Contacts of the helix formed by residues 632 - 645 (chain N) in PDB entry 1CZA
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 ASP 632 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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612N ASP 4.7 0.5 - - - +
613N ALA* 3.4 22.5 - - - +
614N GLY 3.3 23.3 + - - -
615N ILE* 3.4 19.9 - - + +
631N HIS* 1.3 70.8 - - - +
633N VAL* 1.3 58.3 + - - +
634N VAL* 2.9 21.2 + - - +
635N THR* 3.2 27.8 + - - +
636N LEU* 3.0 24.8 + - - +
638N ARG* 5.8 1.4 + - - -
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Residues in contact with VAL 633 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575N PHE* 3.9 12.5 - - + -
600N PHE* 4.0 10.0 - - + -
602N PHE* 3.7 37.2 - - + -
606N CYS* 4.6 1.3 - - - -
614N GLY 2.9 21.4 + - - +
616N LEU* 4.1 20.9 - - + -
628N CYS* 5.8 0.4 - - + -
631N HIS 3.3 2.0 + - - +
632N ASP* 1.3 68.5 - - - +
634N VAL* 1.3 62.1 + - + +
636N LEU* 3.3 19.9 + - + +
637N LEU* 3.0 26.7 + - - +
654N VAL* 4.0 26.7 - - + -
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Residues in contact with VAL 634 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600N PHE* 5.1 4.0 - - + -
612N ASP* 3.2 26.9 - - - +
632N ASP* 2.9 13.7 + - - +
633N VAL* 1.3 73.7 - - + +
635N THR* 1.3 55.9 + - - +
637N LEU* 3.2 6.6 + - - +
638N ARG* 2.7 79.4 + - - +
651N VAL* 3.7 24.7 - - + +
654N VAL* 4.0 25.8 - - + +
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Residues in contact with THR 635 (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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632N ASP* 3.2 30.7 + - - +
634N VAL* 1.3 78.3 - - - +
636N LEU* 1.3 54.0 + - + +
638N ARG* 3.8 13.3 + - + +
639N ASP* 2.7 52.6 + - - +
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Residues in contact with LEU 636 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571N GLY* 5.7 5.6 - - - -
572N GLU 6.0 0.2 - - - +
575N PHE* 3.7 37.5 - - + +
627N ASP 4.3 5.6 - - - +
628N CYS* 4.1 20.4 - - - -
631N HIS* 4.0 35.4 - - + +
632N ASP 3.0 15.2 + - - +
633N VAL* 3.6 22.2 - - + +
634N VAL 3.3 0.2 - - - -
635N THR* 1.3 77.7 - - + +
637N LEU* 1.3 62.3 + - - +
639N ASP* 3.5 12.5 + - + +
640N ALA* 3.1 23.0 + - - +
643N ARG* 4.9 1.2 + - - -
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Residues in contact with LEU 637 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531N LEU* 3.9 15.9 - - + -
575N PHE* 3.7 16.3 - - + -
578N ILE* 4.0 20.6 - - + -
579N VAL* 3.8 22.4 - - + -
582N ILE* 4.5 3.8 - - + -
598N LEU* 4.3 7.4 - - + -
600N PHE* 3.9 24.0 - - + -
633N VAL 3.0 14.2 + - - +
634N VAL 3.2 7.4 + - - +
636N LEU* 1.3 74.1 - - - +
638N ARG* 1.3 65.0 + - - +
640N ALA* 3.1 4.6 + - - +
641N ILE* 3.0 36.1 + - + +
651N VAL* 4.0 23.8 - - + -
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Residues in contact with ARG 638 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612N ASP* 3.5 25.1 + - - -
632N ASP* 5.8 1.2 + - - -
634N VAL* 2.7 46.3 + - + +
635N THR* 3.8 12.3 + - + +
637N LEU* 1.3 72.2 - - - +
639N ASP* 1.3 62.2 + - - +
641N ILE* 3.3 12.5 + - + +
642N LYS* 3.1 41.3 + - - +
649N LEU 6.1 1.1 - - - +
650N ASP* 5.6 0.8 + - - -
651N VAL* 3.0 42.2 + - + +
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Residues in contact with ASP 639 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635N THR* 2.7 41.2 + - - +
636N LEU* 3.7 12.7 - - + +
638N ARG* 1.3 72.2 - - - +
640N ALA* 1.3 63.7 + - - +
642N LYS* 3.2 16.2 + - - +
643N ARG* 2.9 43.3 + - - +
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Residues in contact with ALA 640 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575N PHE* 3.5 31.0 - - + +
576N ASP* 4.0 4.9 - - - +
579N VAL* 3.6 16.3 - - + +
636N LEU 3.1 14.3 + - - +
637N LEU* 3.1 4.5 + - - +
639N ASP* 1.3 80.2 - - - +
641N ILE* 1.3 61.1 + - - +
643N ARG* 3.5 28.1 + - - +
644N ARG* 3.3 15.8 + - - +
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Residues in contact with ILE 641 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579N VAL* 3.7 20.9 - - + -
582N ILE* 5.5 0.4 - - + -
637N LEU* 3.0 35.1 + - + +
638N ARG* 3.6 12.1 - - + +
639N ASP 3.2 0.2 - - - -
640N ALA* 1.3 73.3 - - - +
642N LYS* 1.3 64.7 + - + +
644N ARG* 3.2 6.1 + - - +
645N GLU* 3.1 18.4 + - - -
647N PHE* 3.4 39.7 - - + +
648N ASP* 4.3 15.0 - - - +
649N LEU* 4.0 31.0 - - + +
651N VAL* 4.6 7.9 - - + -
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Residues in contact with LYS 642 (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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638N ARG* 3.1 30.0 + - - +
639N ASP* 3.5 18.0 + - - +
641N ILE* 1.3 77.5 - - + +
643N ARG* 1.3 62.4 + - + +
645N GLU* 3.2 27.6 + - - +
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Residues in contact with ARG 643 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572N GLU* 3.2 54.5 + - - +
575N PHE* 4.6 2.4 - - - +
576N ASP* 2.9 33.4 + - - +
636N LEU 4.9 1.2 + - - -
639N ASP* 2.9 35.6 + - + +
640N ALA* 3.5 23.4 - - - +
641N ILE 3.3 0.2 - - - -
642N LYS* 1.3 76.5 - - + +
644N ARG* 1.3 63.4 + - - +
645N GLU* 4.1 3.6 - - - +
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Residues in contact with ARG 644 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576N ASP 5.0 1.4 + - - -
579N VAL* 3.7 21.3 - - + +
580N SER* 3.6 30.0 + - - +
583N SER* 3.7 25.1 + - - -
640N ALA 3.3 9.7 + - - +
641N ILE 3.2 9.8 + - - +
643N ARG* 1.3 76.1 - - - +
645N GLU* 1.3 73.6 + - - +
646N GLU* 3.2 39.8 + - + +
647N PHE* 4.1 14.6 - - + -
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Residues in contact with GLU 645 (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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641N ILE 3.1 10.1 + - - -
642N LYS* 3.2 21.1 + - - +
643N ARG 4.1 3.4 - - - +
644N ARG* 1.3 80.4 - - - +
646N GLU* 1.3 63.8 + - - +
647N PHE 5.4 0.4 - - - -
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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