Contacts of the helix formed by residues 674 - 686 (chain A) in PDB entry 6P0D
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 674 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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672A ARG 4.4 2.2 - - - +
673A GLU* 1.3 98.8 - - + +
675A LEU* 1.3 66.5 + - - +
676A SER* 3.8 13.0 - - - +
677A ARG* 2.9 22.0 + - + -
678A ARG* 3.0 10.1 + - - +
727A LEU 3.6 13.9 - - - +
728A ASP* 4.2 19.5 - - - +
731A ALA* 3.5 9.4 - - + +
732A THR* 4.6 4.2 - - + +
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Residues in contact with LEU 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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564A THR* 4.1 15.0 - - + -
566A GLU* 5.5 2.9 - - - +
660A PHE 4.6 7.0 - - - +
661A ASP* 3.9 16.8 - - - +
674A PRO* 1.3 72.6 - - - +
676A SER* 1.3 55.4 + - - +
678A ARG* 3.5 26.5 - - - +
679A ARG* 2.7 54.1 + - + +
725A LYS* 3.6 33.4 - - + -
726A THR 3.5 26.5 - - - +
727A LEU* 3.4 8.5 + - + +
731A ALA 2.9 14.4 + - - +
742A TRP* 5.2 2.0 - - - +
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Residues in contact with SER 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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674A PRO* 3.8 8.5 - - - +
675A LEU* 1.3 75.4 - - - +
677A ARG* 1.3 59.9 + - - +
679A ARG* 4.1 7.4 + - - +
680A GLN* 3.2 27.9 + - - +
727A LEU* 2.9 29.5 + - - +
728A ASP* 2.7 30.5 + - - -
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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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668A GLU* 2.9 40.5 + - - -
670A LEU* 3.6 7.1 - - - +
673A GLU* 3.1 33.6 + - + +
674A PRO* 2.9 20.3 + - + +
676A SER* 1.3 81.2 + - - +
678A ARG* 1.3 65.9 + - - +
679A ARG 3.2 0.2 - - - -
680A GLN* 3.1 6.6 + - + +
681A LEU* 2.9 44.4 + - + +
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Residues in contact with ARG 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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661A ASP* 2.8 43.3 + - - +
662A LEU* 3.4 27.6 - - - +
663A ILE* 5.1 0.4 - - - +
670A LEU* 3.4 34.5 - - + -
673A GLU* 2.7 35.7 + - + +
674A PRO 3.0 10.5 + - - +
675A LEU* 3.4 25.8 - - + +
677A ARG* 1.3 76.3 - - - +
679A ARG* 1.3 58.2 + - - +
681A LEU* 3.3 6.8 + - - +
682A LEU* 2.9 27.9 + - - +
731A ALA 2.8 19.8 + - - -
732A THR 3.4 12.5 + - - -
733A TYR* 3.6 19.6 - - - +
742A TRP* 4.4 8.3 - - - +
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Residues in contact with ARG 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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564A THR* 3.4 18.1 + - - +
566A GLU* 4.9 11.2 + - - -
660A PHE 5.8 2.7 - - - +
661A ASP* 6.3 0.9 - - - +
675A LEU* 2.7 33.9 + - + +
676A SER* 4.1 7.5 + - - +
678A ARG* 1.3 70.4 - - - +
680A GLN* 1.3 60.9 + - - +
682A LEU* 3.2 13.7 + - + +
683A ARG* 2.8 81.9 + - + +
698A SER* 4.6 5.3 + - - -
700A ASP* 2.8 41.2 + - - -
727A LEU* 3.6 24.5 - - - +
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Residues in contact with GLN 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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676A SER 3.2 17.0 + - - +
677A ARG* 3.1 8.3 + - + +
679A ARG* 1.3 80.2 + - - +
681A LEU* 1.3 63.5 + - + +
683A ARG* 3.4 30.1 + - - +
684A GLU* 3.0 66.6 + - - +
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Residues in contact with LEU 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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662A LEU* 3.6 16.6 - - + +
665A LEU* 4.1 14.6 - - + -
668A GLU* 4.5 2.9 - - - +
670A LEU* 3.9 34.8 - - + -
677A ARG* 2.9 49.7 + - + +
678A ARG 3.6 1.3 - - - +
680A GLN* 1.3 78.1 - - + +
682A LEU* 1.3 61.1 + - - +
684A GLU* 4.9 5.6 - - - +
685A ASN* 2.9 45.2 + - - +
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Residues in contact with LEU 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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618A LEU* 3.5 31.9 - - + -
659A ALA* 4.2 17.7 - - + +
660A PHE* 3.9 9.2 - - - +
661A ASP* 3.8 28.0 - - - +
662A LEU* 3.6 13.8 - - + +
678A ARG 2.9 13.0 + - - +
679A ARG* 3.2 16.8 + - + +
681A LEU* 1.3 78.5 - - - +
683A ARG* 1.3 63.9 + - + +
684A GLU 3.3 0.9 + - - -
686A PHE* 3.4 29.3 + - + -
693A PHE* 4.7 0.4 - - + -
695A PHE* 3.5 27.7 - - + -
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Residues in contact with ARG 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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679A ARG* 2.8 75.8 + - + +
680A GLN* 3.6 33.3 + - - +
682A LEU* 1.3 75.3 - - + +
684A GLU* 1.3 61.6 + - + +
686A PHE 3.8 10.2 - - - +
695A PHE* 3.7 32.2 - - + +
698A SER* 4.0 14.3 + - - -
700A ASP* 5.0 2.6 + - - -
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Residues in contact with GLU 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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610A LEU* 3.4 17.7 - - - +
680A GLN* 3.0 55.6 + - - +
681A LEU* 5.0 5.4 - - - +
682A LEU 3.2 0.2 - - - -
683A ARG* 1.3 79.9 - - + +
685A ASN* 1.3 69.2 + - - +
686A PHE 3.5 2.4 - - - +
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Residues in contact with ASN 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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610A LEU* 3.1 34.2 + - - +
612A SER* 4.3 12.8 + - - -
613A VAL* 3.5 19.3 - - + +
665A LEU* 3.7 22.1 - - + +
666A ASN* 5.5 3.1 + - - -
681A LEU* 2.9 40.5 + - - +
684A GLU* 1.3 86.0 + - - +
686A PHE* 1.3 71.8 + - + +
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Residues in contact with PHE 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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608A ILE* 3.1 21.3 - - + +
609A LYS* 4.0 11.2 - - + -
610A LEU* 5.3 0.5 - - - +
613A VAL* 4.4 6.7 - - + -
616A PHE* 3.7 42.2 - + + -
618A LEU* 3.8 24.2 - - + -
662A LEU* 3.8 31.2 - - + -
665A LEU* 4.4 3.1 - - + -
682A LEU* 3.4 28.6 + - + +
683A ARG 3.8 7.8 - - - +
684A GLU 4.6 1.7 - - - +
685A ASN* 1.3 92.5 + - + +
687A VAL* 1.3 65.6 + - - +
693A PHE* 4.0 14.6 - + + -
695A PHE* 3.7 17.8 - - + -
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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