Contacts of the helix formed by residues 265 - 278 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A LYS* 5.9 1.7 - - - +
159A GLY 5.3 2.7 + - - -
262A PRO* 4.6 14.9 + - - -
263A GLY 4.1 0.4 - - - -
264A LEU* 1.3 75.8 - - - +
266A GLU* 1.3 69.1 + - - +
267A GLN* 3.4 9.7 + - - +
268A ASP* 2.4 37.2 + - - -
269A VAL* 3.2 20.5 + - - +
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Residues in contact with GLU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A SER* 1.3 75.2 - - - +
267A GLN* 1.3 63.6 + - - +
269A VAL* 3.3 9.7 + - + +
270A ARG* 3.1 47.0 + - + +
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Residues in contact with GLN 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A HIS* 3.6 15.8 + - - -
158A LYS* 5.0 19.3 - - + +
265A SER* 3.2 8.4 + - - +
266A GLU* 1.3 77.3 - - - +
268A ASP* 1.3 64.6 + - - +
270A ARG* 2.9 36.8 + - - +
271A ASP* 2.7 52.8 + - - +
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Residues in contact with ASP 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A THR* 3.7 9.5 + - - +
158A LYS* 3.5 14.9 + - - +
159A GLY* 2.7 39.6 + - - -
262A PRO 5.4 0.2 - - - +
263A GLY 4.0 1.7 - - - +
264A LEU* 3.8 20.7 - - + -
265A SER* 2.4 41.1 + - - +
267A GLN* 1.3 73.5 - - - +
269A VAL* 1.3 52.6 + - - +
271A ASP* 2.8 12.6 + - - +
272A LEU* 2.6 40.9 + - - +
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Residues in contact with VAL 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A LEU* 4.0 15.9 - - + +
265A SER 3.2 11.9 + - - +
266A GLU* 3.6 11.4 - - + +
268A ASP* 1.3 75.1 - - - +
270A ARG* 1.3 65.9 + - + +
272A LEU* 3.1 2.6 + - - +
273A ARG* 2.9 44.0 + - + +
300A ALA* 4.0 26.7 - - + -
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Residues in contact with ARG 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A HIS* 3.9 11.0 + - - +
266A GLU* 3.1 46.9 + - + +
267A GLN* 2.9 44.4 + - - +
269A VAL* 1.3 74.6 - - + +
271A ASP* 1.3 64.7 + - - +
273A ARG* 3.3 9.1 + - - +
274A PHE* 2.9 22.3 + - - +
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Residues in contact with ASP 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A PHE* 3.2 43.4 - - + +
124A HIS* 2.9 16.0 - - - -
155A LEU* 3.5 15.1 - - + +
157A THR* 5.3 2.9 - - - +
158A LYS* 4.9 7.3 + - - +
267A GLN* 2.7 52.8 + - - +
268A ASP* 2.8 12.6 + - - +
270A ARG* 1.3 70.7 - - - +
272A LEU* 1.3 63.8 + - + +
274A PHE* 3.1 6.2 - - - +
275A GLY 3.0 17.3 + - - -
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Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A LEU* 4.4 12.8 - - + -
157A THR* 4.5 9.0 - - - +
264A LEU* 4.1 26.0 - - + -
268A ASP 2.6 21.8 + - - +
269A VAL 3.1 4.0 + - - +
271A ASP* 1.3 72.6 - - + +
273A ARG* 1.3 55.9 + - - +
275A GLY* 2.7 21.3 + - - -
276A VAL* 3.0 16.5 + - - +
283A VAL* 3.8 29.2 - - + -
297A VAL* 4.4 12.8 - - + +
300A ALA* 3.7 30.5 - - + -
301A LEU* 3.7 27.7 - - + +
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Residues in contact with ARG 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A VAL* 2.9 38.9 + - + +
270A ARG* 3.6 8.3 - - - +
272A LEU* 1.3 73.8 - - - +
274A PHE* 1.3 61.6 + - - +
276A VAL* 3.3 15.4 + - - +
277A GLU* 3.1 33.1 + - - +
300A ALA* 2.9 31.2 + - - +
301A LEU 3.9 11.9 + - - -
302A GLY* 4.5 10.0 - - - -
303A PRO* 4.9 6.7 - - - +
304A GLU* 5.1 7.7 - - - +
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Residues in contact with PHE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A PHE* 3.6 25.4 - + - -
124A HIS* 3.4 61.5 - + + +
127A HIS* 4.2 2.9 - - + -
128A ALA* 3.8 13.5 - - + -
131A ILE* 4.0 20.0 - - + -
155A LEU* 4.8 0.4 - - + -
270A ARG 2.9 13.6 + - - +
271A ASP* 3.1 12.8 - - - +
273A ARG* 1.3 75.2 - - - +
275A GLY* 1.3 65.4 + - - +
277A GLU* 3.1 10.7 + - - -
278A HIS* 3.0 63.9 + + - -
280A VAL* 5.8 0.2 - - + -
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Residues in contact with GLY 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A LEU* 3.8 15.0 - - - -
271A ASP 3.0 7.3 + - - -
272A LEU 2.7 15.0 + - - -
274A PHE* 1.3 72.5 - - - +
276A VAL* 1.3 60.3 + - - -
278A HIS* 3.4 0.9 + - - -
279A GLY 3.0 3.5 + - - -
280A VAL* 3.0 53.0 + - - +
301A LEU* 6.3 0.4 - - - -
308A ILE* 4.9 0.2 - - - -
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Residues in contact with VAL 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A LEU 3.0 12.6 + - - +
273A ARG* 3.5 18.4 - - - +
274A PHE 3.2 0.2 - - - -
275A GLY* 1.3 74.8 - - - +
277A GLU* 1.3 61.2 + - + +
279A GLY* 2.9 22.2 + - - -
301A LEU* 3.0 39.9 - - + +
304A GLU* 3.4 44.6 - - + +
305A GLY* 4.7 1.3 - - - -
308A ILE* 4.6 10.8 - - + -
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Residues in contact with GLU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A ARG* 3.1 18.1 + - - +
274A PHE* 3.1 12.3 + - - +
276A VAL* 1.3 82.2 - - + +
278A HIS* 1.3 72.3 + - + +
279A GLY 3.4 0.4 + - - -
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Residues in contact with HIS 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ALA* 4.2 16.2 - - + +
131A ILE* 3.8 26.0 - - + +
135A ARG* 2.5 41.4 + - - +
274A PHE* 3.0 66.1 + + + +
275A GLY* 4.4 1.6 - - - +
277A GLU* 1.3 90.8 + - + +
279A GLY* 1.3 51.8 + - - +
280A VAL 3.4 1.9 + - - -
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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