Contacts of the helix formed by residues 659 - 672 (chain E) in PDB entry 4P6X
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 SER 659 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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610E TRP* 3.5 2.0 - - - -
657E GLN 3.3 3.0 + - - -
658E VAL* 1.3 74.0 - - - +
660E TYR* 1.3 58.6 + - - +
661E GLU* 2.9 23.9 + - - +
662E GLU* 2.7 38.5 + - - +
663E TYR* 2.8 26.9 + - - +
700E ALA 5.3 0.2 + - - -
704E ARG* 4.1 19.1 - - - +
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Residues in contact with TYR 660 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537E GLU* 3.0 45.9 + - + +
540E GLU* 3.4 30.9 - - - +
610E TRP* 3.1 49.6 - + + -
614E ARG* 4.9 16.4 - - - +
659E SER* 1.3 72.0 - - - +
661E GLU* 1.3 64.3 + - - +
663E TYR* 4.1 7.2 - + - -
664E LEU* 2.9 47.4 + - + +
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Residues in contact with GLU 661 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533E VAL* 3.3 26.6 - - + +
537E GLU* 4.3 13.9 - - - +
659E SER* 2.9 24.2 + - - +
660E TYR* 1.3 88.8 + - - +
662E GLU* 1.3 64.4 + - - +
664E LEU* 3.5 0.8 + - - -
665E CYS* 3.3 28.1 + - - -
700E ALA* 4.1 15.9 - - + +
704E ARG* 5.2 3.8 - - - +
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Residues in contact with GLU 662 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658E VAL* 3.3 8.5 - - + -
659E SER* 2.7 41.4 + - - +
661E GLU* 1.3 75.6 - - - +
663E TYR* 1.3 59.8 + - - +
665E CYS* 3.1 4.5 + - - +
666E MET* 2.9 33.4 + - - +
697E LEU* 4.2 8.1 - - + -
700E ALA* 4.3 18.8 - - + +
701E ILE* 3.9 5.6 - - - +
704E ARG* 4.0 11.5 + - - -
714E ARG* 2.4 48.4 + - - -
718E LEU* 3.1 23.1 - - + +
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Residues in contact with TYR 663 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540E GLU* 4.1 11.4 + - - -
606E PHE* 3.3 46.0 - + - -
607E ALA* 3.0 26.7 + - - +
610E TRP* 3.3 67.8 - + + +
653E LEU* 4.6 3.1 - - + -
658E VAL* 3.6 9.1 - - + +
659E SER 2.8 18.0 + - - +
660E TYR* 4.2 10.1 - + - +
662E GLU* 1.3 73.3 - - - +
664E LEU* 1.3 62.7 + - + +
666E MET* 3.7 5.0 - - - +
667E LYS* 2.8 59.9 + - + +
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Residues in contact with LEU 664 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533E VAL* 3.8 16.2 - - + +
536E LEU* 3.6 17.0 - - + +
537E GLU* 3.5 42.8 - - + +
540E GLU* 3.8 34.3 - - + +
577E TRP* 5.2 1.2 - - + +
660E TYR* 2.9 36.2 + - + +
661E GLU* 3.8 4.7 - - - +
662E GLU 3.3 0.8 - - - -
663E TYR* 1.3 88.0 - - + +
665E CYS* 1.3 62.2 + - - +
667E LYS* 3.6 7.8 + - - +
668E VAL* 3.2 27.9 + - - +
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Residues in contact with CYS 665 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533E VAL* 3.7 13.5 - - - -
536E LEU* 4.4 8.1 - - - -
661E GLU 3.3 15.0 + - - -
662E GLU 3.1 7.7 + - - +
664E LEU* 1.3 76.2 - - - +
666E MET* 1.3 60.2 + - - +
668E VAL* 3.3 5.9 + - - +
669E LEU* 3.0 32.2 + - - +
693E TYR* 4.4 5.6 - - + +
696E GLU* 3.6 41.3 - - - -
697E LEU* 3.9 23.8 - - + +
700E ALA* 4.2 2.2 - - - -
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Residues in contact with MET 666 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606E PHE* 3.7 17.0 - - + -
658E VAL* 4.1 17.3 - - - -
662E GLU 2.9 20.7 + - - +
663E TYR 3.7 3.8 - - - +
665E CYS* 1.3 77.3 - - - +
667E LYS* 1.3 55.9 + - - +
669E LEU* 3.2 7.7 + - - +
670E LEU* 2.9 25.6 + - - +
697E LEU* 3.9 18.6 - - + -
718E LEU* 3.2 52.7 - - + +
721E LEU* 4.0 25.1 - - + -
722E LEU* 3.6 29.6 - - + +
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Residues in contact with LYS 667 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540E GLU* 2.7 32.7 + - - -
541E PRO* 5.0 1.8 - - - +
577E TRP* 3.3 32.7 - - + -
603E LEU* 3.3 28.2 - - + +
606E PHE* 3.9 15.0 - - + -
607E ALA* 4.3 12.8 - - + -
663E TYR* 2.8 57.6 + - + +
664E LEU* 3.8 9.3 + - - +
665E CYS 3.2 0.2 - - - -
666E MET* 1.3 77.6 - - - +
668E VAL* 1.3 62.0 + - - +
670E LEU* 3.2 11.6 + - - +
671E LEU 3.3 8.8 + - - -
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Residues in contact with VAL 668 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536E LEU* 3.5 32.8 - - + -
577E TRP* 4.1 19.7 - - + -
581E ILE* 4.2 12.8 - - + -
664E LEU 3.2 16.7 + - - +
665E CYS 3.5 7.2 - - - +
667E LYS* 1.3 76.3 - - - +
669E LEU* 1.3 61.6 - - - +
671E LEU* 3.0 16.6 + - + +
672E LEU* 3.2 18.2 + - + +
693E TYR* 3.6 39.3 - - + -
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Residues in contact with LEU 669 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665E CYS 3.0 19.8 + - - +
666E MET 3.2 7.4 + - - +
668E VAL* 1.3 75.7 - - - +
670E LEU* 1.3 61.9 + - - +
672E LEU* 3.1 15.9 + - + +
673E SER* 3.2 15.9 + - - -
690E ARG* 3.8 19.5 + - + +
693E TYR* 3.8 32.8 - - + +
694E ILE* 3.7 26.2 - - + +
697E LEU* 3.9 20.2 - - + -
722E LEU* 3.8 28.5 - - + -
774E PHE* 4.2 14.4 - - + -
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Residues in contact with LEU 670 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599E SER* 3.4 14.2 - - - -
602E ALA* 4.0 22.4 - - + +
603E LEU* 4.3 7.6 - - + -
606E PHE* 3.4 51.4 - - + -
666E MET 2.9 10.9 + - - +
667E LYS* 3.3 10.1 - - - +
668E VAL 3.1 0.2 - - - -
669E LEU* 1.3 74.9 - - - +
671E LEU* 1.3 64.2 + - - +
672E LEU 3.0 2.0 - - - -
673E SER* 2.8 30.1 + - - +
722E LEU* 3.5 30.7 - - + +
725E MET* 4.1 20.4 - - + -
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Residues in contact with LEU 671 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577E TRP* 3.9 3.8 - - + -
578E ALA* 3.7 17.0 - - + -
581E ILE* 3.5 31.4 - - + -
584E PHE* 4.1 15.9 - - + -
595E LEU* 3.9 21.2 - - + +
596E LEU* 4.0 35.2 - - + +
599E SER* 3.4 24.8 + - - +
603E LEU* 4.0 16.3 - - + +
667E LYS 3.3 3.7 + - - +
668E VAL* 3.0 12.4 + - + +
670E LEU* 1.3 78.2 - - - +
672E LEU* 1.3 63.0 + - + +
673E SER 3.4 1.3 + - - -
674E THR 4.9 1.2 + - - +
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Residues in contact with LEU 672 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581E ILE* 6.3 0.4 - - + -
584E PHE* 5.2 5.4 - - + -
587E LEU* 5.4 2.0 - - + -
595E LEU* 3.9 16.2 - - + -
668E VAL* 3.2 27.6 + - + +
669E LEU* 3.1 13.7 + - + +
670E LEU 3.0 0.6 - - - -
671E LEU* 1.3 86.7 - - + +
673E SER* 1.3 57.0 + - - +
674E THR 3.6 2.0 - - - -
686E PHE* 3.3 47.2 - - + -
689E ILE* 4.0 21.8 - - + +
690E ARG* 3.4 47.8 + - + +
693E TYR* 4.4 2.0 - - + -
772E LEU* 3.6 1.2 - - - +
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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