Contacts of the strand formed by residues 1031 - 1038 (chain A) in PDB entry 4KSC
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 VAL1031 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1029A GLY 3.5 7.1 + - - +
1030A ASN* 1.3 72.9 - - - +
1032A GLN* 1.3 64.0 + - - +
1033A PHE* 3.6 33.5 - - + -
1054A LEU 3.9 0.9 - - - +
1055A GLU* 3.3 25.5 + - - +
1056A VAL* 3.3 24.4 + - + +
1079A LEU* 4.6 22.9 - - + -
1090A VAL* 4.7 1.6 - - + -
1091A PHE 3.2 9.9 - - - +
1092A LEU* 4.6 5.8 - - + -
1192A ILE* 4.1 28.0 - - + -
1222A THR* 5.6 1.8 - - + -
1224A ILE* 5.5 5.8 - - + -
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Residues in contact with GLN1032 (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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1030A ASN* 4.3 10.3 + - - +
1031A VAL* 1.3 73.8 - - - +
1033A PHE* 1.3 67.0 + - - +
1034A SER* 4.3 2.2 - - - -
1054A LEU 3.8 3.3 - - - +
1055A GLU* 3.3 32.3 + - - +
1090A VAL* 3.1 14.4 - - - +
1091A PHE* 2.6 63.1 + - + -
1094A GLY* 5.5 4.0 - - - -
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Residues in contact with PHE1033 (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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1031A VAL* 3.6 25.8 - - + -
1032A GLN* 1.3 77.5 - - - +
1034A SER* 1.3 63.1 + - - +
1036A VAL* 4.2 21.8 - - + -
1052A LEU* 4.2 4.9 - - + +
1053A SER* 3.1 24.3 - - - -
1054A LEU* 2.9 52.6 + - + +
1075A VAL* 4.1 35.0 - - + -
1078A LEU* 5.4 11.9 - - + -
1079A LEU* 5.2 9.4 - - + -
1089A SER 3.9 2.2 - - - -
1090A VAL* 3.4 24.5 - - + -
1224A ILE* 5.5 7.0 - - + -
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Residues in contact with SER1034 (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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1032A GLN* 4.3 2.2 - - - -
1033A PHE* 1.3 76.5 - - - +
1035A GLY* 1.3 67.5 + - - +
1036A VAL* 3.1 3.8 + - - +
1053A SER* 3.4 4.8 + - - -
1088A GLY* 3.6 1.6 - - - -
1089A SER* 3.1 32.7 + - - +
1091A PHE* 4.8 13.5 - - - -
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Residues in contact with GLY1035 (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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1034A SER* 1.3 74.1 + - - +
1036A VAL* 1.3 61.3 + - - +
1037A VAL* 3.6 5.5 + - - +
1051A GLY* 4.9 7.2 - - - -
1052A LEU 4.1 4.7 - - - -
1053A SER* 3.0 14.1 + - - -
1087A ALA* 3.5 3.6 - - - +
1088A GLY* 3.1 18.2 + - - -
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Residues in contact with VAL1036 (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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1033A PHE* 4.2 19.7 - - + -
1034A SER 3.4 13.2 - - - +
1035A GLY* 1.3 75.1 - - - +
1037A VAL* 1.3 72.9 + - - +
1038A PHE* 5.1 0.4 - - + -
1049A LEU* 4.3 4.7 - - + +
1050A GLN 4.2 0.5 - - - -
1051A GLY 3.5 2.1 + - - -
1052A LEU* 3.0 44.2 + - + +
1078A LEU* 4.6 16.2 - - + -
1085A PRO* 4.1 17.7 - - + -
1087A ALA 3.6 3.6 - - - +
1089A SER 3.2 33.0 - - - +
1090A VAL* 5.0 2.2 - - + -
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Residues in contact with VAL1037 (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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1035A GLY 4.4 5.4 - - - +
1036A VAL* 1.3 74.3 - - - +
1038A PHE* 1.3 61.8 + - - +
1047A PRO* 6.2 0.4 - - + -
1049A LEU* 3.2 10.5 - - - +
1050A GLN* 3.7 8.3 - - + -
1051A GLY* 3.3 26.0 - - - +
1085A PRO* 3.2 22.2 - - - +
1086A MET* 3.3 16.8 + - + -
1087A ALA* 3.2 34.7 + - + +
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Residues in contact with PHE1038 (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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1036A VAL* 5.1 0.2 - - + -
1037A VAL* 1.3 77.6 - - - +
1039A ASN* 1.3 81.2 + - - +
1040A TYR* 3.4 31.4 - + + -
1041A PRO* 5.5 0.2 - - + -
1047A PRO* 3.1 19.1 - - - +
1048A VAL* 3.6 6.3 + - + -
1049A LEU* 2.9 48.1 + - + +
1074A THR* 3.8 25.1 - - + -
1077A GLN* 5.5 4.7 - - + -
1078A LEU* 3.5 38.8 - - + -
1083A TYR* 3.3 32.1 - + + -
1085A PRO* 4.6 5.8 - - + -
1086A MET* 4.5 6.3 - - - +
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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