Contacts of the helix formed by residues 257 - 269 (chain B) in PDB entry 2VF8
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 257 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219B ILE 3.4 18.2 - - - -
221B PHE 4.1 2.2 - - - -
222B THR* 2.2 46.4 + - - -
224B GLU 4.2 3.8 + - - -
255B PHE* 3.4 12.3 - - - -
256B SER* 1.3 75.9 + - - +
258B ALA* 1.3 65.6 + - - +
259B ARG* 3.9 1.7 - - - +
260B ARG* 3.3 20.4 + - - +
261B HIS* 3.1 16.6 + - - +
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Residues in contact with ALA 258 (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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168B MET* 3.1 24.0 - - + +
181B VAL* 4.7 4.9 - - + -
183B ALA* 4.4 9.1 - - + +
184B TRP* 3.6 31.7 - - + +
219B ILE* 3.3 6.7 + - + +
220B LEU* 3.9 24.2 - - + +
256B SER 3.5 0.8 + - - -
257B SER* 1.3 68.5 - - - +
259B ARG* 1.3 70.7 + - - +
261B HIS* 3.6 2.4 + - - +
262B VAL* 3.2 15.4 + - - +
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Residues in contact with ARG 259 (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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163B VAL* 3.7 21.5 - - + -
168B MET* 3.3 12.3 - - - +
217B HIS* 6.1 0.2 + - - -
220B LEU 3.5 10.8 + - - +
221B PHE* 2.9 41.4 + - + +
223B ASP* 3.2 35.0 + - - +
257B SER* 3.1 7.4 - - - +
258B ALA* 1.3 83.3 - - - +
260B ARG* 1.3 56.1 + - - +
262B VAL* 2.6 23.2 + - - +
263B LEU* 3.1 30.1 + - + +
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Residues in contact with ARG 260 (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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222B THR 4.7 0.4 - - - +
223B ASP* 3.5 43.8 + - - +
224B GLU 5.0 1.3 - - - -
225B GLN* 2.7 42.9 + - - +
256B SER* 3.9 11.2 - - - +
257B SER* 3.2 19.9 + - - +
259B ARG* 1.3 80.9 - - - +
261B HIS* 1.3 63.9 + - - +
263B LEU* 3.9 5.7 - - - +
264B HIS* 2.9 33.3 + - + +
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Residues in contact with HIS 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ALA 3.7 23.7 + - - -
184B TRP* 4.4 10.2 - - + -
185B PRO* 3.7 41.5 - - + +
256B SER* 3.8 11.2 + - - +
257B SER 3.1 9.6 + - - +
258B ALA 3.9 6.5 + - - +
259B ARG 2.9 0.2 + - - -
260B ARG* 1.3 79.1 - - - +
262B VAL* 1.3 63.4 + - + +
264B HIS* 3.7 3.9 - - + +
265B THR* 2.8 65.3 + - + +
274B MET* 6.1 1.2 - - - -
277B ARG* 5.8 1.8 - - - -
278B VAL* 5.2 5.2 - - + -
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Residues in contact with VAL 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B VAL* 3.5 29.8 - - + -
168B MET* 4.2 2.7 - - + -
183B ALA* 3.9 37.2 - - + +
258B ALA 3.2 10.0 + - - +
259B ARG 2.6 14.3 + - - +
261B HIS* 1.3 78.9 - - + +
263B LEU* 1.3 62.9 + - + +
265B THR* 4.1 0.4 - - - -
266B PHE* 3.3 15.2 + - - +
278B VAL* 3.2 38.3 - - + +
281B TYR* 4.3 11.2 - - + +
282B MET* 4.3 8.4 - - + +
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Residues in contact with LEU 263 (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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161B TYR* 4.6 16.6 - - + +
162B THR* 6.0 0.9 - - - -
163B VAL* 5.6 6.7 - - + -
259B ARG* 3.1 33.5 + - + +
260B ARG* 3.9 8.1 - - - +
262B VAL* 1.3 78.2 - - + +
264B HIS* 1.3 69.8 + - - +
266B PHE* 3.1 18.0 + - + +
267B ALA* 3.2 13.3 + - - +
282B MET* 4.6 18.4 - - + -
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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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260B ARG* 2.9 27.6 + - + +
261B HIS* 3.7 5.6 - - + +
263B LEU* 1.3 70.8 - - - +
265B THR* 1.3 59.0 + - - +
267B ALA* 2.7 27.6 + - - -
268B ASN* 2.8 46.9 + - + +
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Residues in contact with THR 265 (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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261B HIS* 2.8 44.7 + - + +
262B VAL 4.1 3.6 - - - -
264B HIS* 1.3 79.3 + - - +
266B PHE* 1.3 59.9 + - - +
268B ASN* 4.8 3.1 - - - +
269B THR* 2.7 33.6 + - + +
274B MET* 3.5 41.3 - - + +
275B LYS* 4.9 1.4 - - - -
278B VAL* 3.8 20.0 - - + -
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Residues in contact with PHE 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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157B LEU* 4.2 23.6 - - + -
161B TYR* 4.3 24.7 - + + -
262B VAL 3.3 14.4 + - - +
263B LEU* 3.1 14.5 + - + +
264B HIS 2.8 3.4 + - - -
265B THR* 1.3 74.6 - - - +
267B ALA* 1.3 65.4 + - + +
268B ASN 3.6 0.7 + - - -
269B THR 4.7 1.0 + - - +
275B LYS* 3.4 55.4 - - + +
278B VAL* 5.0 2.9 - - + +
279B GLN* 3.0 34.1 - - - -
282B MET* 3.7 23.3 - - + -
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Residues in contact with ALA 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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263B LEU 3.2 9.7 + - - +
264B HIS 2.7 12.9 + - - +
266B PHE* 1.3 79.2 - - + +
268B ASN* 1.3 70.1 + - - +
269B THR 4.0 0.4 - - - -
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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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264B HIS* 2.8 67.4 + - + +
265B THR* 4.3 2.5 - - - -
266B PHE 3.4 0.8 - - - -
267B ALA* 1.3 91.6 - - - +
269B THR* 1.3 66.7 + - - +
270B GLU* 4.0 5.4 + - - +
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Residues in contact with THR 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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265B THR* 2.7 27.2 + - + +
266B PHE 4.7 1.4 + - - +
268B ASN* 1.3 79.2 - - - +
270B GLU* 1.3 62.9 + - - +
271B SER* 3.6 26.8 - - - +
274B MET* 3.4 41.1 - - + +
275B LYS* 4.0 24.6 + - - +
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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