Contacts of the strand formed by residues 681 - 687 (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 ILE 681 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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677A ILE* 5.9 1.6 - - - -
679A SER* 3.0 14.2 + - - -
680A PRO* 1.3 91.5 - - + +
682A GLY* 1.3 74.3 + - - +
683A ILE* 5.6 1.3 - - + -
825A TYR* 3.9 0.3 - - - -
826A ILE* 2.8 47.3 + - + +
828A ALA* 6.0 2.2 - - + +
833A MET* 3.5 42.0 - - + +
836A VAL* 5.3 6.3 - - + -
837A VAL* 3.7 19.1 - - + -
840A LEU* 6.4 1.1 - - + -
858A PHE* 6.0 2.5 - - + -
859A SER 3.6 5.6 - - - -
860A GLY* 3.9 0.9 - - - -
862A PHE* 3.6 26.0 - - + -
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Residues in contact with GLY 682 (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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677A ILE* 5.7 5.8 - - - +
681A ILE* 1.3 82.1 - - - +
683A ILE* 1.3 67.5 + - - +
823A TRP* 5.8 1.6 - - - -
824A ILE 3.0 16.4 - - - -
825A TYR* 4.3 3.1 - - - -
826A ILE* 3.6 3.8 - - - -
858A PHE* 4.0 2.1 - - - +
859A SER* 2.8 32.8 + - - +
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Residues in contact with ILE 683 (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* 5.6 1.1 - - + -
682A GLY* 1.3 79.6 - - - +
684A LYS* 1.3 69.0 + - - +
685A VAL* 6.3 0.2 - - + -
700A ILE* 4.3 31.0 - - + -
822A SER 3.3 1.6 - - - +
823A TRP* 3.0 26.2 - - - +
824A ILE* 3.1 23.2 + - + +
826A ILE* 4.7 12.6 - - + -
840A LEU* 5.0 15.9 - - + -
844A ILE* 5.9 3.6 - - + -
856A VAL* 3.5 26.5 - - + -
857A ALA 3.0 22.2 - - - +
858A PHE* 4.1 23.6 - - + -
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Residues in contact with LYS 684 (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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83A ARG* 3.5 26.7 - - - +
682A GLY 5.7 0.2 - - - -
683A ILE* 1.3 82.9 - - - +
685A VAL* 1.3 60.2 + - - +
686A SER* 3.9 3.1 + - - +
816A GLU* 4.2 21.6 + - + +
821A THR* 4.4 14.4 - - + +
822A SER 3.5 4.7 - - - +
823A TRP* 4.3 19.3 - - + -
855A SER 3.6 0.7 - - - +
856A VAL* 3.3 4.7 - - - +
857A ALA* 2.6 59.8 + - + +
858A PHE 5.5 0.2 + - - -
859A SER* 3.0 38.0 + - - +
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Residues in contact with VAL 685 (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 0.2 - - - -
684A LYS* 1.3 72.5 - - - +
686A SER* 1.3 58.6 + - - +
693A ILE* 3.0 37.9 - - + +
696A MET* 3.6 31.9 - - + -
697A ALA* 4.9 2.7 - - + +
700A ILE* 5.6 6.5 - - + -
821A THR* 3.5 12.3 - - - -
822A SER* 3.1 32.6 + - - +
824A ILE* 5.7 4.9 - - + +
850A LEU* 6.5 0.4 - - + -
854A THR* 4.3 7.2 - - - +
855A SER 3.2 13.7 - - - +
856A VAL* 5.1 9.0 - - + -
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Residues in contact with SER 686 (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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684A LYS* 3.9 5.2 + - - +
685A VAL* 1.3 73.3 - - - +
687A GLY* 1.3 57.9 + - - +
693A ILE* 3.5 0.9 - - - -
816A GLU* 5.4 1.4 - - - +
819A ARG* 3.1 38.5 + - - -
821A THR* 3.1 24.8 - - - +
854A THR* 2.9 31.0 - - - +
855A SER* 3.0 20.8 + - - -
857A ALA* 5.6 3.3 - - - +
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Residues in contact with GLY 687 (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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686A SER* 1.3 76.1 - - - +
688A THR* 1.3 63.0 + - - -
689A VAL 3.5 1.6 - - - -
693A ILE* 3.5 15.2 - - - +
819A ARG* 3.7 13.1 - - - +
820A PRO* 3.1 33.6 + - - +
853A GLY 3.4 12.8 - - - -
854A THR* 3.7 2.7 - - - -
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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