Contacts of the helix formed by residues 680 - 692 (chain A) in PDB entry 2H5G
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 ASN 680 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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587A TYR* 3.8 6.6 + - - -
621A HIS* 4.0 14.1 + - + -
678A VAL* 3.7 3.4 - - - +
679A ASP* 1.3 94.1 + - - +
681A VAL* 1.3 69.5 + - + +
682A GLN* 3.2 15.1 - - - +
683A ASP* 3.0 41.2 + - - +
684A ALA* 3.1 12.3 + - - +
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Residues in contact with VAL 681 (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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587A TYR* 3.6 15.7 + - + +
589A ASP* 4.3 7.6 - - - +
621A HIS* 6.2 0.7 - - + -
680A ASN* 1.3 73.3 - - + +
682A GLN* 1.3 52.7 + - - +
684A ALA* 3.1 4.2 + - - +
685A ILE* 2.8 52.3 + - + +
706A THR* 3.4 36.3 - - + +
709A PHE* 4.3 15.9 - - + -
710A PHE* 4.0 24.7 - - + -
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Residues in contact with GLN 682 (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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680A ASN* 3.2 12.9 + - + +
681A VAL* 1.3 77.4 - - - +
683A ASP* 1.3 56.3 + - - +
685A ILE* 3.3 16.0 + - - +
686A ASP* 2.8 69.4 + - - +
709A PHE* 3.9 26.5 - - + -
713A HIS* 5.8 1.9 - - - -
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Residues in contact with ASP 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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649A LYS* 4.2 8.0 + - - -
677A VAL 5.1 0.2 - - - +
678A VAL* 3.8 15.4 - - + +
679A ASP* 3.2 34.4 + - - +
680A ASN* 3.0 29.4 + - - +
682A GLN* 1.3 74.4 - - - +
684A ALA* 1.3 59.7 + - - +
686A ASP* 3.3 9.9 + - - +
687A HIS* 2.9 30.0 + - - +
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Residues in contact with ALA 684 (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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587A TYR* 3.6 45.8 - - + -
619A LEU* 4.0 12.6 - - + -
678A VAL* 4.2 5.1 - - + +
680A ASN 3.1 5.8 + - - +
681A VAL 3.1 8.3 + - - +
683A ASP* 1.3 79.6 - - - +
685A ILE* 1.3 57.0 + - - +
687A HIS* 3.2 3.1 + - - +
688A ILE* 2.9 35.7 + - - +
710A PHE* 4.5 4.3 - - + -
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Residues in contact with ILE 685 (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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681A VAL* 2.8 30.4 + - + +
682A GLN* 3.6 17.3 - - - +
684A ALA* 1.3 71.2 - - - +
686A ASP* 1.3 64.7 + - - +
688A ILE* 3.3 7.4 + - - +
689A HIS* 3.0 52.5 + - + +
709A PHE* 3.9 34.1 - - + -
710A PHE* 4.1 13.5 - - + -
713A HIS* 4.0 22.4 - - + +
714A VAL* 3.8 17.5 - - + -
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Residues in contact with ASP 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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682A GLN* 2.8 55.7 + - - +
683A ASP* 3.6 9.2 - - - +
685A ILE* 1.3 74.5 - - - +
687A HIS* 1.3 57.5 + - - +
689A HIS* 3.4 9.1 + - - +
690A LYS* 3.0 31.5 + - - +
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Residues in contact with HIS 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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585A HIS* 3.5 27.8 + + - -
617A THR* 3.8 9.1 - - + +
619A LEU* 3.6 33.4 - - + +
664A LEU* 4.1 20.4 - - + +
676A GLU* 4.5 11.6 - - + +
678A VAL* 4.8 5.4 - - + -
683A ASP 2.9 16.4 + - - +
684A ALA* 3.5 5.6 - - - +
686A ASP* 1.3 77.3 - - - +
688A ILE* 1.3 56.6 + - - +
690A LYS* 3.2 1.9 + - - -
691A TYR* 2.8 67.5 + + + +
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Residues in contact with ILE 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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585A HIS* 3.6 37.9 - - + +
587A TYR* 4.9 2.7 - - + -
619A LEU* 3.9 9.0 - - + -
684A ALA* 2.9 23.3 + - + +
685A ILE* 3.3 5.4 + - - +
687A HIS* 1.3 73.9 - - - +
689A HIS* 1.3 61.9 + - - +
692A GLY* 2.9 30.9 + - - -
694A SER* 5.6 1.2 + - - +
697A ASP* 3.5 32.1 - - + +
710A PHE* 3.6 35.9 - - + -
714A VAL* 4.0 17.9 - - + -
716A SER* 4.2 2.2 - - - +
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Residues in contact with HIS 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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685A ILE* 3.0 31.7 + - + +
686A ASP* 3.6 9.0 - - - +
688A ILE* 1.3 82.4 - - - +
690A LYS* 1.3 62.5 + - - +
692A GLY 4.5 5.2 + - - +
713A HIS 2.9 28.3 + - - -
714A VAL* 3.5 10.3 - - + -
715A ASP* 3.3 39.7 + - + +
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Residues in contact with LYS 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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665A ARG* 2.7 45.2 + - - +
686A ASP 3.0 18.7 + - - +
687A HIS* 3.7 4.3 - - - +
689A HIS* 1.3 80.2 - - - +
691A TYR* 1.3 92.0 + - + +
692A GLY 5.0 0.5 - - - +
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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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583A ILE* 3.9 15.1 - - - +
585A HIS* 4.2 4.0 - - - +
664A LEU* 3.4 56.1 - - + +
665A ARG* 3.5 51.0 + - + +
687A HIS* 2.8 57.4 + + + +
690A LYS* 1.3 107.0 - - + +
692A GLY* 1.3 65.5 + - - +
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Residues in contact with GLY 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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581A GLU* 5.1 1.6 - - - +
583A ILE* 3.8 5.8 - - - -
585A HIS* 3.4 21.5 - - - -
688A ILE* 2.9 21.5 + - - +
689A HIS 4.7 4.5 - - - +
690A LYS 3.7 1.2 - - - +
691A TYR* 1.3 82.0 - - - +
693A SER* 1.3 59.4 + - - -
694A SER* 3.4 6.5 + - - -
697A ASP* 5.4 0.9 - - - -
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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