Contacts of the strand formed by residues 270 - 279 (chain M) in PDB entry 2VGL
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 270 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202M MET 3.4 2.8 - - - +
203M LYS* 3.2 5.2 - - - -
204M SER* 2.9 41.4 + - - -
205M TYR* 3.8 19.5 - - - -
268M PRO 4.3 2.3 - - - +
269M ASP* 1.3 76.6 + - - +
271M GLU* 1.3 58.8 + - - -
272M PHE* 4.0 2.1 + - - -
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Residues in contact with GLU 271 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201M VAL* 3.6 26.6 - - + +
202M MET 3.2 5.6 - - - +
203M LYS* 4.0 30.0 - - + +
205M TYR* 5.1 0.8 + - - +
268M PRO* 5.6 0.2 - - - +
269M ASP 3.8 3.1 + - - +
270M GLY* 1.3 72.1 - - - -
272M PHE* 1.3 68.4 + - - +
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Residues in contact with PHE 272 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201M VAL* 3.5 7.0 - - - +
202M MET* 2.7 68.4 + - + +
204M SER* 5.1 0.7 - - - -
249M HIS* 3.5 24.7 - + + +
251M CYS* 4.1 3.1 - - - -
265M PHE* 4.4 0.7 - + - -
267M PRO* 3.7 27.4 - - + -
268M PRO* 3.8 42.6 - - + -
270M GLY 4.3 3.1 - - - -
271M GLU* 1.3 80.7 - - - +
273M GLU* 1.3 75.1 + - - +
274M LEU* 3.7 37.4 + - + -
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Residues in contact with GLU 273 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199M ARG* 3.9 25.8 + - + +
200M VAL 3.8 4.0 - - - +
201M VAL* 4.5 4.0 - - + +
247M THR* 5.6 1.7 - - - +
249M HIS* 3.4 18.4 + - + +
272M PHE* 1.3 83.8 - - - +
274M LEU* 1.3 64.3 + - - +
275M MET* 4.1 11.6 - - - +
276M ARG* 2.7 69.0 + - - +
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Residues in contact with LEU 274 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175M LEU* 5.3 1.3 - - + -
200M VAL* 3.0 27.3 + - + +
202M MET* 4.7 10.3 - - + -
214M PHE* 3.9 35.7 - - + -
248M PHE* 3.5 4.6 - - + +
249M HIS* 2.9 25.9 + - - +
252M VAL* 3.6 28.0 - - + -
263M ILE* 5.1 3.4 - - + -
265M PHE* 3.8 32.3 - - + -
272M PHE* 3.7 25.9 + - + -
273M GLU* 1.3 73.6 - - - +
275M MET* 1.3 67.2 + - + +
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Residues in contact with MET 275 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199M ARG* 3.1 6.8 - - - +
200M VAL* 3.0 50.3 + - + -
214M PHE* 4.6 10.5 - - - -
216M MET* 3.8 34.1 - - + +
220M ILE* 4.8 3.4 - - + -
246M CYS* 3.1 28.9 - - - -
247M THR 3.2 11.2 - - - +
248M PHE* 3.2 27.6 - - + -
263M ILE* 4.8 0.2 - - + -
273M GLU* 4.0 6.8 - - - +
274M LEU* 1.3 86.4 - - + +
276M ARG* 1.3 58.8 + - - +
277M TYR* 4.2 13.7 - - + -
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Residues in contact with ARG 276 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198M GLY 3.6 8.4 + - - +
199M ARG* 4.0 23.1 - - + +
246M CYS* 3.3 2.4 - - - -
247M THR* 2.7 48.2 + - + +
273M GLU* 2.7 40.2 + - - +
275M MET* 1.3 73.7 - - - +
277M TYR* 1.3 64.4 + - - +
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Residues in contact with TYR 277 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177M VAL* 4.0 3.1 - - - +
179M GLU* 2.4 41.9 + - - +
196M VAL* 4.8 2.7 - - + -
197M SER* 3.6 3.1 + - - -
198M GLY* 2.9 55.8 + - - +
199M ARG* 3.3 12.4 + - - -
220M ILE* 3.3 34.1 - - + -
245M ASP* 3.2 15.9 - - - +
246M CYS* 3.9 11.9 - - + +
275M MET* 4.2 15.0 - - + -
276M ARG* 1.3 79.6 - - - +
278M ARG* 1.3 68.9 + - - +
279M THR* 4.7 2.9 - - + -
397M SER* 4.3 7.9 - - - -
399M LEU* 3.3 20.6 - - + +
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Residues in contact with ARG 278 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195M HIS* 4.0 12.6 + - + -
196M VAL 3.3 16.2 - - - +
197M SER* 3.2 24.1 + - - +
242M ALA* 3.9 28.6 - - + +
243M ILE 3.6 20.1 + - - +
244M ASP* 3.2 6.6 - - - +
245M ASP* 2.9 38.7 + - + +
277M TYR* 1.3 76.6 + - - +
279M THR* 1.3 64.5 + - - +
280M THR* 5.7 0.2 - - + -
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Residues in contact with THR 279 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195M HIS* 3.3 5.6 - - - +
196M VAL* 2.7 53.4 + - + +
219M LYS 4.5 10.1 + - - +
220M ILE* 5.1 9.4 - - + -
244M ASP* 3.3 9.5 + - - -
277M TYR* 4.3 9.4 - - + -
278M ARG* 1.3 77.1 - - - +
280M THR* 1.3 64.7 + - - +
281M LYS* 3.8 12.5 + - - +
283M ILE* 3.9 5.5 - - + +
397M SER* 3.7 32.5 - - - +
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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