Contacts of the helix formed by residues 265 - 278 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158B LYS* 6.0 1.6 - - - +
159B GLY 5.3 3.1 + - - -
262B PRO* 4.6 15.8 + - - -
263B GLY 4.2 0.6 - - - -
264B LEU* 1.3 73.9 - - - +
266B GLU* 1.3 66.8 + - - +
267B GLN* 3.3 9.6 + - - +
268B ASP* 2.5 36.0 + - - -
269B VAL* 3.2 20.8 + - - +
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Residues in contact with GLU 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B SER* 1.3 75.2 - - - +
267B GLN* 1.3 64.7 + - - +
269B VAL* 3.4 8.5 + - + +
270B ARG* 3.1 48.1 + - - +
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Residues in contact with GLN 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B HIS* 3.6 14.8 + - - -
158B LYS* 5.2 17.9 - - + +
265B SER* 3.2 8.7 + - - +
266B GLU* 1.3 77.7 - - - +
268B ASP* 1.3 65.0 + - - +
270B ARG* 2.9 36.7 + - - +
271B ASP* 2.7 52.3 + - - +
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Residues in contact with ASP 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B THR* 3.9 10.3 + - - +
158B LYS* 3.7 13.4 + - - +
159B GLY* 2.6 42.1 + - - -
263B GLY 4.4 1.5 - - - -
264B LEU* 3.7 20.6 - - + -
265B SER* 2.5 41.8 + - - +
267B GLN* 1.3 75.4 - - - +
269B VAL* 1.3 54.0 + - - +
271B ASP* 2.8 12.6 + - - +
272B LEU* 2.6 39.9 + - + +
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Residues in contact with VAL 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B LEU* 4.0 15.2 - - + +
265B SER 3.2 11.4 + - - +
266B GLU* 3.6 13.0 - - + +
268B ASP* 1.3 76.6 - - - +
270B ARG* 1.3 65.1 + - + +
272B LEU* 3.2 2.3 + - - +
273B ARG* 2.9 43.4 + - + +
300B ALA* 4.0 25.8 - - + -
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Residues in contact with ARG 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B HIS* 4.0 10.9 + - - +
266B GLU* 3.1 47.4 + - + +
267B GLN* 2.9 43.0 + - - +
269B VAL* 1.3 74.1 - - + +
271B ASP* 1.3 64.9 + - - +
273B ARG* 3.2 10.2 + - - +
274B PHE* 2.9 22.3 + - - +
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Residues in contact with ASP 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B PHE* 3.1 43.7 - - + +
124B HIS* 2.8 15.6 - - - -
155B LEU* 3.4 15.7 - - + +
157B THR* 5.3 3.1 - - - +
158B LYS* 5.0 6.4 + - - +
267B GLN* 2.7 53.9 + - - +
268B ASP* 2.8 12.6 + - - +
270B ARG* 1.3 70.3 - - - +
272B LEU* 1.3 62.5 + - + +
274B PHE* 3.1 5.8 - - - +
275B GLY 3.0 17.0 + - - -
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Residues in contact with LEU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B LEU* 4.3 13.7 - - + -
157B THR* 4.4 9.4 - - - +
264B LEU* 4.1 25.6 - - + -
268B ASP 2.6 21.9 + - - +
269B VAL 3.6 3.8 - - - +
271B ASP* 1.3 69.4 - - - +
273B ARG* 1.3 58.6 + - - +
275B GLY* 2.7 23.6 + - - +
276B VAL* 3.0 16.0 + - - +
283B VAL* 3.8 29.4 - - + -
297B VAL* 4.3 12.8 - - + +
300B ALA* 3.8 28.3 - - + -
301B LEU* 3.6 27.7 - - + +
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Residues in contact with ARG 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B VAL* 2.9 40.6 + - + +
270B ARG* 3.6 8.5 - - - +
272B LEU* 1.3 74.9 - - - +
274B PHE* 1.3 62.7 + - - +
276B VAL* 3.2 16.5 + - - +
277B GLU* 3.1 33.3 + - + +
300B ALA* 2.8 32.2 + - - +
301B LEU 3.8 13.3 + - - -
302B GLY* 4.6 8.9 - - - -
303B PRO* 5.1 5.5 - - - +
304B GLU* 5.2 7.5 - - - +
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Residues in contact with PHE 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B LEU* 5.4 0.2 - - + -
119B PHE* 3.7 25.8 - + - -
124B HIS* 3.3 62.4 - + + +
127B HIS* 4.2 1.8 - - + -
128B ALA* 3.8 12.6 - - + -
131B ILE* 4.0 19.3 - - + -
155B LEU* 4.7 0.7 - - + -
270B ARG 2.9 12.3 + - - +
271B ASP* 3.1 11.0 - - - +
273B ARG* 1.3 75.4 - - - +
275B GLY* 1.3 66.6 + - - +
277B GLU* 3.1 11.7 + - - +
278B HIS* 3.0 65.9 + + - -
280B VAL* 5.8 0.2 - - + -
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Residues in contact with GLY 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B LEU* 3.7 14.6 - - - -
271B ASP 3.0 7.1 + - - -
272B LEU 2.7 14.8 + - - -
274B PHE* 1.3 74.0 - - - +
276B VAL* 1.3 58.1 + - - -
278B HIS 3.5 0.7 + - - -
279B GLY* 3.1 3.1 + - - -
280B VAL* 2.9 55.7 + - - +
301B LEU* 6.4 0.2 - - - -
308B ILE* 4.8 0.2 - - - -
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Residues in contact with VAL 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B LEU 3.0 12.6 + - - +
273B ARG* 3.4 17.9 - - - +
275B GLY* 1.3 75.4 - - - +
277B GLU* 1.3 61.5 + - + +
279B GLY* 2.8 21.7 + - - -
301B LEU* 3.1 41.1 - - + +
304B GLU* 3.5 43.7 - - + +
305B GLY* 4.7 2.2 - - - -
308B ILE* 4.7 10.1 - - + -
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Residues in contact with GLU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B ARG* 3.1 18.4 + - + +
274B PHE* 3.1 15.2 + - - +
276B VAL* 1.3 82.6 - - + +
278B HIS* 1.3 71.9 + - + +
279B GLY 3.3 0.6 + - - -
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Residues in contact with HIS 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ALA* 4.1 17.1 + - + +
131B ILE* 3.8 26.3 - - + +
135B ARG* 2.5 41.3 + - - +
274B PHE* 3.0 66.7 + + + +
275B GLY* 4.5 1.6 - - - +
277B GLU* 1.3 89.7 + - + +
279B GLY* 1.3 53.1 + - - +
280B VAL* 3.3 2.5 + - - +
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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