Contacts of the helix formed by residues 234 - 243 (chain U) in PDB entry 2R2W
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 PHE 234 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91U HIS* 3.9 25.4 - + - -
101U ASN* 3.3 40.8 - - - -
103U ILE* 3.9 28.5 - - + -
179U LYS* 4.1 31.2 - - + -
229U THR* 3.7 22.4 - - + -
230U ARG 3.2 26.5 - - - -
231U VAL 2.9 8.9 + - - +
233U HIS* 1.3 84.2 - - + +
235U LEU* 1.3 66.1 + - - +
236U PRO* 3.2 4.7 - - - -
237U TRP* 3.1 11.7 + - + +
238U ILE* 2.9 23.8 + - + +
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Residues in contact with LEU 235 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123U LEU* 4.4 25.6 - - + -
124U PRO* 3.4 31.4 - - + +
125U SER* 3.5 4.7 - - - +
126U MET* 3.5 41.7 - - + +
231U VAL 3.7 9.1 + - - +
232U SER* 3.9 10.1 - - - +
233U HIS 3.7 0.2 - - - -
234U PHE* 1.3 77.8 - - - +
236U PRO* 1.3 70.2 - - + +
238U ILE* 3.3 9.3 + - + +
239U ARG* 2.9 39.9 + - + +
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Residues in contact with PRO 236 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126U MET* 4.3 22.9 - - + -
127U TYR* 6.4 0.9 - - + -
232U SER 5.3 0.2 - - - +
233U HIS 4.6 5.2 - - - +
234U PHE* 3.3 8.1 - - - +
235U LEU* 1.3 95.8 - - + +
237U TRP* 1.3 62.8 + - - +
239U ARG* 3.4 5.6 + - + +
240U SER* 3.1 26.4 + - - -
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Residues in contact with TRP 237 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89U ILE* 4.1 15.5 - - + -
90U LEU 4.1 1.2 + - - -
91U HIS* 3.6 57.6 + + + +
92U LYS 5.1 1.8 - - - +
103U ILE* 4.0 40.6 - - + -
104U ALA* 4.0 6.5 - - - -
105U LEU* 3.6 34.5 - - + -
234U PHE* 3.1 14.7 + - + +
236U PRO* 1.3 79.3 - - - +
238U ILE* 1.3 75.4 + - + +
240U SER* 3.1 10.1 + - - -
241U HIS* 2.9 57.0 + + - -
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Residues in contact with ILE 238 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47U ILE* 4.5 9.9 - - + -
53U ILE* 3.8 26.7 - - + -
103U ILE* 4.4 5.6 - - + -
105U LEU* 4.4 5.4 - - + -
123U LEU* 4.2 26.7 - - + -
231U VAL* 4.3 19.1 - - + -
234U PHE 2.9 24.1 + - - +
235U LEU* 3.6 13.0 - - + +
237U TRP* 1.3 95.1 - - + +
239U ARG* 1.3 67.4 + - + +
241U HIS* 3.3 1.2 + - - +
242U THR* 3.0 40.5 + - + +
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Residues in contact with ARG 239 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123U LEU* 6.4 1.3 - - + -
235U LEU* 2.9 30.1 + - + +
236U PRO* 3.8 5.2 - - + +
238U ILE* 1.3 80.5 - - + +
240U SER* 1.3 63.2 + - - +
242U THR* 3.3 14.8 + - - -
243U LYS* 3.0 34.6 + - - +
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Residues in contact with SER 240 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236U PRO 3.1 13.8 + - - -
237U TRP* 3.1 17.2 + - - -
239U ARG* 1.3 77.2 - - - +
241U HIS* 1.3 70.3 + - - +
243U LYS* 4.1 21.1 + - - +
244U GLU 5.0 1.9 + - - -
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Residues in contact with HIS 241 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51U TRP* 3.8 12.6 - - - -
89U ILE* 3.8 34.4 - - + +
90U LEU 5.8 1.1 - - - -
105U LEU* 3.7 17.7 - - + -
237U TRP* 2.9 61.1 + + - +
239U ARG 3.2 0.2 - - - -
240U SER* 1.3 90.9 + - - +
242U THR* 1.3 61.8 + - - +
243U LYS 3.4 2.2 + - - -
244U GLU* 4.9 3.3 + - - -
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Residues in contact with THR 242 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47U ILE* 5.0 2.9 - - + -
51U TRP* 3.8 50.1 + - + -
105U LEU* 3.9 21.5 - - + -
238U ILE* 3.0 29.1 + - + +
239U ARG* 3.3 11.6 + - - -
241U HIS* 1.3 77.0 - - - +
243U LYS* 1.3 70.1 + - - +
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Residues in contact with LYS 243 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51U TRP* 5.5 0.2 - - - -
239U ARG* 3.0 35.8 + - - +
240U SER* 4.1 15.0 - - - +
241U HIS 3.4 1.6 - - - -
242U THR* 1.3 85.9 + - - +
244U GLU* 1.3 65.7 + - + +
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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