Contacts of the helix formed by residues 680 - 694 (chain A) in PDB entry 3AR2
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 GLU 680 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489A ARG* 3.7 23.7 - - - +
490A ASP* 3.5 26.7 - - - +
492A LYS* 4.0 8.8 + - - +
679A VAL* 1.3 77.0 - - - +
681A PRO* 1.4 78.0 - - + +
682A SER* 3.2 13.9 + - - +
683A HIS* 2.9 39.9 + - + +
684A LYS* 3.2 8.8 + - - +
706A ASN* 5.7 0.4 - - - -
1002A ACP 5.6 0.2 - - - -
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Residues in contact with PRO 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A ARG* 3.8 25.8 - - + +
679A VAL 4.9 0.2 - - - +
680A GLU* 1.4 93.5 - - + +
682A SER* 1.3 59.3 - - - +
684A LYS* 3.5 5.8 + - + +
685A SER* 3.5 19.6 + - - -
706A ASN* 3.4 49.1 - - + +
709A PRO* 4.3 18.2 - - + +
710A ALA 5.1 0.2 + - - -
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Residues in contact with SER 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A GLU* 3.2 13.0 + - - +
681A PRO* 1.3 76.3 - - - +
683A HIS* 1.3 68.7 + - - +
685A SER* 3.4 8.5 + - - -
686A LYS* 2.9 29.7 + - - +
709A PRO* 5.8 1.3 - - - -
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Residues in contact with HIS 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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655A GLY* 3.7 21.6 + - - -
658A PHE* 4.2 14.6 - + - -
659A ASP* 2.9 41.0 + - - -
678A ARG 5.1 0.7 - - - -
679A VAL* 3.0 27.5 - - + +
680A GLU* 2.9 40.4 + - + +
682A SER* 1.3 85.4 + - - +
684A LYS* 1.3 66.8 + - - +
686A LYS* 3.0 10.4 + - + +
687A ILE* 2.8 29.9 + - + +
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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
----------------------------------------------------------
351A ASP* 2.7 22.2 + - - +
624A ILE* 3.0 56.5 - - + +
625A THR* 3.9 5.4 - - - +
626A GLY 4.7 0.4 - - - +
679A VAL* 3.9 6.3 - - + -
680A GLU 3.2 13.2 + - - +
681A PRO* 4.1 5.2 - - + +
682A SER 3.4 0.4 - - - -
683A HIS* 1.3 76.2 - - - +
685A SER* 1.3 65.3 + - - +
687A ILE* 3.1 5.4 + - - +
688A VAL* 3.1 24.1 + - - +
700A MET* 4.2 7.4 - - + -
706A ASN* 3.1 21.4 - - - +
707A ASP* 2.6 30.3 + - - +
710A ALA* 3.9 16.8 - - + -
1002A ACP 3.1 11.9 + - - -
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Residues in contact with SER 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A PRO 3.5 4.6 + - - -
682A SER* 3.4 11.2 + - - -
684A LYS* 1.3 79.0 - - - +
686A LYS* 1.3 55.6 + - - +
688A VAL* 3.6 2.8 + - - +
689A GLU* 3.0 31.9 + - - +
709A PRO* 3.8 28.4 - - - +
710A ALA* 3.9 14.1 - - - +
713A LYS* 4.1 20.5 - - - +
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Residues in contact with LYS 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A PHE* 4.2 9.6 - - + -
659A ASP* 3.9 13.5 + - - -
663A LEU* 4.5 8.9 - - - +
666A GLN* 3.0 31.3 + - - +
682A SER* 2.9 15.4 + - - +
683A HIS* 3.0 15.2 + - + +
685A SER* 1.3 73.8 - - - +
687A ILE* 1.3 65.3 + - - +
689A GLU* 3.2 14.8 + - + +
690A TYR* 2.8 51.5 + - + -
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Residues in contact with ILE 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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349A CYS* 4.5 6.3 - - - -
622A ILE* 4.9 2.9 - - + -
624A ILE* 4.1 28.3 - - + -
658A PHE* 3.6 26.9 - - + -
670A CYS* 3.8 13.5 - - + -
676A PHE* 3.6 35.2 - - + -
679A VAL* 5.2 0.4 - - + -
683A HIS* 2.8 31.0 + - + +
684A LYS* 3.4 9.4 - - - +
686A LYS* 1.3 71.3 - - - +
688A VAL* 1.3 64.8 + - + +
690A TYR* 2.9 13.2 + - - +
691A LEU* 2.8 33.7 + - + +
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Residues in contact with VAL 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A CYS* 3.8 28.5 - - + -
624A ILE* 6.0 0.7 - - + -
684A LYS 3.1 11.9 + - - +
685A SER* 3.7 8.7 - - - +
687A ILE* 1.3 79.4 - - + +
689A GLU* 1.3 62.8 + - - +
691A LEU* 3.2 13.4 + - - +
692A GLN* 3.1 25.7 + - - +
698A THR* 4.1 10.1 - - + -
700A MET* 4.3 7.4 - - + -
710A ALA* 4.3 16.4 - - + +
713A LYS* 4.2 8.5 - - + -
714A ALA* 3.8 35.0 - - + +
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Residues in contact with GLU 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A SER* 3.0 18.0 + - - +
686A LYS* 3.3 16.8 - - - +
688A VAL* 1.3 76.4 - - - +
690A TYR* 1.3 64.9 + - + +
692A GLN* 2.8 25.3 + - + +
693A SER* 3.0 11.8 + - - -
713A LYS* 3.7 29.8 - - - +
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Residues in contact with TYR 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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658A PHE* 3.4 24.2 - + - -
663A LEU* 3.8 17.2 + - + +
666A GLN* 2.7 33.9 + - + +
667A ARG* 3.6 31.9 - - + -
670A CYS* 3.4 31.4 - - + -
686A LYS* 2.8 46.4 + - + -
687A ILE 2.9 6.0 + - - +
689A GLU* 1.3 71.7 - - + +
691A LEU* 1.3 64.9 + - - +
693A SER* 2.6 27.2 + - - -
694A TYR* 3.6 9.1 + - - -
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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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347A VAL* 4.2 25.4 - - + -
349A CYS* 4.5 4.3 - - - -
620A ARG* 3.2 31.2 - - - +
622A ILE* 5.1 2.0 - - + -
670A CYS* 3.6 20.4 - - + +
671A ARG* 5.0 3.1 - - + -
687A ILE* 2.8 51.0 + - + +
688A VAL* 3.4 9.4 - - - +
690A TYR* 1.3 77.6 - - - +
692A GLN* 1.3 61.5 + - - +
694A TYR* 3.3 22.6 + - + +
696A GLU* 3.6 20.3 - - + +
698A THR* 3.8 17.0 - - + +
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Residues in contact with GLN 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A VAL* 3.1 11.4 + - - +
689A GLU* 2.8 15.4 + - + +
691A LEU* 1.3 73.7 - - - +
693A SER* 1.3 51.0 + - - +
694A TYR 3.0 5.8 - - - -
695A ASP* 2.7 32.1 + - - +
696A GLU 4.0 9.8 - - - +
698A THR* 3.3 17.4 + - - +
713A LYS* 3.0 50.1 + - - +
714A ALA* 3.8 4.2 - - - +
715A GLU* 2.8 41.4 + - - +
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Residues in contact with SER 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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667A ARG* 3.1 41.3 + - - +
689A GLU* 3.0 8.1 + - - -
690A TYR* 2.6 25.1 + - - -
692A GLN* 1.3 76.4 - - - +
694A TYR* 1.3 56.0 + - - +
695A ASP* 3.1 8.6 + - - +
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Residues in contact with TYR 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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664A ALA 5.2 0.3 + - - -
667A ARG* 3.1 65.2 + - + +
668A GLU* 3.5 26.3 + - - -
670A CYS* 5.5 0.2 - - + -
671A ARG* 3.1 51.4 - - + -
690A TYR 3.6 12.6 - - - -
691A LEU* 3.3 13.5 + - - +
692A GLN 3.0 1.2 - - - -
693A SER* 1.3 74.8 + - - +
695A ASP* 1.3 69.2 + - - +
696A GLU* 3.3 18.3 + - + +
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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
------------------------------------------------------------
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