Contacts of the strand formed by residues 277 - 285 (chain C) in PDB entry 4GJ0
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 LEU 277 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180C GLY 3.3 2.9 - - - +
181C THR* 3.2 3.2 - - - -
182C LYS* 2.9 30.2 + - - +
217C THR 5.1 4.7 - - - +
218C GLY 4.2 6.3 - - - +
219C SER 4.0 2.2 - - - -
220C TRP* 3.6 50.3 - - + +
261C MET* 3.6 45.5 - - + -
275C ARG* 4.0 27.6 - - + +
276C LYS* 1.3 82.2 - - - +
278C GLY* 1.3 59.6 + - - +
279C ALA 3.3 10.1 + - - +
280C TRP* 4.8 0.3 - - - -
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Residues in contact with GLY 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C LYS* 3.4 9.5 - - - +
180C GLY 3.0 33.6 + - - -
181C THR* 4.2 10.3 - - - +
215C SER* 5.6 0.7 - - - -
217C THR* 5.5 6.2 + - - -
218C GLY 4.4 3.2 + - - -
277C LEU* 1.3 73.3 - - - +
279C ALA* 1.3 58.6 + - - +
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Residues in contact with ALA 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C GLY 3.3 13.0 - - - +
179C LYS* 4.6 5.2 - - - +
215C SER* 3.5 24.9 - - - +
218C GLY 3.6 7.7 + - - +
219C SER* 3.4 21.5 - - - +
220C TRP* 3.1 16.1 + - - -
277C LEU* 3.3 8.8 - - - +
278C GLY* 1.3 82.5 - - - +
280C TRP* 1.3 71.0 + - - +
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Residues in contact with TRP 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C TYR* 3.7 21.3 - + - -
177C PHE 3.8 0.3 - - - -
178C GLY* 2.8 44.3 + - - +
179C LYS 3.8 14.4 + - - -
180C GLY 3.3 25.6 + - - -
182C LYS* 3.4 38.9 - - + +
187C ALA* 3.8 21.8 - - + -
190C ALA* 3.9 16.8 - - + -
191C CYS* 4.1 4.9 - - - -
194C MET* 3.9 9.0 - - + -
198C LEU* 4.5 2.5 - - + -
219C SER* 4.0 1.9 - - - -
220C TRP* 3.6 15.5 - + + +
277C LEU 4.8 0.9 - - - -
279C ALA* 1.3 85.7 - - - +
281C VAL* 1.3 66.0 + - - +
282C CYS* 3.6 29.6 - - - -
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Residues in contact with VAL 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C TYR* 4.7 1.1 - - + -
176C TYR 3.3 11.7 - - - +
177C PHE* 3.8 37.0 - - + -
191C CYS* 4.2 0.7 - - - -
198C LEU* 3.4 8.7 - - - +
199C VAL* 2.7 49.0 + - + +
210C LEU* 4.2 10.3 - - + -
214C ALA* 5.9 0.4 - - - -
219C SER* 4.1 20.0 - - - +
220C TRP 3.3 8.3 + - - +
262C MET* 4.3 13.7 - - + -
280C TRP* 1.3 80.7 - - - +
282C CYS* 1.3 67.6 + - - +
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Residues in contact with CYS 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C TRP* 3.9 18.2 - - + -
175C TYR* 3.2 5.0 - - - -
176C TYR* 2.8 32.9 + - + -
191C CYS* 2.0 52.3 - - + -
194C MET* 3.6 10.1 - - - -
197C GLN 3.1 10.3 - - - +
199C VAL 4.3 1.1 - - - -
280C TRP* 3.6 20.6 - - - -
281C VAL* 1.3 80.5 - - - +
283C ASP* 1.3 61.7 + - - +
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Residues in contact with ASP 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C TRP* 3.8 3.6 - - - -
173C LYS* 2.9 38.0 + - - -
174C CYS 3.0 13.0 - - - +
175C TYR* 3.9 11.9 - - + -
196C GLY* 3.4 2.4 - - - -
197C GLN* 2.8 39.8 + - - +
198C LEU 4.3 1.6 - - - +
199C VAL* 3.4 11.1 - - + +
200C SER* 3.0 21.5 + - - -
282C CYS* 1.3 75.6 - - - +
284C ARG* 1.3 66.6 + - - +
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Residues in contact with ARG 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C PRO* 3.5 31.9 - - - +
167C TRP* 3.5 33.2 - - + +
173C LYS* 3.4 7.6 - - - +
174C CYS* 2.7 38.4 + - + -
194C MET 3.0 22.6 + - - -
195C GLU* 3.5 40.1 + - - +
196C GLY* 4.3 0.7 - - - -
283C ASP* 1.3 80.0 - - - +
285C LEU* 1.3 70.0 + - - +
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Residues in contact with LEU 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C THR 4.8 0.2 - - - +
172C ARG* 3.8 16.2 - - + +
173C LYS* 4.2 14.8 - - + -
174C CYS* 4.0 2.9 - - - -
284C ARG* 1.3 87.9 + - - +
286C ALA* 1.3 69.3 + - - +
287C THR* 3.9 7.5 + - + +
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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