Contacts of the helix formed by residues 265 - 278 (chain C) in PDB entry 2VGB
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 SER 265 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158C LYS* 6.0 1.7 - - - +
159C GLY 5.4 2.6 + - - -
262C PRO* 4.6 15.7 + - - -
263C GLY 4.2 0.4 - - - -
264C LEU* 1.3 76.7 - - - +
266C GLU* 1.3 68.2 + - - +
267C GLN* 3.2 10.0 + - - +
268C ASP* 2.6 36.1 + - - -
269C VAL* 3.2 20.6 + - - +
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Residues in contact with GLU 266 (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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265C SER* 1.3 76.0 - - - +
267C GLN* 1.3 63.2 + - - +
269C VAL* 3.4 8.8 + - + +
270C ARG* 3.1 46.8 + - - +
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Residues in contact with GLN 267 (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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124C HIS* 3.7 13.9 + - - -
158C LYS* 5.2 17.9 - - + +
265C SER* 3.2 8.1 + - - +
266C GLU* 1.3 75.0 - - - +
268C ASP* 1.3 55.8 + - - +
270C ARG* 2.9 37.2 + - - +
271C ASP* 2.6 67.0 + - - +
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Residues in contact with ASP 268 (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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157C THR* 3.9 9.7 + - - +
158C LYS* 3.6 14.6 + - - +
159C GLY* 2.6 42.0 + - - +
262C PRO 5.2 0.2 - - - +
263C GLY 3.9 1.4 - - - +
264C LEU* 3.7 21.1 - - + -
265C SER* 2.6 40.1 + - - +
267C GLN* 1.3 74.7 - - - +
269C VAL* 1.3 51.5 + - - +
271C ASP* 2.8 14.2 + - - +
272C LEU* 2.6 39.4 + - + +
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Residues in contact with VAL 269 (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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264C LEU* 4.0 26.0 - - + +
265C SER 3.2 12.5 + - - +
266C GLU* 3.6 11.7 - - + +
268C ASP* 1.3 76.7 - - - +
270C ARG* 1.3 64.9 + - + +
272C LEU* 3.1 7.9 + - - +
273C ARG* 2.9 44.2 + - + +
300C ALA* 4.0 12.6 - - + -
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Residues in contact with ARG 270 (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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124C HIS* 3.9 9.8 + - - +
266C GLU* 3.1 47.1 + - + +
267C GLN* 2.9 41.9 + - - +
269C VAL* 1.3 76.2 - - + +
271C ASP* 1.3 64.7 + - - +
273C ARG* 3.2 9.9 + - - +
274C PHE* 3.0 21.7 + - - +
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Residues in contact with ASP 271 (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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119C PHE* 3.2 44.6 - - + +
124C HIS* 2.9 27.9 - - - -
155C LEU* 3.5 14.2 - - + +
157C THR* 5.3 2.7 - - - +
158C LYS* 4.9 7.6 + - - +
267C GLN* 2.6 41.4 + - - +
268C ASP* 2.8 14.1 + - - +
270C ARG* 1.3 69.9 - - - +
272C LEU* 1.3 62.6 + - + +
274C PHE* 3.1 6.5 - - - +
275C GLY 3.0 17.0 + - - -
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Residues in contact with LEU 272 (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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155C LEU* 4.4 13.2 - - + -
157C THR* 4.5 8.3 - - - +
264C LEU* 3.9 26.2 - - + -
268C ASP 2.6 20.5 + - - +
269C VAL 3.6 5.8 - - - +
271C ASP* 1.3 70.5 - - - +
273C ARG* 1.3 66.9 + - - +
275C GLY* 2.8 13.7 + - - +
276C VAL* 3.0 16.1 + - - +
283C VAL* 3.8 29.8 - - + -
297C VAL* 4.3 12.8 - - + +
300C ALA* 3.7 27.4 - - + -
301C LEU* 3.7 27.4 - - + +
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Residues in contact with ARG 273 (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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269C VAL* 2.9 31.0 + - + +
270C ARG* 3.7 8.1 - - - +
272C LEU* 1.3 74.9 - - - +
274C PHE* 1.3 63.6 + - - +
276C VAL* 3.0 16.5 + - - +
277C GLU* 3.0 33.6 + - + +
300C ALA* 2.9 30.3 + - - +
301C LEU 3.9 13.1 + - - -
302C GLY* 4.7 8.3 - - - -
303C PRO* 5.2 4.9 - - - +
304C GLU* 5.2 8.1 - - - +
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Residues in contact with PHE 274 (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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119C PHE* 3.7 24.9 - + - -
124C HIS* 3.3 63.9 - + + +
127C HIS* 4.2 3.1 - - + -
128C ALA* 3.8 13.5 - - + -
131C ILE* 3.9 19.7 - - + -
155C LEU* 4.8 0.7 - - + -
270C ARG 3.0 12.0 + - - +
271C ASP* 3.1 12.6 - - - +
272C LEU 3.0 0.2 - - - -
273C ARG* 1.3 76.3 - - - +
275C GLY* 1.3 64.7 + - - +
277C GLU* 3.2 11.5 + - - -
278C HIS* 3.1 63.4 + + - -
280C VAL* 5.8 0.2 - - + -
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Residues in contact with GLY 275 (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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155C LEU* 3.8 10.8 - - - -
271C ASP 3.0 6.9 + - - -
272C LEU 2.8 8.8 + - - -
274C PHE* 1.3 73.5 - - - +
276C VAL* 1.3 67.9 + - - +
278C HIS* 3.5 0.6 + - - -
279C GLY 3.1 2.9 + - - -
280C VAL* 3.0 55.2 + - - +
308C ILE* 4.8 0.2 - - - -
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Residues in contact with VAL 276 (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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272C LEU 3.0 13.4 + - - +
273C ARG* 3.0 16.1 + - - +
275C GLY* 1.3 74.6 - - - +
277C GLU* 1.3 60.5 + - + +
279C GLY* 2.9 22.9 + - - -
301C LEU* 3.1 41.1 - - + +
304C GLU* 3.5 44.2 - - + +
305C GLY* 4.6 2.0 - - - -
308C ILE* 4.6 9.9 - - + -
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Residues in contact with GLU 277 (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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273C ARG* 3.0 25.2 + - + +
274C PHE* 3.2 14.0 + - - +
276C VAL* 1.3 78.0 - - + +
278C HIS* 1.3 70.2 + - + +
279C GLY 3.3 0.6 + - - -
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Residues in contact with HIS 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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128C ALA* 4.2 16.2 - - + +
131C ILE* 3.8 25.2 - - + +
135C ARG* 2.4 42.1 + - - +
274C PHE* 3.1 65.8 + + + +
275C GLY 3.5 1.1 + - - +
276C VAL 3.2 0.2 - - - -
277C GLU* 1.3 88.7 + - + +
279C GLY* 1.3 53.7 + - - +
280C VAL* 3.4 2.8 + - + +
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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