Contacts of the strand formed by residues 268 - 275 (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 GLY 268 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236G ARG* 4.0 9.0 - - - -
267G GLY* 1.3 74.6 - - - -
269G THR* 1.3 61.1 + - - -
270G TYR* 3.1 14.0 - - - -
291G LEU* 4.8 1.6 - - - -
292G VAL 2.9 35.4 + - - -
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Residues in contact with THR 269 (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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236G ARG* 3.5 3.8 - - - +
237G GLU* 3.0 63.5 + - - +
238G GLY 5.7 0.2 - - - +
268G GLY* 1.3 70.8 - - - -
270G TYR* 1.3 62.6 + - - +
271G ARG* 4.4 2.5 - - - +
289G PRO* 4.1 21.3 - - + -
290G LEU 3.4 6.7 - - - +
291G LEU* 3.1 33.7 - - + +
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Residues in contact with TYR 270 (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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205G LEU* 3.4 16.1 - - + +
221G LEU* 3.6 21.8 - - + -
234G LEU* 3.7 24.0 - - + -
235G SER 3.3 5.4 - - - -
236G ARG* 3.6 39.3 + - + -
261G LEU* 4.0 21.2 - - + +
267G GLY* 3.8 7.8 + - - -
268G GLY 3.1 35.9 - - - -
269G THR* 1.3 75.4 - - - +
271G ARG* 1.3 69.1 + - - +
289G PRO* 3.5 1.0 - - - +
290G LEU* 2.8 37.4 + - + +
292G VAL* 3.6 30.9 - - + +
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Residues in contact with ARG 271 (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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205G LEU* 3.6 4.7 - - - -
233G HIS 3.8 0.2 - - - +
234G LEU* 3.7 3.5 - - - +
235G SER* 2.9 43.0 + - - +
237G GLU* 2.8 40.6 + - - +
269G THR* 4.4 2.4 + - - +
270G TYR* 1.3 77.4 - - - +
272G CYS* 1.3 62.4 + - - +
273G PHE* 4.3 11.9 - - + -
286G PRO* 4.3 14.8 - - + +
287G SER* 3.6 28.0 + - - +
289G PRO* 3.7 35.6 - - + +
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Residues in contact with CYS 272 (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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203G PRO* 3.5 8.0 - - - +
204G SER 3.8 13.7 - - - -
205G LEU* 3.9 15.7 - - + -
223G CYS* 2.0 48.0 - - + -
233G HIS 3.1 11.7 - - - +
234G LEU* 4.7 4.3 - - + -
259G PHE* 5.8 0.4 - - + -
271G ARG* 1.3 75.8 - - - +
273G PHE* 1.3 65.0 + - - +
287G SER* 3.0 46.0 + - - -
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Residues in contact with PHE 273 (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* 4.0 18.4 - - + -
197G THR* 4.0 15.7 - - + -
203G PRO* 4.1 1.3 - - - -
232G TYR* 3.4 9.5 - - - -
233G HIS* 2.9 39.7 + - + +
235G SER* 3.8 23.8 - - - -
271G ARG* 4.3 12.8 - - + -
272G CYS* 1.3 79.8 - - - +
274G GLY* 1.3 59.9 + - - +
283G TRP* 3.4 45.1 - + + -
284G SER* 3.3 26.2 - - - +
286G PRO* 3.4 35.9 - - + -
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Residues in contact with GLY 274 (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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200G TYR* 5.6 0.2 - - - -
203G PRO* 4.1 3.0 - - - +
229G TYR* 3.7 26.6 - - - -
231G MET 3.4 8.1 - - - -
232G TYR* 3.7 7.0 - - - -
233G HIS* 4.5 0.4 - - - -
273G PHE* 1.3 75.6 - - - +
275G SER* 1.3 63.2 + - - -
276G PHE* 5.5 0.2 - - - -
283G TRP* 3.4 3.5 - - - -
284G SER* 2.9 36.6 + - - -
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Residues in contact with SER 275 (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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229G TYR* 3.7 2.1 - - - -
230G ASP 2.8 23.9 + - - -
231G MET* 2.9 25.7 + - - +
233G HIS* 2.7 30.5 + - - -
274G GLY* 1.3 75.3 - - - -
276G PHE* 1.3 73.7 + - - +
279G SER 4.3 5.6 - - - -
280G PRO* 5.5 2.0 - - - +
282G GLU 3.7 18.6 - - - -
283G TRP* 3.8 6.3 - - - -
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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