Contacts of the strand formed by residues 271 - 278 (chain G) in PDB entry 4A63
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 ILE 271 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179G PRO* 4.0 14.6 - - + -
180G VAL 3.3 11.7 - - - +
181G TYR* 3.4 31.9 - - + -
182G LYS* 3.9 3.1 - - - +
191G VAL* 3.9 6.7 - - + -
214G LEU* 4.1 4.7 - - + -
256G PHE* 5.8 0.2 - - + -
260G SER* 5.5 1.6 - - - +
266G MET* 3.5 39.9 - - + -
269G ARG 4.2 1.3 - - - +
270G PRO* 1.4 72.9 - - - +
272G LEU* 1.3 61.7 - - - +
273G ILE* 3.9 30.5 - - + -
291G GLU* 3.2 9.7 - - - +
292G GLY* 2.9 40.3 + - - +
294G ILE* 5.3 6.1 - - + -
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Residues in contact with LEU 272 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118G ASN* 3.7 37.7 - - + +
178G MET 3.8 0.5 - - - +
179G PRO* 3.3 4.3 - - - +
180G VAL* 2.7 42.0 + - + +
181G TYR 5.6 0.9 - - - +
182G LYS* 3.7 41.3 - - + +
271G ILE* 1.3 73.7 - - - +
273G ILE* 1.3 64.3 + - - +
274G ILE* 4.0 10.9 + - + -
289G SER* 4.7 5.6 - - - +
290G PHE* 3.3 14.6 - - - +
291G GLU* 4.0 15.7 - - + +
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Residues in contact with ILE 273 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G LEU* 4.6 3.6 - - + -
177G ALA* 4.9 0.7 - - + -
178G MET 3.7 2.7 - - - +
179G PRO* 4.9 0.4 - - + -
215G ILE* 4.1 22.4 - - + -
256G PHE* 3.8 33.4 - - + -
271G ILE* 3.9 16.2 - - + -
272G LEU* 1.3 73.3 - - - +
274G ILE* 1.3 61.7 + - - +
275G ILE* 3.8 25.9 + - + -
289G SER* 3.2 4.5 - - - -
290G PHE* 2.8 58.0 + - + -
292G GLY* 3.7 28.7 - - - -
294G ILE* 5.3 2.2 - - + -
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Residues in contact with ILE 274 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G PRO* 4.3 11.2 - - + +
117G SER 3.5 18.2 - - - +
118G ASN* 3.9 22.9 - - + -
176G ARG* 3.4 2.4 - - - +
177G ALA* 3.3 4.7 - - - -
178G MET* 3.0 40.0 + - + +
180G VAL* 3.6 30.3 - - + -
272G LEU* 4.6 7.2 - - + +
273G ILE* 1.3 73.3 - - - +
275G ILE* 1.3 63.1 + - - +
276G THR* 3.7 9.4 + - + +
287G ARG* 3.5 33.2 - - + +
288G ARG 3.9 2.0 - - - -
289G SER* 4.1 5.8 - - - -
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Residues in contact with ILE 275 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127G PHE* 3.8 15.2 - - + -
129G VAL* 4.1 18.2 - - + -
161G ILE* 4.9 3.8 - - + -
163G ILE* 4.7 4.3 - - + -
175G ILE* 3.5 30.7 - - + -
176G ARG 3.2 4.3 - - - +
177G ALA* 3.8 25.1 - - + -
254G TYR* 4.2 17.9 - - + +
273G ILE* 3.8 17.5 - - + -
274G ILE* 1.3 71.7 - - - +
276G THR* 1.3 60.3 + - - +
277G LEU 4.3 0.2 - - - -
287G ARG* 3.3 2.6 - - - -
288G ARG 2.8 40.4 + - - +
290G PHE* 3.9 27.4 - - + -
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Residues in contact with THR 276 (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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127G PHE* 4.5 2.2 - - - -
174G ALA 3.7 0.3 - - - +
175G ILE* 3.4 3.6 - - - -
176G ARG* 2.9 41.9 + - - +
274G ILE* 3.7 8.8 + - + +
275G ILE* 1.3 74.3 - - - +
277G LEU* 1.3 61.3 + - - +
278G GLU* 3.2 26.1 + - - +
284G VAL* 5.1 2.9 - - - -
286G GLY 3.4 7.2 - - - -
287G ARG* 2.7 59.6 + - + +
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Residues in contact with LEU 277 (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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125G HIS* 4.7 7.4 - - + -
127G PHE* 3.8 41.7 - - + -
165G VAL* 4.3 12.3 - - + -
169G PRO* 4.4 13.2 - - + -
173G THR* 3.6 24.7 - - + -
174G ALA 3.4 2.0 - - - -
175G ILE* 3.7 25.1 - - + +
240G TYR* 4.3 11.2 - - + -
276G THR* 1.3 69.2 - - - +
278G GLU* 1.3 59.0 + - - +
284G VAL* 3.9 1.2 - - - +
285G LEU* 2.9 41.3 + - + +
286G GLY 2.9 18.2 + - - +
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Residues in contact with GLU 278 (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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173G THR* 3.3 6.2 - - - +
174G ALA* 2.8 44.3 + - + +
176G ARG* 2.9 50.0 + - + +
237G VAL* 5.4 3.3 - - - +
276G THR* 3.2 26.5 + - - +
277G LEU* 1.3 76.0 - - - +
279G MET* 1.3 66.7 + - - +
282G GLY* 4.4 20.0 - - - +
283G GLN 3.4 10.5 - - - +
284G VAL* 5.1 6.9 - - + +
285G LEU* 4.2 6.5 - - - +
287G ARG* 5.5 1.0 + - - -
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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