Contacts of the strand formed by residues 1222 - 1225 (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 THR1222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1028A GLU 4.5 0.7 + - - -
1029A GLY* 3.3 20.6 + - - +
1031A VAL* 5.6 2.0 - - + -
1056A VAL* 3.6 35.4 - - + -
1057A LYS 3.8 2.7 - - - +
1058A LYS* 3.1 26.5 - - - +
1059A GLY 3.2 4.7 + - - +
1060A GLN 3.6 6.5 - - - +
1191A HIS 3.3 12.7 + - - -
1192A ILE* 3.6 10.1 - - + -
1193A LEU* 2.9 25.4 + - - +
1221A ARG* 1.3 75.6 - - - +
1223A CYS* 1.3 66.0 + - - +
1224A ILE* 5.5 3.1 - - + -
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Residues in contact with CYS1223 (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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1060A GLN 3.3 5.7 + - - +
1061A THR* 2.8 36.8 - - - -
1062A LEU* 2.8 27.7 + - - +
1193A LEU* 3.4 21.8 - - + -
1195A LEU* 4.3 9.9 - - + -
1218A ARG* 3.5 32.3 - - + -
1221A ARG 3.5 1.1 + - - +
1222A THR* 1.3 80.3 - - - +
1224A ILE* 1.3 67.9 + - - +
1225A VAL* 5.0 1.1 - - - -
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Residues in contact with ILE1224 (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* 5.5 5.2 - - + -
1033A PHE* 5.5 8.5 - - + -
1056A VAL* 5.0 13.0 - - + -
1062A LEU* 3.4 34.8 - - + +
1064A LEU* 4.6 6.1 - - + -
1075A VAL* 5.1 16.8 - - + -
1076A VAL* 5.1 6.3 - - + +
1079A LEU* 4.8 9.6 - - + -
1192A ILE* 5.8 2.0 - - + -
1193A LEU 3.1 7.8 + - - +
1194A LEU* 3.7 25.4 - - + +
1195A LEU* 2.7 36.0 + - - +
1222A THR* 5.5 3.4 - - + -
1223A CYS* 1.3 78.6 - - - +
1225A VAL* 1.3 57.1 + - - +
1226A ILE* 4.4 18.6 - - + +
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Residues in contact with VAL1225 (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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1061A THR* 4.1 12.1 - - + -
1062A LEU 3.5 6.2 + - - +
1063A ALA* 4.0 0.6 - - - -
1064A LEU* 3.2 21.8 + - - +
1195A LEU* 3.5 22.0 - - + -
1211A GLN* 5.9 2.5 - - - +
1214A LEU* 6.1 3.8 - - + -
1218A ARG* 3.9 22.4 - - - +
1223A CYS* 5.0 1.6 - - - -
1224A ILE* 1.3 73.0 - - - +
1226A ILE* 1.3 61.2 + - - +
1227A ALA* 3.5 26.9 + - + +
1233A ILE* 3.6 28.5 - - + +
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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