Contacts of the helix formed by residues 265 - 278 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158D LYS* 6.0 1.6 - - - +
159D GLY 5.4 1.7 + - - -
262D PRO* 4.5 15.2 + - - +
263D GLY 4.2 0.2 - - - -
264D LEU* 1.3 77.1 - - - +
266D GLU* 1.3 65.1 + - - +
267D GLN* 3.4 9.3 + - - +
268D ASP* 2.4 33.6 + - - -
269D VAL* 3.1 23.7 + - - +
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Residues in contact with GLU 266 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265D SER* 1.3 75.3 - - - +
267D GLN* 1.3 63.4 + - - +
269D VAL* 3.3 8.8 + - + +
270D ARG* 3.0 50.3 + - + +
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Residues in contact with GLN 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D HIS* 3.6 16.0 + - - -
158D LYS* 5.1 17.9 - - + +
265D SER* 3.2 8.4 + - - +
266D GLU* 1.3 75.3 - - - +
268D ASP* 1.3 56.2 + - - +
270D ARG* 2.9 35.1 + - - +
271D ASP* 2.6 68.8 + - - +
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Residues in contact with ASP 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D THR* 3.8 9.0 + - - +
158D LYS* 3.6 15.3 + - - +
159D GLY* 2.7 39.3 + - - +
262D PRO 5.3 0.2 - - - +
263D GLY 4.0 3.9 - - - +
264D LEU* 3.8 19.0 - - + -
265D SER* 2.4 41.0 + - - +
267D GLN* 1.3 75.1 - - - +
269D VAL* 1.3 54.2 + - - +
271D ASP* 2.8 11.1 + - - +
272D LEU* 2.7 39.8 + - + +
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Residues in contact with VAL 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264D LEU* 3.9 25.1 - - + +
265D SER 3.1 15.6 + - - +
266D GLU* 3.6 12.1 - - + +
268D ASP* 1.3 75.7 - - - +
270D ARG* 1.3 65.2 + - + +
272D LEU* 3.2 1.5 + - - +
273D ARG* 3.0 43.2 + - + +
300D ALA* 4.1 16.6 - - + -
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Residues in contact with ARG 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D HIS* 4.0 10.9 + - - +
266D GLU* 3.0 46.6 + - - +
267D GLN* 2.9 39.8 + - - +
269D VAL* 1.3 76.7 - - + +
271D ASP* 1.3 63.4 + - - +
273D ARG* 3.2 10.2 + - - +
274D PHE* 3.0 21.8 + - - +
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Residues in contact with ASP 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D PHE* 3.2 44.0 - - + +
124D HIS* 2.9 15.1 - - - -
155D LEU* 3.4 16.0 - - + +
157D THR* 5.2 3.6 - - - +
158D LYS* 4.9 6.6 + - - +
267D GLN* 2.6 55.2 + - - +
268D ASP* 2.8 12.2 + - - +
270D ARG* 1.3 71.0 - - - +
272D LEU* 1.3 63.1 + - - +
274D PHE* 3.1 5.9 - - - +
275D GLY 3.0 16.8 + - - -
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Residues in contact with LEU 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D LEU* 4.4 10.5 - - + -
157D THR* 4.4 13.2 - - - +
264D LEU* 4.1 25.1 - - + -
268D ASP 2.7 21.6 + - - +
269D VAL 3.7 3.8 - - - +
271D ASP* 1.3 69.6 - - - +
273D ARG* 1.3 67.0 + - - +
275D GLY* 2.8 13.7 + - - -
276D VAL* 2.9 15.9 + - - +
283D VAL* 3.9 28.9 - - + -
297D VAL* 4.2 13.7 - - + +
300D ALA* 3.6 29.6 - - + -
301D LEU* 3.8 26.4 - - + +
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Residues in contact with ARG 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D VAL* 3.0 35.4 + - + +
270D ARG* 3.6 7.9 - - - +
272D LEU* 1.3 74.1 - - - +
274D PHE* 1.3 63.8 + - - +
276D VAL* 3.1 16.2 + - - +
277D GLU* 3.0 33.9 + - + +
300D ALA* 2.9 31.3 + - - +
301D LEU 3.9 13.3 + - - -
302D GLY* 4.7 9.1 - - - -
303D PRO* 5.2 5.7 - - - +
304D GLU* 5.2 8.3 - - - +
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Residues in contact with PHE 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D LEU* 5.5 0.2 - - + -
119D PHE* 3.7 24.5 - + - -
124D HIS* 3.4 63.3 - + + +
127D HIS* 4.2 2.7 - - + -
128D ALA* 3.8 14.1 - - + -
131D ILE* 3.9 19.5 - - + -
155D LEU* 4.7 0.7 - - + -
270D ARG 3.0 12.9 + - - +
271D ASP* 3.1 12.1 - - - +
273D ARG* 1.3 75.9 - - - +
275D GLY* 1.3 68.0 + - - +
277D GLU* 3.1 10.2 + - - -
278D HIS* 3.0 62.4 + + - -
280D VAL* 5.7 0.2 - - + -
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Residues in contact with GLY 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D LEU* 3.8 14.4 - - - -
271D ASP 3.0 4.0 + - - -
272D LEU 2.8 14.1 + - - -
274D PHE* 1.3 74.0 - - - +
276D VAL* 1.3 63.6 - - - -
278D HIS 3.4 0.5 + - - -
279D GLY 3.0 3.1 + - - -
280D VAL* 3.0 54.0 + - - +
301D LEU* 6.3 0.2 - - - -
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Residues in contact with VAL 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272D LEU 2.9 17.5 + - - +
273D ARG* 3.1 17.0 + - - +
275D GLY* 1.3 76.0 - - - +
277D GLU* 1.3 61.4 + - + +
279D GLY* 2.9 21.0 + - - -
301D LEU* 3.1 41.0 - - + +
304D GLU* 3.6 43.3 - - + +
305D GLY* 4.7 1.8 - - - -
308D ILE* 4.7 10.3 - - + -
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Residues in contact with GLU 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D ARG* 3.0 21.9 + - + +
274D PHE* 3.1 11.6 + - - +
276D VAL* 1.3 83.3 - - + +
278D HIS* 1.3 70.7 + - + +
279D GLY 3.3 0.8 + - - -
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Residues in contact with HIS 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D ALA* 4.1 18.1 - - + +
131D ILE* 3.7 25.8 - - + +
135D ARG* 2.4 40.9 + - - +
274D PHE* 3.0 67.2 + + + +
275D GLY 3.7 1.1 - - - +
277D GLU* 1.3 91.0 + - + +
279D GLY* 1.3 53.6 + - - +
280D VAL* 3.3 3.0 + - + +
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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