Contacts of the helix formed by residues 687 - 698 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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683A PHE 4.2 11.6 - - - +
684A LYS 5.4 1.8 - - - +
685A HIS 3.6 9.2 - - - +
686A HIS* 1.4 88.1 - - - +
688A LYS* 1.3 66.8 + - - +
689A ASP* 4.5 6.7 - - + +
690A ASN* 2.9 43.2 + - + +
691A LEU* 3.2 9.4 + - - +
610B PRO* 6.4 2.5 - - + -
615B GLN* 6.1 3.1 - - - +
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Residues in contact with LYS 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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679A LEU* 3.8 33.4 + - + -
681A GLY 5.2 4.5 - - - +
683A PHE* 3.8 28.8 + - + +
686A HIS 3.5 2.0 + - - -
687A PRO* 1.3 71.1 - - - +
689A ASP* 1.3 62.7 + - - +
691A LEU* 3.1 7.7 + - - +
692A ILE* 3.0 41.1 + - + +
613B ALA* 4.8 3.4 - - + -
614B VAL* 2.9 32.8 + - - +
615B GLN* 4.3 18.5 - - + +
616B SER* 4.1 20.3 - - - +
768B MET* 5.1 4.6 - - - +
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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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687A PRO* 3.2 4.8 - - + +
688A LYS* 1.3 78.7 - - - +
690A ASN* 1.3 67.5 + - - +
692A ILE* 3.6 6.3 + - - +
693A LYS* 3.2 49.3 + - - +
610B PRO* 6.5 0.2 - - + -
611B GLY* 3.3 14.3 - - - +
612B ASP* 3.1 34.7 + - - +
613B ALA* 3.9 21.8 - - + +
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Residues in contact with ASN 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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618A LEU* 3.4 44.6 - - + +
621A MET* 6.0 1.9 - - + +
686A HIS* 5.1 1.8 - - + -
687A PRO* 2.9 36.5 + - + +
689A ASP* 1.3 84.3 + - - +
691A LEU* 1.3 67.6 + - + +
693A LYS* 3.3 7.5 + - - +
694A LEU* 3.0 31.8 + - + +
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Residues in contact with LEU 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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679A LEU* 4.0 21.5 - - + -
683A PHE* 3.6 43.3 - - + -
686A HIS* 3.8 23.3 - - + +
687A PRO 3.7 8.7 - - - +
688A LYS* 3.1 6.5 + - - +
690A ASN* 1.3 76.0 - - + +
692A ILE* 1.3 59.9 + - - +
694A LEU* 3.2 7.0 + - + +
695A VAL* 2.9 35.2 + - + +
738A ILE* 4.6 2.9 - - + -
760A SER* 4.3 11.2 - - - -
763A PHE* 3.9 26.6 - - + -
764A ILE* 4.1 11.9 - - + -
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Residues in contact with ILE 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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679A LEU* 3.5 15.7 - - + -
688A LYS* 3.0 32.9 + - + +
689A ASP* 3.8 7.2 - - - +
690A ASN 3.3 0.2 - - - -
691A LEU* 1.3 75.6 - - - +
693A LYS* 1.3 64.8 + - + +
695A VAL* 3.4 2.3 + - - +
696A THR* 3.0 32.6 + - - +
702A ILE* 4.0 30.2 - - + +
613B ALA* 3.8 28.5 - - + -
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Residues in contact with LYS 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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618A LEU* 4.6 24.4 - - + +
622A LEU* 4.1 18.4 - - + +
689A ASP* 3.2 41.6 + - - +
690A ASN* 3.3 9.7 + - - +
692A ILE* 1.3 80.4 - - + +
694A LEU* 1.3 57.4 + - - +
696A THR* 3.5 6.0 + - - -
697A ALA* 2.9 30.5 + - - +
612B ASP* 4.1 17.3 + - - -
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Residues in contact with LEU 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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618A LEU* 4.1 9.4 - - + -
621A MET* 3.5 39.5 - - + -
622A LEU* 4.0 16.2 - - + -
625A LEU* 3.2 26.6 - - + +
672A PHE* 4.2 1.2 - - - -
690A ASN* 3.0 26.6 + - + +
691A LEU* 3.2 3.8 + - + +
693A LYS* 1.3 73.4 - - - +
695A VAL* 1.3 62.5 + - - +
697A ALA* 4.5 0.7 - - - -
698A GLY* 2.9 26.2 + - - -
763A PHE* 3.6 30.3 - - + -
764A ILE* 3.9 22.7 - - + -
767A VAL* 4.7 2.7 - - + -
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Residues in contact with VAL 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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672A PHE* 4.4 4.8 - - - -
677A PHE* 3.7 27.8 - - + -
679A LEU* 5.2 4.3 - - + -
691A LEU* 2.9 22.3 + - + +
692A ILE 3.7 4.5 - - - +
694A LEU* 1.3 79.1 - - - +
696A THR* 1.3 60.4 + - - +
698A GLY 3.3 1.4 + - - -
699A GLY 3.2 2.9 + - - -
700A GLY* 2.9 49.0 + - - +
701A GLN 3.8 2.5 - - - +
702A ILE* 3.7 31.0 - - + -
763A PHE* 3.6 24.6 - - + -
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Residues in contact with THR 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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670A LYS* 5.1 1.6 - - - +
692A ILE* 3.0 24.8 + - - +
693A LYS* 3.7 6.5 - - - -
695A VAL* 1.3 76.3 - - - +
697A ALA* 1.3 60.8 + - - +
699A GLY* 3.1 14.2 + - - -
700A GLY 4.2 8.4 + - - +
702A ILE* 4.8 6.6 - - - +
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Residues in contact with ALA 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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622A LEU* 3.8 21.1 - - + -
625A LEU* 3.7 19.6 - - + +
626A ASN* 4.0 20.1 + - - +
670A LYS* 3.3 24.0 - - - +
693A LYS 2.9 19.4 + - - +
694A LEU 3.9 3.1 - - - +
696A THR* 1.3 76.7 - - - +
698A GLY* 1.3 56.7 + - - +
699A GLY 3.2 0.2 - - - -
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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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625A LEU* 3.9 16.8 - - - +
670A LYS* 3.2 14.6 - - - +
671A LEU 4.7 0.4 - - - -
672A PHE* 2.8 40.3 + - - -
694A LEU 2.9 18.3 + - - -
695A VAL 3.5 1.3 - - - -
696A THR 3.2 0.2 - - - -
697A ALA* 1.3 75.3 - - - +
699A GLY* 1.3 58.3 + - - +
700A GLY 3.3 3.4 - - - -
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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