Contacts of the helix formed by residues 671 - 686 (chain A) in PDB entry 2P6U
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 GLY 671 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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667A ALA 3.2 16.9 + - - -
668A SER 5.4 0.4 - - - -
670A ILE* 1.3 79.4 - - - +
672A ARG* 1.3 53.9 + - - -
673A GLY 3.3 2.0 - - - -
674A ILE* 3.9 12.6 - - - -
675A ALA* 2.6 42.1 + - - +
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Residues in contact with ARG 672 (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 ALA* 3.4 23.4 + - + +
671A GLY* 1.3 70.6 - - - -
673A GLY* 1.3 66.6 + - - +
674A ILE* 4.8 0.2 - - - +
675A ALA* 3.3 1.2 - - - +
676A GLU* 2.9 22.8 + - - +
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Residues in contact with GLY 673 (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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671A GLY 3.3 0.4 - - - -
672A ARG* 1.3 77.4 - - - +
674A ILE* 1.3 69.9 + - - +
676A GLU* 2.8 22.0 + - - +
677A ARG* 3.0 11.5 + - - +
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Residues in contact with ILE 674 (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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638A ARG* 5.3 0.4 - - - +
644A ARG* 3.2 45.8 - - - +
670A ILE* 3.6 23.3 - - + +
671A GLY* 3.9 21.5 - - - +
673A GLY* 1.3 74.1 - - - +
675A ALA* 1.3 56.8 + - - +
677A ARG* 3.2 7.6 + - + +
678A VAL* 2.7 39.5 + - + +
705A PO4 4.3 7.2 - - - +
709A PO4 3.9 8.5 - - - +
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Residues in contact with ALA 675 (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 ARG* 5.2 4.0 - - + +
666A VAL* 4.6 12.1 - - + -
667A ALA* 3.3 31.2 - - + +
670A ILE* 4.8 2.4 - - - +
671A GLY 2.6 26.9 + - - +
672A ARG 3.3 4.9 - - - +
674A ILE* 1.3 75.9 - - - +
676A GLU* 1.3 64.2 + - - +
678A VAL* 3.2 11.3 + - - +
679A VAL* 3.1 24.9 + - + +
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Residues in contact with GLU 676 (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 ARG* 4.3 21.5 + - - +
672A ARG 2.9 13.1 + - - +
673A GLY* 2.8 17.9 + - - +
675A ALA* 1.3 73.0 - - - +
677A ARG* 1.3 63.5 + - - +
679A VAL* 3.3 6.3 + - - +
680A GLU* 3.1 23.5 + - + +
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Residues in contact with ARG 677 (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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638A ARG* 2.5 58.4 - - - +
673A GLY 3.0 8.1 + - - +
674A ILE* 3.5 11.7 - - - +
676A GLU* 1.3 77.9 - - - +
678A VAL* 1.3 64.8 + - + +
680A GLU* 3.2 25.4 - - - +
681A GLY 3.6 2.9 + - - -
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Residues in contact with VAL 678 (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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637A ILE* 4.4 12.6 - - + +
638A ARG* 4.8 12.0 - - + +
640A ILE* 4.1 24.9 - - + -
659A ILE* 4.7 12.3 - - + -
666A VAL* 6.0 0.2 - - + -
670A ILE* 4.8 10.3 - - + -
674A ILE* 2.7 40.8 + - + +
675A ALA* 3.4 7.9 - - - +
677A ARG* 1.3 74.5 - - - +
679A VAL* 1.3 62.9 + - + +
681A GLY* 3.3 10.7 + - - -
682A ILE* 3.4 19.0 + - + +
709A PO4 4.1 19.7 - - - +
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Residues in contact with VAL 679 (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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659A ILE* 4.9 15.5 - - + +
660A VAL* 4.8 23.8 - - + -
663A ARG* 4.0 44.4 - - + +
666A VAL* 5.8 2.0 - - + -
675A ALA* 3.1 20.1 + - + +
676A GLU 3.8 4.0 - - - +
678A VAL* 1.3 72.6 - - + +
680A GLU* 1.3 67.3 + - - +
681A GLY 2.9 4.5 + - - -
682A ILE* 3.2 17.7 + - + +
683A SER* 3.3 19.2 + - - +
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Residues in contact with GLU 680 (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 ARG* 5.7 0.4 - - - +
676A GLU* 3.1 14.4 + - + +
677A ARG* 3.2 23.8 + - - +
679A VAL* 1.3 76.2 - - - +
681A GLY* 1.3 55.3 + - - +
683A SER* 4.1 4.1 + - - -
684A VAL* 3.1 34.7 - - + +
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Residues in contact with GLY 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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638A ARG* 6.0 4.9 - - - -
677A ARG 3.6 3.6 + - - -
678A VAL 3.3 7.1 + - - -
679A VAL 2.9 3.0 + - - -
680A GLU* 1.3 80.2 - - - +
682A ILE* 1.3 65.6 + - - +
684A VAL* 3.6 6.6 + - - +
685A LYS* 3.4 20.8 + - - +
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Residues in contact with ILE 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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637A ILE* 3.6 31.1 - - + +
656A ALA* 4.0 33.7 - - + +
659A ILE* 4.4 15.0 - - + -
660A VAL* 4.2 21.5 - - + -
678A VAL* 3.4 20.0 - - + +
679A VAL* 3.2 9.8 + - - +
681A GLY* 1.3 73.6 - - - +
683A SER* 1.3 65.6 + - - +
685A LYS* 3.0 18.1 + - + +
686A SER* 3.0 21.6 + - - -
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Residues in contact with SER 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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660A VAL* 5.7 4.6 - - - +
679A VAL* 3.3 20.6 + - - +
680A GLU* 4.1 7.6 + - - -
682A ILE* 1.3 78.9 - - - +
684A VAL* 1.3 69.7 + - - +
685A LYS 2.9 2.4 + - - -
686A SER* 3.3 20.5 + - - +
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Residues in contact with VAL 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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680A GLU* 3.1 29.6 - - + +
681A GLY* 3.8 9.2 - - - +
682A ILE 3.4 0.4 - - - -
683A SER* 1.3 78.9 - - - +
685A LYS* 1.3 60.0 + - - +
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Residues in contact with LYS 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 GLY 3.4 9.6 + - - +
682A ILE* 3.0 10.9 + - - +
683A SER 2.9 1.6 + - - -
684A VAL* 1.3 81.6 - - - +
686A SER* 1.3 67.4 + - - +
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Residues in contact with SER 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 ILE* 3.0 21.2 + - - -
683A SER* 3.7 13.4 - - - +
685A LYS* 1.3 85.2 - - - +
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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