Contacts of the strand formed by residues 1060 - 1065 (chain A) in PDB entry 1Y1S
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 LYS1060 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1056A GLU* 3.3 4.7 - - - -
1057A LEU 2.8 27.3 + - - +
1058A ASP 4.1 7.0 - - - +
1059A GLY* 1.3 83.8 - - - +
1061A ALA* 1.3 67.0 + - - +
1062A VAL* 3.8 1.4 - - - +
1253A LEU* 3.4 59.7 + - + +
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Residues in contact with ALA1061 (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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1016A LEU 3.4 24.5 - - - +
1017A GLN* 3.4 23.6 - - + +
1018A GLY 4.6 0.4 - - - -
1019A ALA* 3.1 23.6 - - + +
1020A GLN 4.2 2.8 + - - -
1021A LEU 4.9 0.7 + - - +
1054A ARG* 4.8 5.6 - - - +
1055A ALA 3.7 6.5 - - - +
1056A GLU* 4.8 3.6 - - - +
1059A GLY 4.1 1.2 + - - -
1060A LYS* 1.3 76.1 - - - +
1062A VAL* 1.3 64.0 + - - +
1253A LEU* 5.1 1.7 - - - +
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Residues in contact with VAL1062 (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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1019A ALA* 4.1 0.4 - - - -
1021A LEU* 3.9 26.9 - - + +
1023A ILE* 4.6 5.6 - - + -
1038A MET* 4.0 26.0 - - + -
1053A TRP 4.1 0.2 - - - +
1054A ARG* 3.5 4.9 - - - +
1055A ALA* 2.9 37.0 + - - +
1057A LEU* 3.8 27.8 - - + -
1060A LYS 3.8 2.9 - - - +
1061A ALA* 1.3 80.8 - - - +
1063A ILE* 1.3 75.8 + - - +
1064A VAL* 4.2 1.0 + - - +
1253A LEU* 4.0 19.5 - - + -
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Residues in contact with ILE1063 (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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1011A LEU* 5.6 1.1 - - + -
1016A LEU* 3.7 42.6 - - + -
1019A ALA* 4.0 9.6 - - + -
1021A LEU 3.2 10.4 + - - +
1022A ALA* 3.1 11.0 - - + -
1023A ILE 2.9 23.8 + - - -
1044A LEU* 3.5 28.5 - - + -
1052A SER* 4.9 5.4 - - - -
1053A TRP 3.6 4.0 - - - +
1054A ARG* 4.1 9.4 - - + -
1062A VAL* 1.3 78.8 - - - +
1064A VAL* 1.3 77.7 + - - +
1065A CYS* 4.3 11.4 - - + +
1081A LEU* 4.4 13.9 - - + -
1086A ILE* 4.2 4.9 - - + -
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Residues in contact with VAL1064 (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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1023A ILE* 3.3 17.0 - - + +
1025A PRO* 4.2 6.7 - - + -
1031A VAL* 3.5 36.2 - - + +
1034A ILE* 3.9 22.2 - - + -
1035A ALA* 4.4 6.3 - - + -
1038A MET* 3.5 32.5 - - + -
1052A SER* 3.2 2.3 - - - -
1053A TRP* 2.8 41.7 + - + +
1062A VAL 4.9 0.4 - - - +
1063A ILE* 1.3 82.5 - - - +
1065A CYS* 1.3 62.5 + - - +
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Residues in contact with CYS1065 (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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1009A LEU* 4.4 23.1 - - - -
1022A ALA* 5.5 0.4 - - + +
1023A ILE 3.1 6.9 + - - +
1024A VAL* 3.3 26.5 - - - +
1025A PRO* 3.8 3.8 - - - -
1050A PHE* 4.7 6.3 - - - -
1051A THR 3.4 7.2 - - - -
1052A SER* 4.0 20.4 - - - -
1063A ILE* 4.2 3.3 - - + +
1064A VAL* 1.3 76.4 - - - +
1066A SER* 1.3 77.3 + - - +
1067A THR* 3.9 0.2 - - - +
1077A ALA* 4.8 2.7 - - - -
1081A LEU* 4.0 31.4 - - + -
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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