Contacts of the helix formed by residues 263 - 277 (chain B) in PDB entry 2VES
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 263 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142B LYS* 4.9 7.6 - - - +
238B LYS* 5.4 5.4 - - - -
261B LYS 3.6 3.0 + - - -
262B SER* 1.3 75.1 + - - +
264B HIS* 1.3 61.7 + - - -
265B ALA* 3.2 3.3 + - - -
266B LEU* 3.3 6.8 + - - +
267B ASN* 2.9 36.3 + - - -
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Residues in contact with HIS 264 (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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60B THR* 3.8 22.5 + - + +
61B THR 5.5 0.4 - - - -
62B MET 3.2 21.1 + - - -
63B SER* 3.6 9.4 - - - -
64B THR* 3.4 18.9 + - - +
77B GLU* 3.1 13.8 + - + -
241B ASP* 3.8 21.6 + - + +
245B ASP* 2.6 31.5 + - - +
263B GLY* 1.3 72.8 - - - -
265B ALA* 1.3 57.3 + - - +
267B ASN* 3.7 1.4 - - - +
268B ASN* 3.0 29.6 + - - +
1290B GVR 2.8 36.4 + - - +
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Residues in contact with ALA 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B THR* 3.2 32.2 + - - +
139B GLU* 4.5 11.9 - - - +
263B GLY* 3.2 0.6 - - - -
264B HIS* 1.3 78.0 - - - +
266B LEU* 1.3 58.2 + - - +
268B ASN* 3.4 3.6 + - - +
269B GLN* 3.0 28.5 + - - +
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Residues in contact with LEU 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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137B VAL* 3.4 26.9 - - + +
138B GLU 3.9 9.6 - - - +
139B GLU* 3.8 29.4 + - + +
142B LYS* 3.6 19.1 - - + +
143B ARG* 3.5 43.1 - - - +
144B ALA* 3.6 2.0 - - + +
262B SER* 3.4 16.4 - - - +
263B GLY 3.3 9.7 + - - +
265B ALA* 1.3 74.9 - - - +
267B ASN* 1.3 60.5 + - - +
269B GLN* 3.1 9.7 + - + +
270B LEU* 2.9 29.8 + - - +
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Residues in contact with ASN 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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144B ALA* 5.2 0.2 - - - -
156B PHE* 5.2 2.1 - - - -
238B LYS 5.6 0.2 + - - -
241B ASP* 4.4 2.4 - - - +
242B ALA* 3.8 19.8 - - - +
245B ASP* 3.0 38.6 + - + +
246B LEU* 4.7 5.3 - - + +
257B PHE* 3.5 23.4 - - - -
262B SER* 2.8 28.0 + - - -
263B GLY* 2.9 23.3 + - - +
264B HIS* 3.7 5.1 + - - +
266B LEU* 1.3 77.5 - - - +
268B ASN* 1.3 62.4 + - - +
270B LEU* 3.3 7.4 + - - +
271B LEU* 3.1 27.1 + - - +
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Residues in contact with ASN 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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54B ALA* 3.4 31.7 + - - +
57B VAL* 3.5 31.9 - - + +
60B THR* 4.8 1.5 - - + +
64B THR* 6.4 0.4 - - + -
245B ASP* 5.4 0.9 - - - +
248B LEU* 4.8 3.3 - - + +
264B HIS 3.0 18.8 + - - +
265B ALA* 3.7 5.8 - - - +
267B ASN* 1.3 76.5 - - - +
269B GLN* 1.3 59.7 + - - +
271B LEU* 3.1 10.5 + - - +
272B ARG* 2.9 55.5 + - - +
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Residues in contact with GLN 269 (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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137B VAL* 4.1 16.6 - - + -
138B GLU 6.1 0.2 - - - +
265B ALA 3.0 14.3 + - - +
266B LEU* 3.1 18.6 + - + +
268B ASN* 1.3 77.3 + - - +
270B LEU* 1.3 56.3 + - - +
272B ARG* 3.4 14.9 + - - +
273B THR* 2.8 38.5 + - - +
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Residues in contact with LEU 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B VAL* 3.6 35.0 - - + +
136B SER* 4.2 1.3 - - - -
137B VAL* 3.8 16.7 - - + +
144B ALA* 3.8 20.2 - - + +
145B VAL 4.0 5.4 - - - +
146B PHE* 3.5 33.4 - - + -
246B LEU* 4.9 2.0 - - + -
257B PHE* 3.5 34.5 - - + -
266B LEU 2.9 12.4 + - - +
267B ASN 3.5 8.1 - - - +
269B GLN* 1.3 76.3 - - - +
271B LEU* 1.3 56.6 + - - +
273B THR* 3.3 1.6 + - - -
274B LEU* 2.8 29.8 + - - +
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Residues in contact with LEU 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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54B ALA* 3.9 16.8 - - + -
146B PHE* 3.8 7.6 - - + -
245B ASP 3.2 25.8 - - - +
246B LEU* 3.6 26.2 - - + -
248B LEU* 3.9 17.5 - - + -
249B LEU* 3.5 41.0 - - + +
267B ASN 3.1 17.1 + - - +
268B ASN* 3.1 13.7 + - - +
270B LEU* 1.3 75.0 - - - +
272B ARG* 1.3 59.7 + - - +
274B LEU* 3.2 4.6 + - - +
275B ILE* 2.9 35.6 + - - +
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Residues in contact with ARG 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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54B ALA* 3.1 27.7 + - + +
55B GLU* 3.5 24.0 + - + +
57B VAL 3.0 26.7 + - - -
268B ASN* 2.9 39.6 + - - +
269B GLN* 3.9 14.8 - - - +
271B LEU* 1.3 75.2 - - - +
273B THR* 1.3 61.7 + - - +
275B ILE* 3.6 8.8 + - + +
276B ALA* 3.2 24.4 + - - +
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Residues in contact with THR 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B VAL* 3.7 14.6 - - + -
136B SER 4.6 3.4 - - - +
137B VAL* 3.4 22.0 - - + +
269B GLN* 2.8 26.5 + - - +
270B LEU 3.7 3.8 - - - -
272B ARG* 1.3 74.2 - - - +
274B LEU* 1.3 65.1 + - - +
276B ALA* 3.4 5.0 + - - +
277B ASP* 3.0 46.3 + - - +
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Residues in contact with LEU 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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129B ILE* 4.7 8.3 - - + -
131B ILE* 3.7 33.7 - - + -
135B VAL* 3.8 28.6 - - + +
146B PHE* 3.7 21.1 - - + -
249B LEU* 4.1 25.6 - - + -
270B LEU 2.8 20.5 + - - +
271B LEU 3.6 3.4 - - - +
273B THR* 1.3 72.3 - - - +
275B ILE* 1.3 62.5 + - - +
277B ASP* 3.0 12.8 + - - +
280B ALA* 4.1 5.4 - - + +
281B TRP* 2.8 44.6 + - + -
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Residues in contact with ILE 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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53B ARG* 6.1 2.2 - - - +
54B ALA* 3.8 24.2 - - + -
55B GLU* 3.7 27.1 - - - +
248B LEU 5.7 0.2 - - - +
249B LEU* 3.9 24.7 - - + +
271B LEU 2.9 24.4 + - - +
272B ARG* 3.9 8.3 - - + +
274B LEU* 1.3 75.1 - - + +
276B ALA* 1.3 61.4 + - - +
278B LYS* 4.1 8.0 - - - +
281B TRP* 3.3 29.5 + - + +
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Residues in contact with ALA 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 ARG 3.2 14.8 + - - +
273B THR* 3.7 6.3 - - - +
274B LEU 3.2 0.4 - - - -
275B ILE* 1.3 81.0 - - - +
277B ASP* 1.3 65.0 + - - +
278B LYS* 3.1 10.2 + - - +
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Residues in contact with ASP 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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135B VAL* 4.3 9.6 - - + +
273B THR* 3.0 32.1 + - - +
274B LEU* 3.0 9.0 + - - +
276B ALA* 1.3 80.1 - - - +
278B LYS* 1.3 59.0 + - - +
279B ASP* 3.2 9.6 - - - +
280B ALA* 2.9 30.3 + - + +
281B TRP* 3.3 11.1 - - - -
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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