Contacts of the helix formed by residues 424 - 433 (chain A) in PDB entry 6B0O
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 ARG 424 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400A THR* 3.8 34.1 + - + +
403A ARG* 4.5 0.9 - - - +
411A PHE* 3.4 13.2 - - - -
422A PHE* 3.9 3.3 - - - +
423A ALA* 1.3 86.5 - - + +
425A SER* 1.3 65.7 + - - +
426A ASP* 2.6 37.3 + - - +
427A GLU* 3.1 27.8 + - + +
428A LEU 3.4 4.3 + - - -
3B C 3.2 35.2 - - - +
4B G 2.9 48.3 + - - -
5B T 3.2 21.1 + - - +
9C C 6.0 0.4 - - - +
10C A 3.5 0.2 - - - +
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Residues in contact with SER 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A PHE* 3.4 28.8 - - - -
424A ARG* 1.3 74.8 - - - +
426A ASP* 1.3 62.3 + - - +
428A LEU* 3.1 6.4 + - - +
429A VAL* 2.9 33.7 + - - +
8C C 3.2 48.2 + - - +
9C C 5.2 3.6 + - - -
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Residues in contact with ASP 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A ARG* 2.6 50.9 + - - +
425A SER* 1.3 74.8 + - - +
427A GLU* 1.3 62.2 + - - +
429A VAL* 3.8 10.6 - - + +
430A ARG* 3.2 29.3 + - - +
3B C 4.5 3.7 + - - -
9C C 4.3 23.4 + - + -
10C A 3.2 23.2 + - + +
11C C 4.3 3.8 + - - -
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Residues in contact with GLU 427 (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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422A PHE* 3.6 26.8 - - + -
423A ALA* 3.3 17.4 + - - +
424A ARG* 3.1 40.3 + - + +
425A SER 3.2 0.4 - - - -
426A ASP* 1.3 80.1 - - - +
428A LEU* 1.3 62.9 + - - +
430A ARG* 3.4 8.1 + - - +
431A HIS* 3.1 22.0 + - - +
2B G 3.3 38.7 + - + +
3B C 4.0 29.8 + - + +
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Residues in contact with LEU 428 (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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411A PHE* 3.8 34.1 - - + -
412A SER 3.2 20.2 - - - +
413A CYS* 3.6 17.5 - - + +
422A PHE* 3.9 25.1 - - + -
424A ARG 3.4 2.0 + - - -
425A SER* 3.1 9.4 + - - +
427A GLU* 1.3 75.8 - - - +
429A VAL* 1.3 61.4 + - + +
431A HIS* 3.2 2.3 + - + +
432A HIS* 2.8 62.7 + - + +
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Residues in contact with VAL 429 (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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425A SER* 2.9 24.0 + - - +
426A ASP* 3.8 9.9 - - - +
427A GLU 3.3 0.2 - - - -
428A LEU* 1.3 77.7 - - + +
430A ARG* 1.3 63.8 + - + +
432A HIS* 3.3 17.9 + - - +
433A ASN* 3.4 23.8 + - - +
9C C 4.2 18.6 - - - +
10C A 5.8 3.6 - - - +
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Residues in contact with ARG 430 (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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426A ASP* 3.2 17.9 + - - +
427A GLU* 3.8 6.5 - - - +
429A VAL* 1.3 79.3 - - + +
431A HIS* 1.3 63.7 + - - +
433A ASN* 3.3 27.9 + - - +
434A MET* 4.1 12.2 + - + +
1B A 5.4 2.7 - - - -
2B G 2.7 31.1 + - - -
3B C 3.4 10.3 - - - +
11C C 3.5 25.7 - - - +
12C G 2.7 26.6 + - - -
13C C 3.9 5.3 - - - +
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Residues in contact with HIS 431 (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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413A CYS* 3.5 14.3 - - + +
418A CYS* 3.0 14.7 - - - -
420A LYS* 4.6 2.9 - - + -
422A PHE* 3.4 41.7 - + + -
427A GLU 3.1 11.4 + - - +
428A LEU* 3.2 6.9 + - + +
430A ARG* 1.3 76.7 - - - +
432A HIS* 1.3 64.0 + - - +
434A MET* 3.1 42.1 + - + +
435A HIS* 3.9 11.2 + + - -
503A ZN 2.1 37.0 - - - -
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Residues in contact with HIS 432 (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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412A SER 4.7 0.7 - - - -
413A CYS* 2.8 47.0 + - - -
415A TRP* 6.0 2.0 - + - -
428A LEU* 2.8 49.6 + - + +
429A VAL* 3.7 10.1 - - - +
430A ARG 3.3 0.6 - - - -
431A HIS* 1.3 72.5 - - - +
433A ASN* 1.3 62.7 + - - +
434A MET 3.1 1.1 + - - -
435A HIS* 3.1 28.1 + + - +
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Residues in contact with ASN 433 (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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429A VAL* 3.4 23.7 + - - +
430A ARG* 3.4 18.9 - - - +
431A HIS 3.1 1.0 - - - -
432A HIS* 1.3 78.3 - - - +
434A MET* 1.3 57.9 + - + +
435A HIS 3.3 4.6 + - - +
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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