Contacts of the strand formed by residues 685 - 698 (chain A) in PDB entry 2W77
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 685 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680A GLU* 3.4 4.7 - - - +
681A LEU* 3.0 56.9 + - + +
682A ALA* 2.8 36.3 + - + +
683A PRO 3.2 1.2 + - - -
684A GLY* 1.3 71.5 - - - -
686A GLN* 1.3 61.9 + - - +
687A VAL* 5.7 0.2 - - + -
717A THR* 3.0 32.6 + - + +
718A SER 3.4 13.2 - - - -
719A TYR* 3.8 22.9 - + + +
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Residues in contact with GLN 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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145A GLY 3.7 14.8 + - - +
146A SER* 3.4 18.9 + - - +
147A TYR* 2.7 46.7 + - + +
628A ARG* 4.7 1.8 + - - +
679A GLY* 3.3 17.0 - - - -
680A GLU* 3.2 33.5 - - - +
683A PRO 5.8 1.3 + - - +
684A GLY 5.3 2.5 - - - +
685A TRP* 1.3 76.5 + - - +
687A VAL* 1.3 55.7 + - - +
717A THR* 2.7 25.0 + - - -
718A SER* 2.9 25.7 + - - +
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Residues in contact with VAL 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A TYR* 3.8 10.5 - - - +
629A LEU* 4.9 0.2 - - + -
677A ILE* 4.7 12.6 - - + -
678A SER* 3.1 5.2 - - - -
679A GLY 2.8 36.5 + - - +
681A LEU* 3.5 43.3 - - + -
685A TRP* 5.7 0.4 - - + -
686A GLN* 1.3 69.1 - - - +
688A GLN* 1.4 64.3 + - - +
689A ALA* 5.0 2.5 - - + +
715A LEU* 5.0 14.4 - - + -
716A TYR 3.2 7.6 - - - +
717A THR* 3.3 25.8 - - - +
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Residues in contact with GLN 688 (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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147A TYR* 4.0 8.9 - - + +
170A THR* 3.6 20.8 - - - +
171A VAL 3.0 27.5 + - - +
172A VAL* 4.2 6.2 - - - +
176A ASN* 3.3 27.2 + - - +
191A HIS 4.3 4.3 - - - +
193A PRO* 3.9 23.5 - - + +
676A GLU* 5.3 1.5 + - + -
677A ILE 3.3 6.5 - - - +
678A SER* 3.9 19.4 + - - -
687A VAL* 1.4 73.8 - - - +
689A ALA* 1.3 64.1 - - - +
714A SER* 4.5 0.7 - - - -
715A LEU* 3.6 0.7 - - - -
716A TYR* 2.8 41.5 + - + +
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Residues in contact with ALA 689 (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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193A PRO* 4.5 6.9 - - - +
676A GLU* 3.2 4.4 - - - +
677A ILE* 2.8 47.9 + - + +
687A VAL* 5.3 2.7 - - + -
688A GLN* 1.3 78.6 - - - +
690A GLY* 1.3 57.1 + - - +
713A LEU* 5.5 2.0 - - + -
714A SER 2.9 17.3 - - - +
715A LEU* 3.7 23.8 - - + -
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Residues in contact with GLY 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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193A PRO* 4.1 16.8 - - - +
194A GLY 6.1 0.7 - - - -
675A ALA 2.9 11.9 - - - -
676A GLU* 3.8 7.4 - - - -
689A ALA* 1.3 74.8 - - - +
691A TYR* 1.3 63.5 + - - +
692A THR* 5.4 0.7 - - - -
713A LEU* 3.4 6.9 - - - +
714A SER 2.8 31.0 + - - +
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Residues in contact with TYR 691 (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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673A TYR* 4.0 31.5 + + - -
674A GLU* 3.2 4.4 - - - +
675A ALA* 2.5 47.0 + - + +
690A GLY* 1.3 76.5 - - - +
692A THR* 1.3 74.4 + - - +
693A HIS* 4.2 2.7 - - + -
711A ASP* 2.7 31.8 + - + +
712A GLN 3.3 20.9 - - - -
713A LEU* 4.1 20.6 - - + -
736A TRP* 4.9 7.9 - + - -
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Residues in contact with THR 692 (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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193A PRO 4.8 0.3 - - - -
194A GLY* 3.5 16.4 + - - +
210A ARG* 5.8 5.6 - - + +
636A PHE* 4.4 11.9 - - + -
673A TYR 3.5 9.9 - - - +
674A GLU* 2.7 39.4 + - + +
691A TYR* 1.3 77.7 + - - +
693A HIS* 1.3 70.4 + - - +
694A LYS* 5.0 4.5 - - + +
710A GLN 3.7 1.0 - - - +
711A ASP* 3.5 3.5 - - - -
712A GLN* 2.9 52.9 + - - +
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Residues in contact with HIS 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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636A PHE* 4.0 3.1 - - - -
671A LYS 4.8 1.0 + - - -
672A GLY* 3.0 29.4 - - - -
673A TYR* 2.8 60.4 + + + +
691A TYR* 4.2 2.4 - - + -
692A THR* 1.3 76.3 - - - +
694A LYS* 1.3 71.3 + - - +
695A ILE* 4.1 28.0 + - + +
710A GLN* 3.2 16.2 + - - -
711A ASP* 3.0 29.7 + - - +
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Residues in contact with LYS 694 (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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210A ARG* 5.0 5.8 - - - -
211A GLY* 4.9 2.9 - - - +
636A PHE* 5.0 5.4 - - + -
670A THR* 4.8 10.5 - - + -
671A LYS 3.5 8.5 - - - +
672A GLY* 5.0 0.2 - - - -
692A THR* 5.2 4.5 - - + +
693A HIS* 1.3 80.6 - - - +
695A ILE* 1.3 79.1 + - - +
696A ILE* 4.0 16.4 - - + +
704A VAL 4.8 1.4 + - - -
705A SER 3.2 14.1 + - - -
706A THR* 5.0 0.8 - - - +
708A GLU* 2.6 69.7 + - - +
709A PRO 3.4 16.7 + - - +
710A GLN* 2.8 31.9 + - - +
712A GLN* 6.3 0.9 - - - +
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Residues in contact with ILE 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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669A LYS 3.7 1.2 - - - +
670A THR* 3.5 1.5 - - - -
671A LYS* 2.9 35.2 + - + +
693A HIS* 4.1 18.1 + - + +
694A LYS* 1.3 85.7 - - - +
696A ILE* 1.3 63.0 + - - +
697A ARG* 4.1 28.9 - - + +
703A LYS* 4.0 33.9 - - + -
710A GLN* 3.6 28.7 - - - +
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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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211A GLY* 3.7 20.2 - - - +
212A PHE* 3.7 28.5 - - + -
643A ARG* 4.2 3.8 - - - +
668A ALA* 4.6 5.4 - - + -
669A LYS 3.1 14.6 - - - +
670A THR* 3.1 26.5 - - + +
694A LYS* 4.0 7.9 - - + +
695A ILE* 1.3 74.3 - - - +
697A ARG* 1.3 62.8 + - - +
703A LYS* 3.6 4.5 - - - +
704A VAL* 2.7 64.4 + - + +
705A SER* 3.6 14.6 - - - +
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Residues in contact with ARG 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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668A ALA* 3.1 7.2 - - - +
669A LYS* 2.7 38.5 + - + +
671A LYS* 6.5 0.9 - - - +
695A ILE* 4.1 28.5 - - + +
696A ILE* 1.3 78.7 - - - +
698A ASP* 1.3 63.0 + - - +
701A GLY* 3.1 27.6 + - - +
702A LYS 3.3 13.5 - - - +
703A LYS* 3.5 28.4 - - - +
704A VAL* 4.9 2.9 - - - -
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Residues in contact with ASP 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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643A ARG* 5.2 3.1 - - - -
645A GLU* 4.1 6.2 - - - +
666A ILE* 3.6 20.2 - - + +
667A LYS 3.3 15.0 - - - +
668A ALA* 3.9 5.6 - - + +
697A ARG* 1.3 75.9 - - - +
699A ASP* 1.3 55.7 + - - +
700A SER* 2.6 36.0 + - - -
701A GLY* 2.8 17.7 + - - -
702A LYS* 3.3 36.9 + - - +
704A VAL* 4.6 10.9 - - + +
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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