Contacts of the helix formed by residues 238 - 240 (chain A) in PDB entry 1XGS
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 238 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 3.5 28.3 - - - +
34A ALA* 3.8 14.7 - - - +
35A GLU* 3.0 26.2 + - - +
38A GLU* 2.9 42.8 + - - -
51A PRO* 4.1 3.2 - - - +
64A THR* 2.9 24.2 + - - -
65A PRO* 2.8 33.0 + - - +
66A TYR* 3.9 5.8 - - - +
67A LYS* 4.4 9.8 - - + +
204A LEU 4.8 0.2 + - - -
236A ALA* 3.8 5.5 - - + +
237A TYR* 1.3 80.2 - - - +
239A TRP* 1.3 73.3 + - + +
240A LEU 3.0 1.2 + - - -
241A GLN* 3.2 32.3 + - - +
242A ASN* 4.3 6.8 + - - -
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Residues in contact with TRP 239 (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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35A GLU* 5.4 0.4 - - - -
38A GLU* 3.0 25.1 + - - -
48A PRO* 4.0 32.3 - - + -
50A PHE* 4.2 1.3 - - - -
51A PRO* 3.7 33.0 - - + -
225A LYS* 5.3 1.6 - - - -
230A TYR* 3.4 52.3 + + + +
234A PRO 3.9 7.6 - - - -
235A PHE* 3.6 26.2 - - + -
236A ALA* 3.2 23.0 + - + +
237A TYR 3.1 0.2 + - - -
238A ARG* 1.3 93.5 - - + +
240A LEU* 1.3 60.6 + - + +
242A ASN* 4.5 8.3 + - - +
243A ASP* 4.6 4.9 - - - +
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Residues in contact with LEU 240 (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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222A LEU* 4.0 18.2 - - + -
225A LYS* 3.9 12.3 - - + -
226A ILE* 4.9 3.6 - - + -
230A TYR* 3.8 27.4 - - + +
235A PHE* 3.9 30.5 - - + -
236A ALA 4.3 7.2 - - - +
237A TYR* 2.9 12.4 + - - +
239A TRP* 1.3 77.4 - - - +
241A GLN* 1.3 58.3 + - - +
242A ASN 2.9 12.4 + - - -
243A ASP* 3.2 35.6 + - + +
244A MET 4.0 2.3 + - - -
249A LEU* 3.6 32.3 - - + +
253A LEU* 4.5 8.7 - - + -
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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