Contacts of the helix formed by residues 688 - 703 (chain N) in PDB entry 5A31
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 688 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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607N GLU* 3.6 39.3 - - + +
608N LYS 4.8 0.9 - - - +
686N LYS 3.6 7.9 - - - +
687N MET* 1.3 84.7 - - + +
689N VAL* 1.3 66.5 + - - +
690N ALA* 3.3 6.7 - - + +
691N LEU* 3.2 10.4 + - + +
692N LEU* 3.1 17.7 + - - +
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Residues in contact with VAL 689 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678N LEU* 4.8 12.6 - - + -
679N GLU* 6.1 2.7 - - + -
682N SER* 4.1 21.8 - - - +
687N MET 3.7 0.6 + - - -
688N PRO* 1.3 72.5 - - - +
690N ALA* 1.3 55.0 + - - +
692N LEU* 3.2 1.7 + - - +
693N ARG* 2.7 57.6 + - + +
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Residues in contact with ALA 690 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688N PRO* 3.2 5.9 + - + +
689N VAL* 1.3 79.3 - - - +
691N LEU* 1.3 60.4 + - + +
693N ARG* 3.7 6.7 + - - +
694N ARG* 3.1 37.9 + - - +
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Residues in contact with LEU 691 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607N GLU* 3.3 47.8 - - + +
609N LEU* 5.8 2.5 - - + -
640N THR* 4.0 18.6 - - + +
687N MET* 3.8 19.1 - - + -
688N PRO* 3.2 10.3 + - + +
690N ALA* 1.3 79.7 - - + +
692N LEU* 1.3 60.9 + - - +
694N ARG* 3.2 23.3 + - + +
695N ARG* 2.9 39.6 + - - +
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Residues in contact with LEU 692 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666N ILE* 3.5 20.6 - - + -
678N LEU* 3.0 27.8 - - + +
681N LEU* 3.5 35.0 - - + +
682N SER* 3.0 36.8 - - - +
685N VAL* 4.9 0.4 - - + -
687N MET* 3.8 23.6 - - + +
688N PRO 3.1 13.5 + - - +
689N VAL* 3.8 6.1 - - - +
691N LEU* 1.3 76.0 - - - +
693N ARG* 1.3 51.3 + - + +
695N ARG* 3.7 1.0 - - - +
696N MET* 2.7 37.9 + - + +
713N PHE* 4.8 3.8 - - + -
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Residues in contact with ARG 693 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678N LEU* 3.7 26.9 - - + +
689N VAL* 2.7 43.0 + - + +
690N ALA* 3.8 6.7 - - - +
692N LEU* 1.3 70.7 - - + +
694N ARG* 1.3 60.7 + - + +
696N MET* 3.4 16.0 - - + +
697N SER* 2.9 34.5 + - - +
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Residues in contact with ARG 694 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690N ALA* 3.1 25.0 + - - +
691N LEU* 3.2 28.4 + - + +
693N ARG* 1.3 77.6 - - + +
695N ARG* 1.3 67.0 + - - +
697N SER* 3.5 8.2 - - - -
698N VAL* 3.4 24.6 + - - +
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Residues in contact with ARG 695 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640N THR* 3.6 27.7 + - - -
641N LEU* 5.9 1.4 - - - +
660N THR* 3.3 34.7 + - - +
662N VAL* 3.3 42.1 - - + +
663N GLN* 3.3 35.2 + - + +
666N ILE* 4.7 5.6 - - + -
687N MET* 4.5 6.5 - - + +
691N LEU* 2.9 26.4 + - - +
692N LEU 4.1 2.2 - - - +
694N ARG* 1.3 81.0 - - - +
696N MET* 1.3 65.6 + - - +
698N VAL* 3.3 3.8 + - + +
699N TRP* 3.1 24.8 + - - +
729N LEU 5.4 3.2 + - - -
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Residues in contact with MET 696 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666N ILE* 5.6 0.8 - - - +
678N LEU* 3.5 27.4 - - + -
692N LEU* 2.7 26.3 + - + +
693N ARG* 3.4 17.7 - - + +
695N ARG* 1.3 69.2 - - - +
697N SER* 1.3 60.9 + - - +
699N TRP* 3.4 6.2 + - - +
700N LEU* 2.9 37.0 + - + +
705N LEU* 5.8 2.6 - - - +
707N GLU* 4.6 8.5 - - - +
712N THR* 3.2 36.1 - - - +
713N PHE* 3.2 46.9 - - + -
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Residues in contact with SER 697 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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693N ARG 2.9 23.5 + - - -
694N ARG* 3.5 10.3 - - - -
696N MET* 1.3 76.1 - - - +
698N VAL* 1.3 58.7 + - - +
700N LEU* 3.5 9.1 + - - +
701N GLN* 3.0 43.5 + - - +
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Residues in contact with VAL 698 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663N GLN* 3.2 30.5 - - - +
694N ARG 3.4 14.1 - - - +
695N ARG* 3.3 4.9 + - + +
696N MET 3.2 0.8 - - - -
697N SER* 1.3 75.2 - - - +
699N TRP* 1.3 65.0 + - - +
701N GLN* 3.4 14.5 + - - +
702N GLN* 3.0 22.0 + - + +
728N VAL* 3.3 16.8 - - + +
730N ILE* 3.1 36.1 - - + +
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Residues in contact with TRP 699 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657N VAL* 3.5 19.7 - - + -
659N VAL* 3.5 10.8 - - + -
663N GLN* 3.1 60.0 + - + +
664N ALA 4.3 0.2 - - - -
666N ILE* 4.1 20.0 - - + +
667N LEU* 3.3 37.9 - - + +
695N ARG 3.1 14.9 + - - +
696N MET* 3.8 4.7 - - - +
698N VAL* 1.3 76.7 - - - +
700N LEU* 1.3 58.8 + - - +
702N GLN* 3.1 9.3 + - + +
703N GLY 2.9 24.4 + - - -
704N VAL* 3.1 35.6 + - + -
705N LEU* 3.4 28.5 + - + -
713N PHE* 5.1 3.4 - + - -
728N VAL* 3.3 24.9 - - + -
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Residues in contact with LEU 700 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696N MET* 2.9 23.0 + - + +
697N SER* 3.6 9.2 - - - +
699N TRP* 1.3 76.3 - - - +
701N GLN* 1.3 63.6 + - + +
703N GLY* 3.2 11.4 + - - -
705N LEU* 3.4 27.4 - - + +
706N ARG* 4.2 2.2 - - + -
707N GLU* 3.3 57.2 - - + +
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Residues in contact with GLN 701 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697N SER* 3.0 28.4 + - - +
698N VAL* 3.5 14.6 - - - +
700N LEU* 1.3 78.8 - - + +
702N GLN* 1.3 62.5 + - - +
703N GLY* 3.3 1.2 + - - -
730N ILE* 5.6 6.4 - - - +
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Residues in contact with GLN 702 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698N VAL* 3.0 15.3 + - - +
699N TRP* 3.1 17.5 + - + +
701N GLN* 1.3 76.1 - - - +
703N GLY* 1.3 59.8 + - - +
704N VAL* 3.8 21.4 - - + +
721N PRO* 4.8 3.3 - - + +
726N ASN* 2.6 34.5 + - - +
727N MET 4.9 1.6 + - - -
728N VAL* 3.3 36.4 - - + +
730N ILE* 6.0 2.6 - - - +
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Residues in contact with GLY 703 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699N TRP 2.9 5.9 + - - -
700N LEU 3.2 13.1 + - - -
701N GLN 4.3 0.9 - - - -
702N GLN* 1.3 77.9 - - - +
704N VAL* 1.3 60.4 + - - +
705N LEU 3.1 7.9 - - - -
716N ILE* 3.0 29.5 - - - +
719N GLU* 3.2 12.4 - - - +
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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