Contacts of the helix formed by residues 779 - 786 (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 779 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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724A ILE* 5.4 0.2 - - - -
777A ARG 3.5 1.8 + - - -
778A ASP* 1.3 83.9 - - - +
780A PRO* 1.3 70.8 - - - +
781A GLN* 3.9 9.2 + - - +
782A ALA* 2.6 35.6 + - - +
783A LEU* 2.9 15.4 + - - +
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Residues in contact with PRO 780 (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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724A ILE* 3.7 24.6 - - + -
779A SER* 1.3 87.4 - - - +
781A GLN* 1.3 63.5 + - - +
783A LEU* 2.9 8.9 + - + -
784A ARG* 2.8 40.3 + - - +
804A ILE* 2.9 20.9 - - + +
806A VAL* 4.4 15.7 - - + -
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Residues in contact with GLN 781 (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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779A SER* 3.1 9.9 + - - +
780A PRO* 1.3 77.2 - - - +
782A ALA* 1.3 65.1 + - - +
784A ARG* 2.9 43.8 + - - +
785A GLN* 3.0 35.4 + - - +
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Residues in contact with ALA 782 (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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775A SER 4.5 3.8 - - - +
776A TRP* 3.2 35.1 - - - +
777A ARG 4.4 0.2 - - - -
778A ASP* 3.8 2.9 - - + +
779A SER* 2.6 36.5 + - - +
781A GLN* 1.3 73.6 - - - +
783A LEU* 1.3 55.1 + - - +
785A GLN* 3.0 12.8 + - - +
786A LEU* 2.8 25.6 + - - -
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Residues in contact with LEU 783 (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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724A ILE* 3.8 39.9 - - + -
726A VAL* 5.0 7.2 - - + -
751A VAL* 4.0 32.5 - - + -
776A TRP 4.3 10.8 - - - +
777A ARG* 4.5 10.3 - - - +
779A SER 2.9 11.0 + - - +
780A PRO* 2.9 13.2 + - + +
782A ALA* 1.3 78.3 - - - +
784A ARG* 1.3 63.3 + - - +
786A LEU* 2.9 23.1 + - + +
798A LEU* 3.3 24.3 - - + +
804A ILE* 3.5 8.5 - - + -
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Residues in contact with ARG 784 (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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780A PRO* 2.8 55.9 + - - +
781A GLN* 2.9 30.8 + - - +
783A LEU* 1.3 72.0 - - - +
785A GLN* 1.3 63.4 + - + +
797A THR* 3.5 5.0 - - - -
799A ALA* 3.0 46.4 + - + +
804A ILE* 3.3 44.4 + - + +
805A LYS* 5.1 2.0 - - - +
806A VAL* 5.4 5.3 - - - +
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Residues in contact with GLN 785 (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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776A TRP* 5.0 9.5 - - + -
781A GLN* 3.0 35.8 + - + +
782A ALA* 3.0 10.8 + - - +
783A LEU 3.0 0.6 - - - -
784A ARG* 1.3 79.0 - - + +
786A LEU* 1.3 68.4 + - - +
787A PRO* 2.9 10.0 - - - +
797A THR* 3.2 20.5 - - + +
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Residues in contact with LEU 786 (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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746A PHE* 4.1 14.8 - - + -
751A VAL* 3.6 28.5 - - + -
772A TYR* 3.6 31.6 - - + -
776A TRP* 4.2 18.8 - - + +
777A ARG* 5.9 0.2 - - + -
782A ALA 2.8 7.7 + - - +
783A LEU* 2.9 19.6 + - + +
785A GLN* 1.3 72.8 - - - +
787A PRO* 1.3 76.1 - - + +
788A ILE* 3.3 23.3 - - + -
797A THR* 3.1 2.1 - - - -
798A LEU* 2.6 41.7 + - + -
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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