Contacts of the helix formed by residues 456 - 461 (chain B) in PDB entry 2A1A
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 456 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454B TYR 4.1 0.8 + - - -
455B MET* 1.3 77.8 - - - +
457B PRO* 1.4 76.8 - - - +
458B GLU* 3.4 16.4 + - - -
459B GLN* 3.1 6.6 + - - +
460B ILE* 3.1 21.3 + - - +
469B VAL* 2.9 32.5 + - - +
472B TYR* 3.5 32.6 - - - +
526B ARG* 4.0 0.4 - - - -
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Residues in contact with PRO 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B MET 4.8 0.2 - - - +
456B SER* 1.4 84.2 - - - +
458B GLU* 1.3 70.0 + - + +
460B ILE* 3.5 10.5 + - + +
461B SER* 3.0 33.6 + - - -
472B TYR* 3.5 23.6 - - + +
499B ARG* 5.5 4.4 - - - +
521B LYS* 4.6 20.0 - - + +
526B ARG* 4.3 1.1 - - - +
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Residues in contact with GLU 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B SER* 3.2 10.2 + - - -
457B PRO* 1.3 89.3 - - + +
459B GLN* 1.3 64.4 + - - +
461B SER* 4.4 3.4 - - - -
462B SER* 3.0 41.2 + - - +
464B ASP 4.6 2.5 - - - +
465B TYR* 4.1 19.4 - - + +
468B GLU* 4.3 6.9 - - - +
469B VAL* 4.2 5.9 + - - +
521B LYS 4.2 3.1 - - - +
523B PRO* 4.0 23.5 - - + +
526B ARG* 2.5 45.4 + - - -
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Residues in contact with GLN 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B ARG* 2.9 46.4 + - - +
435B LEU* 4.6 6.1 - - - +
446B TPO 4.9 2.1 - - - +
447B ARG* 5.4 0.3 - - - -
448B SER* 3.4 22.1 + - - +
455B MET* 3.6 36.6 - - + +
456B SER* 3.1 13.5 + - - +
458B GLU* 1.3 79.7 - - - +
460B ILE* 1.3 61.5 + - - +
461B SER 4.8 0.3 - - - -
462B SER 4.5 3.8 - - - +
465B TYR* 3.9 26.3 + - + +
469B VAL* 3.4 29.0 - - + +
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Residues in contact with ILE 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447B ARG* 5.3 4.2 + - - -
448B SER* 3.5 18.4 + - - +
452B LEU* 3.7 30.5 - - + +
455B MET* 3.6 25.1 - - + +
456B SER 3.1 18.6 + - - +
457B PRO* 3.9 7.4 - - + +
459B GLN* 1.3 78.5 - - - +
461B SER* 1.3 60.6 + - - +
499B ARG* 3.4 29.2 - - - +
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Residues in contact with SER 461 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B ARG* 3.4 32.4 + - - +
457B PRO* 3.0 19.3 + - - +
458B GLU* 4.4 1.4 - - - -
459B GLN 4.8 0.6 - - - +
460B ILE* 1.3 80.9 - - - +
462B SER* 1.3 73.7 + - - +
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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