Contacts of the strand formed by residues 240 - 246 (chain G) in PDB entry 3WUW
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 ALA 240 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234G LEU 5.3 0.2 - - - +
235G SER* 5.2 0.2 - - - -
236G ARG* 3.8 40.7 + - - +
238G GLY 3.4 2.8 + - - -
239G GLY* 1.3 80.2 - - - +
241G HIS* 1.3 70.6 + - - +
242G GLU* 3.3 6.1 + - - +
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Residues in contact with HIS 241 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239G GLY 4.1 2.8 + - - -
240G ALA* 1.3 76.1 - - - +
242G GLU* 1.3 76.4 + - - +
243G ARG* 3.5 6.4 + - - +
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Residues in contact with GLU 242 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112G LEU* 5.0 10.0 - - + +
233G HIS* 4.5 6.5 - - + +
234G LEU 3.2 14.4 - - - +
235G SER* 3.7 24.2 - - - +
240G ALA 3.3 5.8 + - - +
241G HIS* 1.3 83.1 + - - +
243G ARG* 1.3 65.8 + - - +
244G ARG* 4.1 6.3 + - + +
283G TRP* 3.8 33.8 - - + -
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Residues in contact with ARG 243 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233G HIS* 3.3 5.4 - - - +
234G LEU* 2.9 44.2 + - + +
241G HIS 4.6 4.3 - - - +
242G GLU* 1.3 75.7 - - - +
244G ARG* 1.3 61.7 + - - +
245G LEU* 4.9 3.0 - - + +
259G PHE* 3.4 43.0 - - + +
260G PRO* 3.1 29.8 + - - +
261G LEU* 3.2 33.7 - - - +
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Residues in contact with ARG 244 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231G MET* 3.2 38.6 - - - +
232G TYR 3.3 4.5 - - - +
233G HIS* 3.3 35.2 - - - +
242G GLU* 4.1 8.3 + - + +
243G ARG* 1.3 78.2 - - - +
245G LEU* 1.3 75.2 + - - +
259G PHE* 3.8 0.2 - - - -
283G TRP* 5.8 0.4 - - - -
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Residues in contact with LEU 245 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231G MET* 3.4 8.1 - - - +
232G TYR 2.9 31.7 + - - -
243G ARG* 4.9 2.7 - - - +
244G ARG* 1.3 84.2 - - - +
246G PRO* 1.3 79.8 - - + +
257G ALA* 4.1 8.9 - - + +
258G ASP 3.2 31.0 - - - +
259G PHE* 3.4 37.0 - - + -
260G PRO* 4.7 4.3 - - + -
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Residues in contact with PRO 246 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230G ASP 3.6 9.4 - - - +
231G MET* 4.4 8.9 - - + -
245G LEU* 1.3 98.9 - - + +
247G ALA* 1.3 66.4 + - - +
248G VAL* 3.9 9.6 + - + +
256G GLN 4.1 0.3 - - - +
257G ALA* 3.4 13.4 - - - +
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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