Contacts of the strand formed by residues 688 - 701 (chain A) in PDB entry 3BJY
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 CYS 688 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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669A MET* 4.0 11.0 - - + +
670A ARG 3.1 30.3 - - - +
671A ARG* 3.8 3.4 - - - -
672A CYS* 3.6 11.7 - - - -
685A MET* 3.2 48.0 - - + +
686A GLY 3.4 4.0 + - - -
687A ARG* 1.3 78.5 - - - +
689A ASP* 1.3 64.2 + - - +
690A SER 4.3 0.3 + - - -
726A ARG* 3.7 15.7 - - - -
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Residues in contact with ASP 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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668A LEU 3.6 0.5 - - - +
669A MET* 3.6 3.8 - - - -
670A ARG* 2.8 32.4 + - + +
671A ARG 4.8 0.9 - - - +
672A CYS* 3.7 29.6 - - - +
673A LYS 4.7 1.9 + - - -
688A CYS* 1.3 75.8 - - - +
690A SER* 1.3 63.7 + - - +
691A PHE* 3.8 23.0 - - + -
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Residues in contact with SER 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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667A LYS* 3.8 13.7 + - - -
668A LEU 3.5 4.9 - - - -
669A MET* 3.1 25.3 - - - +
688A CYS 4.3 0.4 + - - -
689A ASP* 1.3 71.0 - - - +
691A PHE* 1.3 72.8 + - - +
7P C 3.9 25.0 + - - -
8P C 3.5 29.2 + - - -
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Residues in contact with PHE 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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667A LYS* 3.4 2.9 - - - +
668A LEU* 2.8 55.1 + - + -
670A ARG* 4.3 27.4 - - + -
689A ASP* 3.8 31.9 - - + -
690A SER* 1.3 87.6 - - - +
692A SER* 1.3 61.8 + - - +
718A LEU* 3.9 35.6 - - + +
720A CYS* 6.3 0.7 - - + -
7P C 3.7 7.4 - - - -
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Residues in contact with SER 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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665A THR* 3.5 21.1 - - - +
666A LEU 3.6 4.4 + - - -
667A LYS* 4.0 12.0 - - - +
691A PHE* 1.3 76.6 - - - +
693A ARG* 1.3 66.9 + - - +
718A LEU* 3.9 8.1 - - - +
6P C 3.7 23.7 + - - +
7P C 3.1 46.4 + - - -
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Residues in contact with ARG 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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665A THR* 3.4 3.4 - - - -
666A LEU 3.0 31.2 + - - +
692A SER* 1.3 77.9 + - - +
694A SER* 1.3 72.7 + - - +
695A SER* 6.1 0.6 - - - -
714A LEU* 3.6 30.2 - - + +
717A THR* 3.4 37.6 + - - +
718A LEU* 3.9 16.7 - - + +
6P C 3.7 21.1 + - - +
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Residues in contact with SER 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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663A GLN* 4.1 17.2 + - - -
664A ILE 3.1 6.5 - - - -
665A THR* 3.1 24.7 - - - -
693A ARG* 1.3 88.4 + - - +
695A SER* 1.3 65.5 + - - +
714A LEU* 4.3 3.1 - - - +
733A ASN* 4.7 0.2 - - - -
5P T 3.9 15.1 + - - +
6P C 2.7 24.7 + - - -
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Residues in contact with SER 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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663A GLN* 3.4 6.7 - - - +
664A ILE* 2.8 34.4 + - - +
693A ARG* 6.1 0.9 - - - -
694A SER* 1.3 77.9 - - - +
696A ARG* 1.3 70.6 + - - +
697A LEU* 3.8 1.6 + - - +
710A GLU* 2.7 41.9 + - - +
714A LEU* 3.8 8.7 - - - +
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Residues in contact with ARG 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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662A SER 3.5 8.3 - - - +
663A GLN* 3.5 14.8 - - - +
695A SER* 1.3 80.0 - - - +
697A LEU* 1.3 68.0 + - - +
698A GLY 3.9 0.5 + - - -
734A LYS* 2.7 49.5 - - - +
4P C 3.7 24.7 + - - +
5P T 2.8 42.2 + - - +
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Residues in contact with LEU 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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661A THR* 3.5 24.2 - - - +
662A SER* 2.7 25.7 + - - +
663A GLN* 4.3 1.8 - - - +
664A ILE* 4.2 33.0 - - + -
695A SER* 4.5 2.7 - - - +
696A ARG* 1.3 81.0 - - - +
698A GLY* 1.3 68.4 + - - +
699A ILE* 3.2 13.9 + - - +
700A PRO* 5.1 0.5 - - - +
701A THR* 3.6 19.3 - - + -
706A ILE* 4.3 17.0 - - + -
707A ILE* 4.2 15.3 - - + -
710A GLU* 4.5 12.6 - - + -
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Residues in contact with GLY 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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696A ARG 3.9 1.6 + - - -
697A LEU* 1.3 74.0 - - - +
699A ILE* 1.3 68.9 + - - +
700A PRO* 4.5 2.1 - - - +
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Residues in contact with ILE 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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661A THR 4.6 0.2 - - - -
697A LEU* 4.0 7.1 - - - +
698A GLY* 1.3 83.3 - - - +
700A PRO* 1.4 89.4 - - + +
701A THR* 3.1 17.1 + - - +
706A ILE* 5.8 0.7 - - - +
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Residues in contact with PRO 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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660A THR* 3.1 25.5 - - - +
661A THR 3.3 10.3 - - - +
662A SER* 3.8 14.4 - - - -
697A LEU 5.1 0.2 - - - +
698A GLY 4.5 2.9 - - - +
699A ILE* 1.4 99.0 - - + +
701A THR* 1.3 57.0 + - - +
736A VAL* 3.6 35.0 - - + -
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Residues in contact with THR 701 (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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660A THR* 3.4 9.3 - - - -
661A THR* 2.9 28.3 + - - +
697A LEU* 3.6 26.0 - - + -
699A ILE* 3.4 13.5 - - - +
700A PRO* 1.3 76.6 - - - +
702A ASN* 1.3 69.4 + - - +
703A GLU* 2.6 29.9 + - - +
706A ILE* 4.1 25.6 - - + +
707A ILE* 4.0 7.7 - - + +
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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