Contacts of the helix formed by residues 253 - 272 (chain A) in PDB entry 1VZP
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 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A LEU* 6.1 0.2 - - - -
251A VAL 3.7 3.4 + - - -
252A LEU* 1.3 74.3 - - - +
254A ALA* 1.3 66.1 + - - +
255A SER* 3.3 10.3 + - - -
256A ARG* 2.8 34.8 + - - +
257A ARG* 2.8 26.1 + - - +
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Residues in contact with ALA 254 (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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203A ARG* 3.4 31.4 - - - +
207A LEU* 4.8 11.4 - - + +
252A LEU 3.9 0.4 + - - -
253A SER* 1.3 72.7 - - - +
255A SER* 1.3 56.8 - - - +
257A ARG* 3.1 4.8 + - - -
258A GLU* 2.8 26.5 + - - +
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Residues in contact with SER 255 (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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253A SER* 3.1 9.0 + - - -
254A ALA* 1.3 76.8 - - - +
256A ARG* 1.3 66.9 + - - +
258A GLU* 3.2 11.2 + - - +
259A VAL* 3.2 28.7 + - - +
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Residues in contact with ARG 256 (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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241A ALA* 2.7 28.5 + - - +
242A GLY 2.7 23.0 + - - -
243A ILE* 3.6 30.7 - - + +
252A LEU* 4.4 12.1 - - + +
253A SER* 2.8 33.1 + - - +
255A SER* 1.3 78.9 - - - +
257A ARG* 1.3 57.3 + - - +
259A VAL* 3.2 9.9 + - - +
260A LEU* 2.9 28.2 + - - +
319A GLN* 4.1 4.9 + - - -
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Residues in contact with ARG 257 (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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203A ARG* 3.9 14.4 - - + -
206A ALA* 2.6 39.1 + - + +
207A LEU* 3.6 26.4 + - + +
209A ALA* 4.7 4.8 - - - +
210A LEU 5.3 3.2 + - - +
212A GLN* 5.7 3.4 - - - +
216A VAL* 3.6 10.9 - - - +
219A THR* 5.0 4.4 - - - +
225A TYR* 4.0 12.7 + - - -
249A GLY* 3.7 17.6 + - - -
252A LEU* 3.6 39.8 - - + +
253A SER 2.8 23.1 + - - +
254A ALA* 3.1 8.5 + - - +
256A ARG* 1.3 73.4 - - - +
258A GLU* 1.3 67.0 + - - +
260A LEU* 3.4 21.4 - - - +
261A VAL* 3.0 29.5 + - - +
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Residues in contact with GLU 258 (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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202A HIS* 2.8 33.2 + - - -
203A ARG* 2.7 48.8 + - + +
254A ALA 2.8 15.3 + - - +
255A SER* 3.3 13.0 - - - +
257A ARG* 1.3 77.1 - - - +
259A VAL* 1.3 63.0 + - + +
261A VAL* 3.1 4.6 - - - +
262A ASP* 3.0 35.7 + - - +
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Residues in contact with VAL 259 (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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240A ARG 4.3 5.2 - - - +
241A ALA* 3.9 25.6 - - + +
255A SER* 3.2 19.1 + - - +
256A ARG* 3.8 10.5 - - - +
258A GLU* 1.3 76.6 - - + +
260A LEU* 1.3 64.5 + - - +
262A ASP* 3.6 9.4 - - + +
263A HIS* 2.8 33.2 + - + +
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Residues in contact with LEU 260 (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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201A PHE* 6.0 0.7 - - + -
216A VAL* 4.1 14.4 - - + -
220A LEU* 4.5 13.7 - - + -
225A TYR* 4.9 3.4 - - - +
237A ALA* 5.2 0.2 - - + -
238A LEU* 3.9 21.1 - - + -
241A ALA* 4.3 1.5 - - - +
243A ILE* 4.0 7.6 - - + -
252A LEU* 4.4 6.7 - - + -
256A ARG 2.9 16.7 + - - +
257A ARG* 3.4 39.5 - - - +
258A GLU 3.2 0.2 - - - -
259A VAL* 1.3 79.9 - - - +
261A VAL* 1.3 67.3 + - + +
263A HIS* 3.1 31.1 - - + +
264A VAL* 3.0 36.8 + - + +
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Residues in contact with VAL 261 (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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201A PHE* 3.5 37.3 - - + +
202A HIS* 3.3 44.4 - - + +
203A ARG 3.6 9.0 - - - +
206A ALA* 3.8 11.2 - - + -
225A TYR* 4.8 1.1 - - - +
257A ARG 3.0 13.4 + - - +
258A GLU 3.1 13.9 - - - +
260A LEU* 1.3 78.7 - - + +
262A ASP* 1.3 66.5 + - - +
264A VAL* 3.3 9.2 + - - +
265A VAL* 3.2 26.3 + - + +
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Residues in contact with ASP 262 (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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202A HIS* 2.6 34.9 + - - -
258A GLU* 3.0 27.7 + - - +
259A VAL* 3.6 11.1 - - + +
260A LEU 3.1 0.6 - - - -
261A VAL* 1.3 82.6 - - - +
263A HIS* 1.3 63.0 + - + +
265A VAL* 3.2 17.0 + - - +
266A GLU* 3.3 10.8 + - - +
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Residues in contact with HIS 263 (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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237A ALA* 2.5 45.3 + - + +
240A ARG* 3.5 26.4 - - + +
241A ALA* 3.2 36.9 - - + +
259A VAL* 2.8 23.0 + - + +
260A LEU* 3.1 28.9 + - + +
262A ASP* 1.3 75.9 - - + +
264A VAL* 1.3 74.8 + - + +
265A VAL 3.0 1.6 - - - -
266A GLU* 3.2 11.0 - - + +
267A PHE* 2.8 36.6 + - - +
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Residues in contact with VAL 264 (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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196A ILE* 3.9 13.7 - - + -
201A PHE* 3.8 26.9 - - + -
220A LEU* 5.6 8.1 - - + -
229A LEU* 4.1 20.9 - - + -
233A ILE* 5.2 2.6 - - + +
237A ALA* 3.8 15.0 - - + -
260A LEU* 3.0 29.3 + - + +
261A VAL* 3.4 11.4 - - - +
263A HIS* 1.3 96.5 + - + +
265A VAL* 1.3 51.9 + - - +
267A PHE* 4.2 0.9 - - - +
268A SER* 2.6 34.5 + - - -
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Residues in contact with VAL 265 (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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196A ILE* 3.4 27.4 - - + +
197A LEU* 3.9 19.5 - - + +
198A SER 5.7 0.7 - - - +
201A PHE* 5.3 4.7 - - + +
202A HIS* 6.0 3.4 - - + -
261A VAL 3.2 13.0 + - - +
262A ASP* 3.3 10.8 - - - +
263A HIS 3.0 0.4 - - - -
264A VAL* 1.3 79.5 - - + +
266A GLU* 1.3 55.7 + - + +
268A SER* 2.5 20.0 + - - -
269A THR* 2.7 32.7 + - - +
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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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240A ARG* 2.7 48.3 + - - +
262A ASP 3.3 8.4 + - - +
263A HIS* 2.9 19.8 + - + +
265A VAL* 1.3 82.5 - - + +
267A PHE* 1.3 70.4 + - - +
269A THR* 3.5 7.5 + - - -
270A ALA* 3.0 27.5 + - - +
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Residues in contact with PHE 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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233A ILE* 4.9 7.6 - - + +
236A GLU* 2.9 62.6 - - + -
237A ALA* 4.0 8.3 - - + -
240A ARG* 3.5 35.0 - - + -
263A HIS 2.8 13.6 + - - +
264A VAL* 4.2 3.8 - - - +
266A GLU* 1.3 81.6 - - - +
268A SER* 1.3 60.9 + - - +
269A THR 3.1 1.3 - - - -
270A ALA* 3.2 10.7 + - + +
271A TRP* 2.8 28.2 + - - +
279A ARG* 3.8 22.2 - - - -
282A HIS 4.9 5.8 - - - -
284A GLN* 4.0 17.0 - - + -
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Residues in contact with SER 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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196A ILE* 3.4 19.5 - - - +
197A LEU* 3.4 13.9 - - - +
229A LEU* 6.0 0.2 - - - -
233A ILE* 4.9 12.4 - - - +
264A VAL* 2.6 17.9 + - - -
265A VAL* 2.5 25.3 + - - -
267A PHE* 1.3 78.8 - - - +
269A THR* 1.3 59.9 + - - +
271A TRP* 3.2 30.9 + - - +
272A LEU* 3.2 17.6 + - - +
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Residues in contact with THR 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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197A LEU* 3.5 16.8 - - - +
265A VAL* 2.7 28.8 + - - +
266A GLU* 3.6 8.3 - - - -
267A PHE 3.1 0.2 - - - -
268A SER* 1.3 73.8 - - - +
270A ALA* 1.3 62.7 + - - +
272A LEU* 3.3 25.7 - - + +
273A GLN* 3.0 18.9 + - - +
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Residues in contact with ALA 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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266A GLU* 3.0 22.1 + - - +
267A PHE* 3.2 19.0 + - + +
269A THR* 1.3 72.7 - - - +
271A TRP* 1.3 64.4 + - - +
272A LEU 3.0 1.6 - - - -
273A GLN* 2.8 38.5 + - - +
279A ARG* 6.1 0.2 - - - +
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Residues in contact with TRP 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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193A THR* 4.9 14.1 - - + -
196A ILE* 6.1 3.8 - - + -
228A GLY 5.6 7.2 - - - -
233A ILE* 4.5 15.7 - - + -
267A PHE 2.8 13.5 + - - +
268A SER* 3.2 28.7 + - - +
270A ALA* 1.3 76.6 - - - +
272A LEU* 1.3 79.5 + - + +
273A GLN* 2.8 2.3 + - - +
274A GLY 3.7 6.6 + - - -
279A ARG* 4.0 45.9 - - + +
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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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193A THR* 5.8 3.8 - - - +
197A LEU* 4.7 18.4 - - + -
268A SER 3.2 14.2 + - - +
269A THR* 3.3 31.4 - - + +
270A ALA 3.0 0.4 - - - -
271A TRP* 1.3 96.1 - - + +
273A GLN* 1.3 68.3 + - - +
274A GLY 3.0 3.8 + - - +
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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