Contacts of the helix formed by residues 335 - 338 (chain A) in PDB entry 2XB2
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 335 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A THR* 5.6 0.3 - - - +
283A PHE* 4.6 0.8 - - - -
284A CYS 4.1 3.9 + - - +
285A ASN* 5.1 6.8 + - - -
334A THR* 1.3 75.1 - - - +
336A VAL* 1.3 58.7 + - - +
337A TRP 3.1 0.9 - - - -
338A ALA* 2.7 35.5 + - + +
339A ARG* 4.3 1.9 + - - +
356A ASN* 5.1 2.4 + - - +
360A LEU* 3.5 27.6 - - + +
364A ARG* 2.7 45.8 + - - -
2E U 4.8 6.6 - - - +
3E U 3.9 25.7 + - - +
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Residues in contact with VAL 336 (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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115A THR* 3.6 39.3 + - + +
117A GLU* 4.5 13.0 - - - +
307A MET* 4.2 4.7 - - + +
308A HIS* 4.2 8.7 - - - -
309A GLY 4.9 3.1 - - - +
316A ARG* 4.5 8.5 - - - +
333A SER* 3.3 18.6 - - - +
334A THR* 2.7 20.0 + - - +
335A ASP* 1.3 80.8 - - - +
337A TRP* 1.3 64.0 + - + +
338A ALA 3.1 2.0 + - - -
339A ARG 4.5 3.8 + - - +
341A LEU* 4.7 5.5 - - - +
3E U 3.6 4.1 + - - -
4E U 3.5 30.7 - - - +
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Residues in contact with TRP 337 (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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117A GLU* 5.7 0.7 - - + -
281A VAL* 4.1 21.3 - - + -
283A PHE* 3.7 12.2 - - + -
307A MET* 3.4 39.5 - - + +
320A MET* 3.5 16.2 - - - -
323A PHE* 3.5 26.2 - + - -
331A LEU* 3.6 13.9 - - + +
333A SER* 3.7 18.8 - - - +
334A THR 3.1 4.4 + - - +
336A VAL* 1.3 81.2 - - + +
338A ALA* 1.3 61.9 + - - +
339A ARG* 3.4 2.6 - - - -
341A LEU* 3.7 34.0 - - + +
343A VAL* 3.2 33.4 - - + -
346A VAL* 5.1 1.6 - - + -
367A ARG* 3.6 33.7 - - + -
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Residues in contact with ALA 338 (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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283A PHE* 3.9 9.6 - - + -
335A ASP* 2.7 36.5 + - - +
336A VAL 3.1 0.2 - - - -
337A TRP* 1.3 79.1 - - - +
339A ARG* 1.3 60.7 + - + +
360A LEU* 3.6 27.4 - - + -
363A HIS* 3.0 31.6 - - - +
364A ARG* 4.4 7.0 - - + -
367A ARG* 3.6 4.0 + - - -
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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