - +
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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