Contacts of the helix formed by residues 462 - 470 (chain A) in PDB entry 1CVU
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 462 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A MET* 3.4 27.0 + - - +
461A GLN* 1.3 80.3 - - - +
463A LEU* 1.3 64.2 + - - +
464A ASN* 3.3 6.2 + - - +
465A GLU* 3.1 33.5 + - - +
466A TYR* 3.2 12.9 + - - -
499A ASP 3.3 26.9 + - - -
501A MET 3.6 9.4 - - - -
502A GLU* 5.1 0.4 - - - +
503A LEU 4.8 1.3 - - - -
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Residues in contact with LEU 463 (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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462A SER* 1.3 71.8 - - - +
464A ASN* 1.3 63.9 + - - +
466A TYR* 3.2 5.4 + - - +
467A ARG* 2.9 38.8 + - - +
475A TYR* 4.0 23.8 - - + -
481A LEU* 4.4 6.3 - - + -
498A ILE* 4.9 3.8 - - + -
501A MET* 2.8 35.7 + - + +
502A GLU 3.8 10.8 - - - +
503A LEU* 4.0 20.2 - - + +
506A ALA* 3.7 28.3 - - + -
510A GLU* 6.3 0.2 - - - -
521A THR* 4.2 22.2 - - + +
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Residues in contact with ASN 464 (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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462A SER* 3.2 7.2 + - - +
463A LEU* 1.3 82.1 - - - +
465A GLU* 1.3 65.2 - - + +
467A ARG* 3.6 12.9 - - - +
468A LYS* 3.0 30.9 + - + +
474A PRO* 3.3 19.1 - - + +
475A TYR* 2.9 42.1 + - - +
498A ILE* 3.9 9.7 + - - +
499A ASP* 2.7 36.8 - - - +
501A MET 4.7 0.2 + - - -
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Residues in contact with GLU 465 (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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38A SER 4.7 2.3 - - - +
39A ASN* 3.6 34.8 - - - +
152A LEU* 3.8 8.1 - - + +
163A MET 5.9 0.2 - - - +
461A GLN* 3.5 30.4 - - + +
462A SER* 3.1 26.7 + - - +
464A ASN* 1.3 77.5 - - - +
466A TYR* 1.3 58.5 + - - +
468A LYS* 3.3 33.5 + - - +
469A ARG* 2.8 27.2 + - - +
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Residues in contact with TYR 466 (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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150A ARG* 3.7 6.4 + - - -
151A ALA* 4.3 2.9 - - + -
152A LEU* 3.5 34.3 + - + +
380A GLU* 2.5 49.5 + - + +
460A TYR* 4.1 15.8 - + - -
461A GLN* 3.3 31.8 + - + -
462A SER 3.2 20.5 + - - -
463A LEU 3.2 7.6 + - - +
465A GLU* 1.3 78.4 - - - +
467A ARG* 1.3 64.5 + - - +
469A ARG* 3.2 3.0 + - - -
470A PHE* 3.1 36.5 + + - +
503A LEU* 3.9 26.9 - - + -
521A THR* 6.1 0.7 - - + -
525A LEU* 4.1 16.8 - - + +
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Residues in contact with ARG 467 (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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463A LEU* 2.9 24.4 + - + +
464A ASN* 3.6 18.8 - - - +
465A GLU 3.2 0.4 - - - -
466A TYR* 1.3 75.8 - - - +
468A LYS* 1.3 58.4 + - - +
470A PHE 3.1 6.6 + - - -
472A LEU* 2.7 56.5 + - + +
473A LYS* 2.6 42.9 + - - +
474A PRO* 4.0 1.3 - - + +
475A TYR* 3.7 44.3 + - - -
510A GLU* 4.0 0.4 + - - -
520A GLU* 2.7 31.7 + - - -
521A THR* 2.7 39.3 + - + +
525A LEU* 5.2 0.4 - - - -
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Residues in contact with LYS 468 (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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42A GLN* 3.0 33.1 + - - +
44A ARG* 6.0 0.7 - - - +
464A ASN* 3.0 23.5 + - + +
465A GLU* 3.4 35.1 + - - +
467A ARG* 1.3 75.4 - - - +
469A ARG* 1.3 64.6 + - - +
471A SER* 2.8 15.6 + - - +
472A LEU 3.7 6.7 - - - +
474A PRO* 4.2 29.6 - - + -
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Residues in contact with ARG 469 (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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44A ARG* 3.1 50.3 - - - +
123A LEU* 2.8 37.3 + - - +
124A ILE* 4.4 2.2 - - - +
125A ASP* 3.7 13.7 + - - +
151A ALA* 3.5 25.6 + - - +
152A LEU* 3.6 29.1 - - + +
465A GLU 2.8 15.6 + - - +
466A TYR* 3.3 15.9 - - + +
468A LYS* 1.3 77.5 - - - +
470A PHE* 1.3 89.2 + - + +
471A SER* 3.8 1.0 + - - -
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Residues in contact with PHE 470 (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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123A LEU* 4.1 24.1 - - + +
124A ILE* 4.1 11.0 - - + -
151A ALA* 4.2 12.8 - - + -
466A TYR* 3.1 18.8 + + - +
467A ARG 3.1 4.2 + - - +
468A LYS 2.8 1.4 + - - -
469A ARG* 1.3 110.0 - - + +
471A SER* 1.3 69.0 + - - +
472A LEU* 3.2 16.8 + - + +
524A GLU* 3.5 21.3 - - - +
525A LEU* 3.3 42.0 - - + -
528A PRO* 4.0 17.5 - - + -
529A PHE* 3.8 24.7 - + - -
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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