Contacts of the helix formed by residues 422 - 428 (chain A) in PDB entry 4HXG
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 422 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A HIS* 3.6 0.6 + - - -
261A ASP* 3.6 15.3 - - - -
262A ARG* 3.2 12.7 - - - +
421A TYR* 1.3 75.8 - - - +
423A GLU* 1.3 66.0 + - - +
424A ASP* 4.1 9.2 - - - +
425A PHE* 2.8 37.8 + - - +
426A ALA* 3.2 5.5 + - - +
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Residues in contact with GLU 423 (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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234A LYS* 2.6 34.1 + - - -
241A SER 5.1 0.9 - - - +
242A GLU* 3.8 18.2 - - - +
243A HIS* 3.0 45.5 + - + +
261A ASP* 3.1 23.5 + - - +
422A SER* 1.3 69.9 - - - +
424A ASP* 1.3 66.5 + - - +
426A ALA* 3.0 6.7 + - - +
427A LEU* 3.0 36.1 + - + +
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Residues in contact with ASP 424 (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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261A ASP* 4.5 2.7 + - - +
422A SER* 3.0 8.6 - - - +
423A GLU* 1.3 80.7 - - - +
425A PHE* 1.3 62.7 + - - +
427A LEU* 3.1 23.8 + - - +
428A ARG* 3.1 24.4 + - + +
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Residues in contact with PHE 425 (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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361A LEU* 4.2 24.2 - - + -
362A GLU 5.6 2.7 - - - -
363A LEU* 4.4 12.3 - - + -
414A ASN 3.5 13.9 - - - -
415A PRO 3.6 10.8 - - - -
416A ARG* 3.3 35.8 - - + -
417A GLY* 2.7 26.7 + - - -
418A SER* 3.6 14.4 - - - -
421A TYR* 3.4 45.1 - + + -
422A SER* 2.8 30.6 + - - +
424A ASP* 1.3 74.9 - - - +
426A ALA* 1.3 52.7 + - - +
428A ARG* 3.8 15.2 - - - +
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Residues in contact with ALA 426 (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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241A SER* 4.5 8.5 - - - +
243A HIS* 4.7 2.5 - - + -
389A LYS* 4.0 26.9 - - + +
417A GLY* 3.2 33.5 - - - +
418A SER 4.0 7.6 - - - +
422A SER 3.2 7.7 + - - +
423A GLU* 3.0 13.5 + - - +
425A PHE* 1.3 79.1 - - - +
427A LEU* 1.3 63.5 + - - +
429A VAL* 3.3 11.6 - - - +
430A LEU* 5.1 0.9 - - - +
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Residues in contact with LEU 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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239A TYR* 4.2 23.8 - - + -
241A SER* 3.5 40.8 - - - +
242A GLU* 4.1 4.5 - - + +
423A GLU* 3.0 42.5 + - + +
424A ASP* 3.1 13.0 + - - +
426A ALA* 1.3 72.1 - - - +
428A ARG* 1.3 63.4 + - - +
429A VAL 3.0 7.0 + - - -
430A LEU* 3.0 38.9 + - + +
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Residues in contact with ARG 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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360A ASP* 3.2 27.4 + - - -
361A LEU* 3.9 33.1 - - - +
416A ARG* 3.4 30.3 - - + +
424A ASP* 3.1 23.1 + - + +
425A PHE* 3.8 18.9 - - - +
426A ALA 3.2 1.0 - - - -
427A LEU* 1.3 76.7 - - - +
429A VAL* 1.3 60.3 + - - +
430A LEU 3.3 0.8 - - - +
432A ARG* 3.6 20.3 - - - +
436A GLU* 4.6 3.1 - - - +
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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