Contacts of the helix formed by residues 656 - 667 (chain A) in PDB entry 4B9N
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 GLN 656 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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654A TYR 3.6 2.0 + - - -
655A SER* 1.3 77.9 - - - +
657A ILE* 1.3 64.8 + - - +
658A GLU* 3.2 9.1 + - - +
659A LEU* 3.4 23.9 + - + +
660A ARG* 3.1 21.3 + - - +
675A PHE* 4.2 19.3 - - + -
681A ILE* 4.0 19.6 - - + +
682A HIS* 3.5 24.6 + - - -
713A VAL* 5.8 0.7 - - - +
830A ASP* 5.5 0.6 + - - -
1877A SO4 4.8 1.0 + - - -
1880A SO4 2.6 44.1 + - - +
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Residues in contact with ILE 657 (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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654A TYR* 3.6 41.1 - - + +
655A SER 3.2 4.6 + - - -
656A GLN* 1.3 76.1 - - - +
658A GLU* 1.3 78.1 + - - +
660A ARG* 3.3 7.6 + - - +
661A VAL* 2.9 35.1 + - + +
800A ALA* 4.1 19.7 - - + +
803A ILE* 3.8 38.6 - - + -
804A ILE* 5.6 0.2 - - + -
829A HIS 5.9 0.2 - - - +
830A ASP* 4.2 13.4 + - + +
862A LEU* 4.1 16.2 - - + -
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Residues in contact with GLU 658 (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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615A ARG* 4.3 15.1 + - - -
656A GLN* 3.9 5.9 - - - +
657A ILE* 1.3 93.3 + - - +
659A LEU* 1.3 57.1 + - - +
661A VAL* 3.3 4.7 + - - +
662A LEU* 3.0 23.4 + - - +
713A VAL* 3.7 34.8 - - + +
714A TYR* 5.0 3.4 + - - -
796A ILE* 3.5 23.6 - - + +
797A GLN* 4.1 14.6 - - - +
800A ALA* 4.2 16.2 - - + +
830A ASP* 4.5 13.6 - - - +
13B T 4.6 4.5 - - - +
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Residues in contact with LEU 659 (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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656A GLN* 3.4 28.6 + - - +
658A GLU* 1.3 77.9 + - - +
660A ARG* 1.3 57.9 + - - +
662A LEU* 3.3 24.8 + - + +
663A ALA* 2.9 22.9 + - - +
671A LEU* 3.9 8.5 - - + +
675A PHE* 3.5 24.7 - - + -
681A ILE* 3.8 27.8 - - + -
682A HIS* 4.6 1.3 - - + -
709A ASN* 4.1 31.6 - - + +
712A ILE* 4.8 3.4 - - + -
713A VAL* 3.6 26.5 - - + -
739A TYR* 5.0 3.1 - - - +
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Residues in contact with ARG 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655A SER* 3.0 28.6 + - - -
656A GLN* 3.1 14.4 + - - +
657A ILE* 3.6 5.2 - - - +
659A LEU* 1.3 74.5 - - - +
661A VAL* 1.3 64.9 + - - +
663A ALA* 3.2 3.8 + - - +
664A HIS* 3.0 19.6 + - - +
675A PHE* 3.6 56.6 + - + +
678A ASP* 3.3 25.1 + - - -
679A LEU 5.9 0.2 + - - -
858A LEU* 4.6 2.0 - - - +
860A VAL* 3.6 16.9 - - + +
861A PRO* 2.8 42.7 + - - +
862A LEU* 4.3 19.7 - - + +
863A LYS* 3.6 25.8 - - - +
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Residues in contact with VAL 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A ILE* 2.9 25.5 + - + +
658A GLU 3.6 4.9 - - - +
660A ARG* 1.3 75.8 - - - +
662A LEU* 1.3 58.3 + - - +
664A HIS* 3.2 9.6 + - + +
665A ILE* 2.9 38.6 + - + +
766A LEU* 5.9 2.0 - - + -
795A PRO 4.0 8.7 - - - +
796A ILE* 4.1 11.7 - - - +
799A SER* 3.8 21.8 - - - -
800A ALA* 4.4 10.3 - - + +
803A ILE* 3.9 27.8 - - + -
858A LEU* 4.2 11.0 - - + -
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Residues in contact with LEU 662 (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 GLU 3.0 13.0 + - - +
659A LEU* 3.5 18.2 - - + +
661A VAL* 1.3 75.5 - - - +
663A ALA* 1.3 64.8 + - - +
665A ILE* 3.8 7.2 - - + -
666A ALA* 2.9 34.1 + - + +
671A LEU* 4.0 17.0 - - + -
712A ILE* 3.5 31.0 - - + -
713A VAL* 6.1 0.2 - - + -
739A TYR* 4.3 2.2 - - - +
746A VAL* 3.9 20.4 - - + -
749A TYR* 3.9 24.7 - - + -
750A MET* 4.8 0.7 - - + -
796A ILE* 3.7 26.9 - - + +
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Residues in contact with ALA 663 (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 LEU 2.9 14.0 + - - +
660A ARG 3.2 8.5 + - - +
662A LEU* 1.3 76.4 - - - +
664A HIS* 1.3 57.1 + - - +
667A GLU* 2.9 28.4 + - - -
668A ASP 3.6 2.8 + - - +
671A LEU* 3.7 26.9 - - + -
672A MET* 3.5 24.1 - - + +
675A PHE* 4.1 13.0 - - + -
860A VAL* 4.2 6.3 - - + -
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Residues in contact with HIS 664 (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 ARG 3.0 13.0 + - - +
661A VAL* 3.4 10.3 - - + +
663A ALA* 1.3 77.1 - - - +
665A ILE* 1.3 79.7 + - + +
667A GLU* 3.4 9.4 - - - +
766A LEU* 4.0 14.9 - - + +
857A THR 4.6 3.6 - - - -
858A LEU* 3.5 37.2 - - + +
859A ARG* 2.9 85.7 + - + +
860A VAL* 4.9 2.4 - - + +
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Residues in contact with ILE 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A VAL* 2.9 37.3 + - + +
662A LEU* 3.6 8.7 - - + +
664A HIS* 1.3 88.3 - - + +
666A ALA* 1.3 62.1 + - - +
667A GLU* 4.3 6.9 - - - +
749A TYR* 3.6 46.2 - - + +
766A LEU* 4.6 10.1 - - + -
795A PRO* 4.4 13.5 - - + +
796A ILE* 3.8 20.2 - - + -
799A SER* 5.2 1.6 - - - +
859A ARG* 4.8 1.5 + - - +
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Residues in contact with ALA 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A LEU* 2.9 22.8 + - + +
665A ILE* 1.3 77.3 - - - +
667A GLU* 1.3 70.7 + - - +
668A ASP* 3.2 5.0 + - + +
745A GLY* 3.7 23.5 - - - +
746A VAL* 4.0 9.6 - - + +
748A ARG* 5.4 2.4 + - - +
749A TYR* 3.6 30.7 - - + -
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Residues in contact with GLU 667 (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 ALA 2.9 14.0 + - - -
664A HIS 3.4 15.0 - - - +
665A ILE 3.4 5.8 - - - +
666A ALA* 1.3 80.6 - - - +
668A ASP* 1.3 64.1 + - - +
669A ASP* 3.3 8.5 + - - +
672A MET* 3.5 18.8 - - + +
745A GLY* 5.1 1.2 - - - -
748A ARG* 5.4 3.1 + - - -
859A ARG* 3.6 35.6 + - - +
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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