Contacts of the helix formed by residues 689 - 707 (chain A) in PDB entry 3KSS
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 VAL 689 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687A GLY 3.5 0.4 - - - -
688A THR* 1.3 85.2 - - + +
690A LEU* 1.3 70.9 - - + +
691A ALA* 3.2 14.1 + - + +
692A ASP* 3.2 44.7 + - - +
693A ILE* 3.6 17.0 + - - +
820A PRO* 5.2 2.0 - - - -
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Residues in contact with LEU 690 (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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689A VAL* 1.3 76.4 - - + +
691A ALA* 1.3 63.8 + - - +
692A ASP 3.3 0.3 + - - -
693A ILE* 3.3 12.3 - - + +
694A ASP* 3.1 35.3 + - + +
810A PRO* 5.6 7.9 - - + -
813A LEU* 4.8 25.4 - - + -
814A LYS 6.0 1.8 - - - +
820A PRO* 4.6 20.6 - - + +
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Residues in contact with ALA 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A VAL* 3.2 12.7 - - + +
690A LEU* 1.3 79.3 - - - +
692A ASP* 1.3 70.9 + - - +
694A ASP* 3.8 4.5 - - - +
695A ALA* 3.3 20.1 + - - +
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Residues in contact with ASP 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A THR* 5.3 3.1 + - - -
689A VAL* 3.2 32.7 + - - +
691A ALA* 1.3 79.9 - - - +
693A ILE* 1.3 62.8 + - - +
695A ALA* 3.1 17.7 + - - +
696A MET* 3.3 24.0 + - + +
851A LYS* 4.6 22.7 - - + +
852A PRO 5.1 5.7 - - - +
853A GLY* 5.6 1.2 - - - +
854A THR* 4.4 19.2 - - + +
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Residues in contact with ILE 693 (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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685A VAL* 3.0 40.3 - - + +
686A SER 3.5 21.1 - - - +
687A GLY* 3.5 9.9 - - - +
689A VAL 3.6 10.5 - - - +
690A LEU* 3.3 23.3 - - + +
692A ASP* 1.3 77.0 - - - +
694A ASP* 1.3 61.7 + - - +
696A MET* 3.3 22.9 - - - +
697A ALA 3.5 3.1 + - - -
820A PRO* 3.2 44.2 - - + +
821A THR* 4.1 3.6 - - - +
822A SER* 3.5 10.3 + - - +
854A THR* 4.0 4.9 - - + -
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Residues in contact with ASP 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A LEU* 3.1 33.4 + - + +
691A ALA* 3.8 6.0 - - - +
692A ASP 3.2 0.2 - - - -
693A ILE* 1.3 74.0 - - - +
695A ALA* 1.3 66.7 + - - +
696A MET 3.0 1.8 - - - -
697A ALA* 3.0 18.9 + - - +
698A GLU* 3.4 16.5 + - - +
716A GLU* 4.2 25.8 - - - +
719A GLU* 5.2 7.3 - - - +
822A SER* 4.9 4.9 - - - -
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Residues in contact with ALA 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691A ALA 3.3 9.0 + - - +
692A ASP* 3.1 12.2 + - - +
694A ASP* 1.3 79.2 - - - +
696A MET* 1.3 67.0 + - + +
698A GLU* 3.4 12.6 + - - +
699A GLN* 3.3 20.8 + - - +
851A LYS* 5.8 5.2 - - + -
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Residues in contact with MET 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A VAL* 3.6 29.6 - - + -
692A ASP* 3.3 18.4 - - + +
693A ILE* 3.3 8.7 - - - +
695A ALA* 1.3 78.4 - - - +
697A ALA* 1.3 60.8 + - - +
699A GLN* 3.0 17.8 + - + +
700A ILE* 2.8 36.5 + - + +
850A LEU* 4.9 6.5 - - + -
851A LYS* 3.4 56.1 - - + +
854A THR* 4.1 15.7 - - + +
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Residues in contact with ALA 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A VAL* 4.9 0.8 - - - +
693A ILE 3.5 2.0 + - - -
694A ASP* 3.0 15.5 + - - +
696A MET* 1.3 76.5 - - - +
698A GLU* 1.3 63.0 + - - +
700A ILE* 3.8 1.6 - - - +
701A GLU* 3.0 24.6 + - - +
715A ALA* 4.1 28.4 - - + +
716A GLU* 6.0 0.2 - - + -
822A SER* 4.2 17.3 - - - +
824A ILE* 4.1 26.1 - - + +
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Residues in contact with GLU 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A ASP* 3.7 18.0 - - - +
695A ALA* 3.5 12.8 - - - +
696A MET 3.2 0.4 - - - -
697A ALA* 1.3 79.8 - - - +
699A GLN* 1.3 60.3 + - - +
701A GLU* 3.5 18.4 + - - +
702A GLU* 4.1 4.5 + - - +
715A ALA* 4.0 9.2 - - - +
716A GLU* 2.5 29.8 - - - +
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Residues in contact with GLN 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 ALA 3.3 6.3 + - - +
696A MET* 3.0 30.3 + - + +
698A GLU* 1.3 76.9 - - - +
700A ILE* 1.3 88.2 + - - +
702A GLU* 3.1 38.4 + - - +
703A VAL* 3.6 11.1 - - - +
844A ILE* 5.0 2.9 - - - +
848A VAL* 4.4 25.7 - - - +
849A GLN 4.9 8.2 + - - +
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Residues in contact with ILE 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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683A ILE* 4.3 28.5 - - + -
685A VAL* 5.6 6.5 - - + -
696A MET* 2.8 23.8 + - + +
697A ALA 3.3 0.6 + - - +
699A GLN* 1.3 97.1 - - - +
701A GLU* 1.3 67.5 + - - +
703A VAL* 2.8 19.7 + - + +
704A ALA* 3.0 14.2 + - + +
824A ILE* 3.4 36.6 - - + -
844A ILE* 4.8 17.7 - - + -
856A VAL* 5.3 7.6 - - + -
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Residues in contact with GLU 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697A ALA 3.0 13.5 + - - +
698A GLU* 3.5 14.4 - - - +
699A GLN 3.3 0.4 - - - -
700A ILE* 1.3 76.4 - - - +
702A GLU* 1.3 71.7 + - - +
704A ALA* 2.8 25.5 + - - +
705A ARG* 3.0 30.7 + - - +
713A ALA* 4.1 27.5 - - + +
715A ALA* 5.5 6.7 - - + -
824A ILE* 5.6 1.1 - - + -
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Residues in contact with GLU 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 GLU 4.1 3.2 + - - +
699A GLN* 3.1 30.6 + - - +
701A GLU* 1.3 92.5 + - - +
703A VAL* 1.3 69.7 + - + +
705A ARG* 3.5 3.0 + - - +
706A THR* 3.0 32.2 + - - +
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Residues in contact with VAL 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 GLN* 3.6 26.5 - - - +
700A ILE* 2.8 16.2 + - + +
702A GLU* 1.3 85.3 - - + +
704A ALA* 1.3 56.1 + - - +
706A THR* 3.2 22.6 - - + +
707A VAL* 3.2 16.8 - - + +
840A LEU* 3.7 22.9 - - + +
843A ALA* 5.8 6.7 - - + -
844A ILE* 5.1 13.9 - - + -
848A VAL* 5.2 15.3 - - + -
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Residues in contact with ALA 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 ILE* 3.0 14.5 + - + +
701A GLU* 2.8 11.3 + - - +
703A VAL* 1.3 75.6 - - - +
705A ARG* 1.3 64.5 + - - +
706A THR 3.2 0.2 - - - -
707A VAL* 3.2 25.2 - - - +
709A GLY 4.2 7.1 - - - +
711A ALA* 5.7 2.6 - - - +
713A ALA* 3.9 13.0 - - + -
826A ILE* 3.5 32.7 - - + +
840A LEU* 5.2 3.8 - - - -
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Residues in contact with ARG 705 (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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701A GLU* 3.0 26.9 + - - +
702A GLU* 4.1 4.3 - - - +
704A ALA* 1.3 77.2 - - - +
706A THR* 1.3 60.7 + - - +
707A VAL 4.1 3.1 - - - +
709A GLY 4.8 5.8 - - - +
711A ALA 3.2 27.1 + - - -
712A SER* 4.0 18.8 + - - +
713A ALA* 5.0 2.5 - - - +
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Residues in contact with THR 706 (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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702A GLU 3.0 21.0 + - - +
703A VAL* 3.2 22.7 - - + +
705A ARG* 1.3 78.7 - - - +
707A VAL* 1.3 80.1 + - + +
708A PRO* 3.3 6.2 - - - +
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Residues in contact with VAL 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703A VAL* 3.2 19.1 - - + +
704A ALA* 3.2 17.5 - - - +
705A ARG 4.1 2.3 - - - +
706A THR* 1.3 85.5 - - + +
708A PRO* 1.3 72.1 - - + +
709A GLY* 2.6 23.9 + - - +
836A VAL* 4.3 26.0 - - + -
839A ASP* 4.6 19.3 - - + +
840A LEU* 3.9 20.9 - - + -
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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