Contacts of the helix formed by residues 835 - 846 (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 SER 835 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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832A ASP 5.0 3.7 + - - -
833A MET* 3.3 0.9 - - - -
834A VAL* 1.3 79.4 + - - +
836A VAL* 1.3 68.7 + - - +
838A HIS* 3.2 15.1 + - - +
839A ASP* 3.3 22.4 + - - +
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Residues in contact with VAL 836 (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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681A ILE* 5.3 4.5 - - + -
707A VAL* 4.3 19.5 - - + -
708A PRO 4.2 17.3 - - - +
709A GLY* 5.5 4.9 - - - -
833A MET* 4.2 25.1 + - + +
834A VAL 3.5 0.4 - - - -
835A SER* 1.3 80.3 - - - +
837A VAL* 1.3 65.0 + - + +
839A ASP* 3.2 11.0 + - - +
840A LEU* 3.1 40.1 + - + +
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Residues in contact with VAL 837 (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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681A ILE* 3.7 26.7 - - + -
833A MET 4.2 2.7 - - - +
834A VAL* 3.2 23.6 - - + +
836A VAL* 1.3 76.2 - - + +
838A HIS* 1.3 65.3 - - + +
840A LEU* 4.0 10.1 - - + +
841A GLN* 3.3 28.5 + - - +
858A PHE* 4.3 16.7 - - + -
862A PHE* 3.4 46.2 - - + -
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Residues in contact with HIS 838 (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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834A VAL 4.7 4.7 - - - +
835A SER* 3.2 10.4 + - - +
836A VAL 3.1 0.6 - - - -
837A VAL* 1.3 80.3 - - + +
839A ASP* 1.3 68.9 + - - +
840A LEU 3.1 2.0 - - - -
841A GLN* 3.3 36.6 + - - +
842A LYS* 3.3 48.0 + - + +
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Residues in contact with ASP 839 (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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707A VAL* 4.6 17.0 - - + +
708A PRO* 6.1 0.3 - - - +
835A SER* 3.5 20.6 - - - +
836A VAL* 3.2 12.0 + - - +
838A HIS* 1.3 79.6 + - - +
840A LEU* 1.3 59.1 + - - +
842A LYS* 4.6 1.2 - - - +
843A ALA* 2.8 33.7 + - - +
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Residues in contact with LEU 840 (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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681A ILE* 6.4 1.1 - - + -
683A ILE* 5.0 16.6 - - + -
703A VAL* 3.7 40.2 - - + +
704A ALA* 5.2 2.7 - - - +
707A VAL* 3.9 17.5 - - + -
826A ILE* 5.8 9.6 - - + -
836A VAL* 3.1 34.6 + - + +
837A VAL* 4.0 8.5 - - + +
838A HIS 3.1 0.6 - - - -
839A ASP* 1.3 73.9 - - - +
841A GLN* 1.3 59.6 + - - +
842A LYS 3.1 2.0 - - - -
843A ALA* 4.5 3.4 - - + -
844A ILE* 3.0 41.2 + - + +
858A PHE* 4.7 10.1 - - + -
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Residues in contact with GLN 841 (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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837A VAL* 3.3 17.4 + - - +
838A HIS* 3.3 46.3 + - - +
840A LEU* 1.3 79.4 - - - +
842A LYS* 1.3 71.8 + - + +
844A ILE* 4.4 5.1 - - - +
845A ALA* 4.1 14.7 + - - +
858A PHE* 3.7 33.2 - - + -
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Residues in contact with LYS 842 (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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838A HIS* 3.3 44.0 + - + +
839A ASP* 4.6 1.1 - - - +
841A GLN* 1.3 89.5 - - + +
843A ALA* 1.3 65.6 + - - +
844A ILE 3.2 1.6 - - - -
845A ALA* 3.4 6.4 + - - +
846A GLU* 3.0 26.8 + - - +
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Residues in contact with ALA 843 (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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703A VAL* 5.8 6.7 - - + -
839A ASP* 2.8 23.4 + - + +
840A LEU* 4.2 3.8 - - + +
842A LYS* 1.3 74.8 - - - +
844A ILE* 1.3 62.6 + - - +
846A GLU* 2.8 27.6 - - - +
848A VAL* 3.4 10.2 - - + +
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Residues in contact with ILE 844 (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* 5.9 2.9 - - + -
699A GLN* 5.0 1.8 - - - +
700A ILE* 4.8 23.8 - - + -
703A VAL* 5.1 14.3 - - + +
840A LEU* 3.0 28.7 + - + +
841A GLN* 4.4 5.6 - - - +
843A ALA* 1.3 74.3 - - - +
845A ALA* 1.3 65.1 + - + +
848A VAL* 2.5 62.4 + - + +
849A GLN 4.8 4.3 - - - +
850A LEU* 6.2 2.2 - - + -
856A VAL* 5.4 16.4 - - + -
858A PHE* 5.4 7.4 - - + -
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Residues in contact with ALA 845 (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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841A GLN 4.1 11.1 + - - +
842A LYS* 3.4 10.5 + - - +
844A ILE* 1.3 84.8 - - + +
846A GLU* 1.3 58.4 + - + +
847A LYS 3.3 4.9 + - - -
848A VAL 3.9 6.0 - - - +
849A GLN* 5.8 1.9 + - - -
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Residues in contact with GLU 846 (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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842A LYS 3.0 17.6 + - - +
843A ALA* 2.8 18.6 - - - +
845A ALA* 1.3 72.9 - - - +
847A LYS* 1.3 68.7 + - + +
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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