Contacts of the helix formed by residues 694 - 704 (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 TRP 694 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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693A PHE* 1.3 103.9 - + + +
695A ARG* 1.3 60.0 + - - +
696A ILE* 3.0 18.6 + - + +
697A LEU* 3.4 54.9 - - + +
698A LYS* 3.5 7.4 + - - +
828A ARG* 3.9 17.3 - - - -
994A TYR* 3.8 24.0 + + - -
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Residues in contact with ARG 695 (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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692A SER* 3.7 18.1 + - - +
693A PHE 2.8 6.3 + - - +
694A TRP* 1.3 75.2 - - - +
696A ILE* 1.3 55.9 + - - +
697A LEU 3.6 0.2 - - - -
698A LYS* 3.7 19.7 - - + +
699A LEU* 2.8 61.2 + - + +
1005A ILE* 3.6 32.0 - - + +
1006A ARG* 6.2 1.0 - - - +
1009A GLU* 2.7 38.7 + - - +
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Residues in contact with ILE 696 (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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692A SER* 3.7 23.6 - - - +
694A TRP* 3.0 21.3 - - + +
695A ARG* 1.3 78.7 - - - +
697A LEU* 1.3 58.4 + - + +
699A LEU* 3.7 1.5 - - - +
700A ASN* 2.8 50.4 + - - +
821A VAL* 6.0 0.4 - - + -
824A ALA* 6.0 8.5 - - + -
828A ARG* 3.5 24.5 - - - +
994A TYR* 3.6 25.8 - - + +
997A ALA 5.9 0.2 - - - -
998A THR* 4.7 14.8 - - + +
1001A ALA* 3.8 22.4 - - + -
1005A ILE* 4.8 5.2 - - + -
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Residues in contact with LEU 697 (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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694A TRP* 3.4 47.8 - - + +
696A ILE* 1.3 77.3 - - - +
698A LYS* 1.3 77.8 + - + +
700A ASN* 3.7 12.3 - - - +
701A SER* 2.7 39.5 + - - +
828A ARG* 3.5 27.6 - - - +
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Residues in contact with LYS 698 (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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694A TRP* 3.5 12.1 + - - +
695A ARG* 3.2 24.4 + - + +
696A ILE 3.0 0.4 - - - -
697A LEU* 1.3 89.1 - - + +
699A LEU* 1.3 57.7 + - + +
701A SER* 4.2 2.5 - - - -
702A THR* 2.5 34.6 + - - +
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Residues in contact with LEU 699 (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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695A ARG* 2.8 48.7 + - + +
696A ILE* 3.9 2.5 - - - +
698A LYS* 1.3 77.6 - - + +
700A ASN* 1.3 66.6 - - - +
702A THR* 3.3 12.1 - - + +
703A GLU* 2.9 36.2 + - - +
1005A ILE* 3.6 38.4 - - + -
1008A ILE* 5.7 5.2 - - + -
1009A GLU* 5.6 0.7 - - - +
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Residues in contact with ASN 700 (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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696A ILE* 2.8 37.4 + - - +
697A LEU* 3.8 10.1 - - - +
699A LEU* 1.3 77.7 - - - +
701A SER* 1.3 54.1 + - - +
703A GLU* 2.9 12.7 + - - +
704A TRP* 2.8 37.3 + - + +
780A LEU* 4.4 16.5 - - + +
784A LEU* 5.6 3.1 - - - +
821A VAL* 5.2 13.2 + - - +
824A ALA* 5.2 7.3 - - - +
825A THR* 4.0 18.3 + - - +
828A ARG* 6.0 2.2 - - - +
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Residues in contact with SER 701 (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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697A LEU* 2.7 29.4 + - - +
698A LYS* 4.2 2.9 - - - -
700A ASN* 1.3 73.7 - - - +
702A THR* 1.3 59.1 + - - +
704A TRP* 2.9 43.1 - - - +
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Residues in contact with THR 702 (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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698A LYS* 2.5 25.8 + - - +
699A LEU* 3.3 17.4 - - + +
701A SER* 1.3 81.1 - - - +
703A GLU* 1.3 62.7 + - + +
704A TRP 3.7 1.4 + - - -
705A PRO* 5.4 2.3 - - - +
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Residues in contact with GLU 703 (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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699A LEU* 2.9 29.6 + - - +
700A ASN* 2.9 11.3 + - - +
702A THR* 1.3 82.2 - - + +
704A TRP* 1.3 58.9 + - - +
705A PRO* 3.1 13.5 - - - +
779A ILE* 4.4 4.2 - - - +
780A LEU* 4.0 16.7 - - + +
783A ARG* 4.0 30.6 + - - +
784A LEU* 3.7 32.2 - - - +
787A MET* 3.6 27.8 - - - +
1008A ILE* 5.3 2.1 - - - +
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Residues in contact with TRP 704 (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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700A ASN 2.8 16.3 + - - +
701A SER* 2.9 34.8 + - - +
702A THR 4.8 0.4 - - - -
703A GLU* 1.3 76.6 - - - +
705A PRO* 1.3 69.0 - - + +
706A TYR* 5.5 0.7 - - - -
707A PHE* 2.2 91.7 - + + -
711A ILE* 5.7 4.3 - - + -
776A ALA* 3.9 21.4 - - + +
779A ILE* 5.1 3.4 - - + -
780A LEU* 5.1 10.5 - - + -
825A THR* 6.4 3.4 - - + -
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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