Contacts of the helix formed by residues 687 - 698 (chain B) in PDB entry 2R1Z
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 PRO 687 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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683B PHE 4.9 6.9 - - - +
684B LYS 5.5 0.9 - - - +
685B HIS 3.9 7.6 - - - +
686B HIS* 1.4 87.1 - - + +
688B LYS* 1.3 66.2 + - - +
689B ASP* 4.4 4.0 - - + +
690B ASN* 3.0 43.6 + - + +
691B LEU* 3.2 10.4 + - - +
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Residues in contact with LYS 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679B LEU* 3.6 40.8 + - + -
681B GLY 4.7 7.0 + - - +
683B PHE* 4.3 24.2 + - + +
686B HIS 3.3 4.2 + - - -
687B PRO* 1.3 70.7 - - - +
689B ASP* 1.3 60.1 + - - +
691B LEU* 3.1 11.4 + - - +
692B ILE* 3.0 42.9 + - + +
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Residues in contact with ASP 689 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687B PRO* 3.2 4.6 - - + +
688B LYS* 1.3 80.0 - - - +
690B ASN* 1.3 67.8 + - - +
692B ILE* 3.6 16.6 + - - +
693B LYS* 3.1 36.2 + - - +
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Residues in contact with ASN 690 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618B LEU* 3.5 37.5 - - + +
621B MET* 6.4 0.9 - - + -
686B HIS* 5.3 4.6 + - - +
687B PRO* 3.0 36.9 + - + +
689B ASP* 1.3 80.4 - - - +
691B LEU* 1.3 59.9 + - + +
693B LYS* 3.3 16.7 + - - +
694B LEU* 3.1 35.7 + - + +
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Residues in contact with LEU 691 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679B LEU* 3.9 21.3 - - + -
683B PHE* 3.6 41.1 - - + -
686B HIS* 4.1 19.1 - - + +
687B PRO 3.2 9.6 + - - +
688B LYS* 3.1 8.6 + - - +
690B ASN* 1.3 76.2 - - + +
692B ILE* 1.3 59.2 + - - +
694B LEU* 3.3 7.3 + - + +
695B VAL* 2.9 35.8 + - + +
738B ILE* 4.7 3.1 - - + -
760B SER* 4.6 10.5 - - - -
763B PHE* 4.0 27.0 - - + -
764B ILE* 4.2 16.2 - - + -
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Residues in contact with ILE 692 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679B LEU* 3.6 17.5 - - + -
688B LYS* 3.0 30.8 + - + +
689B ASP* 3.8 21.8 - - - +
691B LEU* 1.3 76.4 - - - +
693B LYS* 1.3 62.8 + - + +
695B VAL* 3.4 2.9 + - - +
696B THR* 2.8 35.0 + - - +
702B ILE* 4.0 32.5 - - + -
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Residues in contact with LYS 693 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618B LEU* 4.4 26.4 - - + +
622B LEU* 4.1 11.1 - - + +
689B ASP* 3.1 26.5 + - - +
690B ASN* 3.3 18.2 + - - +
692B ILE* 1.3 75.5 - - + +
694B LEU* 1.3 57.1 + - - +
696B THR* 3.6 5.5 + - - -
697B ALA* 2.9 30.4 + - - +
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Residues in contact with LEU 694 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618B LEU* 3.7 13.5 - - + -
621B MET* 3.7 48.0 - - + -
622B LEU* 3.6 24.0 - - + +
625B LEU* 3.3 20.6 - - + +
672B PHE* 4.5 1.6 - - - -
690B ASN* 3.1 26.6 + - + +
691B LEU* 3.8 4.5 - - + +
692B ILE 3.2 0.2 - - - -
693B LYS* 1.3 73.3 - - - +
695B VAL* 1.3 66.4 + - - +
697B ALA* 4.4 0.2 - - - -
698B GLY* 2.8 20.4 + - - -
763B PHE* 3.8 28.9 - - + -
764B ILE* 4.2 6.5 - - + -
767B VAL* 5.1 2.0 - - + -
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Residues in contact with VAL 695 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672B PHE* 4.4 3.2 - - - -
677B PHE* 3.6 31.9 - - + -
679B LEU* 4.8 5.8 - - + -
691B LEU* 2.9 22.5 + - + +
692B ILE 3.6 4.9 - - - +
694B LEU* 1.3 78.0 - - - +
696B THR* 1.3 60.8 + - - +
698B GLY* 3.2 4.7 + - - -
700B GLY* 2.9 47.9 + - - +
701B GLN 3.8 2.7 - - - +
702B ILE* 3.7 30.5 - - + -
763B PHE* 3.9 19.9 - - + -
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Residues in contact with THR 696 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692B ILE* 2.8 25.4 + - - +
693B LYS* 3.8 5.6 - - - -
695B VAL* 1.3 73.7 - - - +
697B ALA* 1.3 63.9 + - - +
699B GLY* 3.1 14.2 + - - -
700B GLY 4.1 10.0 - - - +
702B ILE* 4.6 7.3 - - - +
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Residues in contact with ALA 697 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622B LEU* 3.6 24.2 - - + +
625B LEU* 3.9 16.8 - - + +
626B ASN* 4.8 9.9 + - - +
670B LYS* 3.1 26.9 - - - +
693B LYS 2.9 19.6 + - - +
694B LEU 3.9 2.9 - - - +
696B THR* 1.3 76.2 - - - +
698B GLY* 1.3 57.1 + - - +
699B GLY 3.2 0.4 - - - -
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Residues in contact with GLY 698 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625B LEU* 3.9 15.9 - - - +
670B LYS* 3.2 13.3 - - - +
671B LEU 3.4 1.5 + - - -
672B PHE* 2.7 42.6 + - - -
694B LEU 2.8 14.8 + - - -
695B VAL 3.2 4.2 + - - -
697B ALA* 1.3 75.5 - - - +
699B GLY* 1.3 56.9 + - - +
700B GLY 3.3 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