Contacts of the helix formed by residues 254 - 270 (chain A) in PDB entry 2VL7
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 ASP 254 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A LYS* 5.3 5.0 - - - +
252A LEU 3.5 3.0 + - - -
253A PRO* 1.3 77.7 - - - +
255A ARG* 1.3 59.9 + - - +
256A GLU* 3.3 8.6 + - - +
257A THR* 2.8 33.9 + - - -
258A ASN* 2.9 23.8 + - - +
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Residues in contact with ARG 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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254A ASP* 1.3 76.8 - - - +
256A GLU* 1.3 65.5 + - + +
258A ASN* 3.5 7.0 + - + +
259A GLY* 3.1 18.5 + - - -
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Residues in contact with GLU 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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223A LYS* 2.9 42.3 + - + -
254A ASP* 3.3 6.5 + - - +
255A ARG* 1.3 76.3 - - + +
257A THR* 1.3 61.7 + - - +
259A GLY* 3.2 3.7 + - - -
260A GLU* 3.0 30.3 + - + +
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Residues in contact with THR 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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223A LYS* 3.4 48.5 + - - +
224A VAL* 3.8 7.2 - - + +
227A TYR* 3.7 21.3 - - + +
253A PRO* 3.9 10.8 - - + -
254A ASP* 2.8 29.2 + - - -
256A GLU* 1.3 74.0 - - - +
258A ASN* 1.3 59.6 + - - +
260A GLU* 3.2 3.4 + - - +
261A LEU* 2.8 30.1 + - + +
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Residues in contact with ASN 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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253A PRO* 3.8 17.1 + - + +
254A ASP 2.9 17.7 + - - +
255A ARG* 3.6 8.5 - - + +
257A THR* 1.3 77.0 - - - +
259A GLY* 1.3 60.9 + - - +
261A LEU* 3.4 5.8 + - - +
262A ILE* 3.1 40.7 + - - +
285A LEU* 4.7 10.7 - - - +
288A VAL* 4.2 23.4 - - - +
289A GLU* 5.1 6.0 - - - +
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Residues in contact with GLY 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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255A ARG 3.1 14.4 + - - -
256A GLU* 3.2 4.9 + - - -
258A ASN* 1.3 77.7 + - - +
260A GLU* 1.3 58.6 + - - +
262A ILE* 3.4 9.7 + - - +
263A VAL* 3.0 30.4 + - - +
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Residues in contact with GLU 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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220A ASP* 3.8 19.4 - - - +
221A ALA* 3.4 21.7 - - + -
222A LYS 4.9 0.3 + - - -
223A LYS* 3.5 42.2 + - - +
224A VAL* 3.4 15.4 + - + +
256A GLU* 3.0 13.9 + - - +
257A THR 3.2 4.0 + - - +
259A GLY* 1.3 72.0 - - - +
261A LEU* 1.3 58.4 + - - +
263A VAL* 3.0 7.7 + - - +
264A VAL* 2.7 36.4 + - - +
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Residues in contact with LEU 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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224A VAL* 3.4 28.0 - - + +
227A TYR* 6.0 1.6 - - + -
253A PRO* 4.5 20.0 - - + -
257A THR* 2.8 18.5 + - + +
258A ASN* 3.5 8.5 - - - +
260A GLU* 1.3 77.1 - - - +
262A ILE* 1.3 59.0 + - - +
264A VAL* 4.0 1.6 - - + -
265A THR* 2.6 44.9 + - - +
281A LEU* 4.0 18.8 - - + +
284A LEU* 4.3 21.8 - - + -
285A LEU* 3.6 33.9 - - + -
288A VAL* 5.0 2.7 - - + -
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Residues in contact with ILE 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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258A ASN* 3.1 33.5 + - - +
259A GLY* 3.6 10.1 - - - +
261A LEU* 1.3 75.3 - - - +
263A VAL* 1.3 58.7 + - + +
265A THR* 3.7 1.6 - - - -
266A ARG* 3.0 55.8 + - - +
285A LEU* 4.0 29.2 - - + +
289A GLU* 4.6 9.9 - - - +
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Residues in contact with VAL 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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219A ILE* 4.8 13.9 - - + -
259A GLY 3.0 18.2 - - - +
260A GLU* 3.0 9.5 + - - +
262A ILE* 1.3 77.2 - - + +
264A VAL* 1.3 64.6 + - - +
266A ARG* 3.2 20.6 + - - +
267A ALA* 3.0 23.3 + - + +
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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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210A ILE* 4.2 20.6 - - + -
213A VAL* 4.0 28.9 - - + -
214A GLU* 6.0 0.4 - - + -
219A ILE* 4.7 8.3 - - + +
221A ALA* 4.4 18.6 - - + -
224A VAL* 4.5 6.7 - - + -
260A GLU 2.7 19.3 + - - +
261A LEU* 3.5 17.5 - - + +
263A VAL* 1.3 70.8 - - - +
265A THR* 1.3 64.0 + - - +
267A ALA* 3.5 4.5 + - - +
268A TYR* 3.0 28.1 + - - +
281A LEU* 4.0 21.4 - - + +
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Residues in contact with THR 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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261A LEU* 2.6 33.4 + - - +
262A ILE 3.7 3.6 - - - -
264A VAL* 1.3 77.5 - - - +
266A ARG* 1.3 57.8 + - - +
268A TYR* 3.2 4.2 + - - +
269A LEU* 2.9 38.4 + - + +
279A SER* 4.9 0.4 - - - +
281A LEU* 3.5 24.8 + - + +
282A LYS* 3.6 37.7 - - + +
285A LEU* 4.0 15.0 - - + +
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Residues in contact with ARG 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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262A ILE* 3.0 45.6 + - - +
263A VAL* 3.7 20.0 + - - +
265A THR* 1.3 77.1 - - - +
267A ALA* 1.3 57.5 + - - +
269A LEU* 3.6 11.1 + - + +
270A ASN* 3.0 46.0 + - - +
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Residues in contact with ALA 267 (chain A).
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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213A VAL* 3.9 13.0 - - + -
217A ASN* 3.3 29.8 + - + +
219A ILE* 5.2 3.8 - - + -
263A VAL* 3.0 17.5 + - + +
264A VAL* 3.8 4.9 - - - +
266A ARG* 1.3 75.8 - - - +
268A TYR* 1.3 65.7 + - - +
270A ASN* 3.3 8.6 + - - +
271A ILE* 3.0 21.1 + - - +
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Residues in contact with TYR 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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209A GLU* 3.3 62.4 + - + +
212A ILE* 4.1 18.4 - - + +
213A VAL* 3.7 15.1 - - + +
264A VAL 3.0 18.2 + - - +
265A THR 3.7 3.6 - - - +
267A ALA* 1.3 74.8 - - - +
269A LEU* 1.3 58.2 + - - +
271A ILE* 2.8 31.2 + - + -
272A ASP* 3.0 47.6 + - - -
278A LYS 4.3 2.7 + - - -
279A SER* 3.4 15.0 - - - -
281A LEU* 4.1 8.3 - - + -
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Residues in contact with LEU 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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265A THR* 2.9 32.7 + - + +
266A ARG* 3.8 10.3 - - + +
267A ALA 3.3 0.2 - - - -
268A TYR* 1.3 76.1 - - - +
270A ASN* 1.3 57.6 + - - +
271A ILE 3.1 0.2 - - - -
272A ASP* 3.3 32.0 + - + +
277A LYS* 3.8 17.0 - - + +
279A SER* 3.6 30.1 - - - +
282A LYS* 3.7 27.6 - - + +
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Residues in contact with ASN 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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217A ASN* 6.2 0.2 - - - +
266A ARG* 3.0 40.6 + - - +
267A ALA* 3.3 8.0 + - - +
268A TYR 3.2 0.4 - - - -
269A LEU* 1.3 75.7 - - - +
271A ILE* 1.3 65.5 + - - +
272A ASP 4.7 2.7 - - - +
273A GLU* 5.5 4.3 - - - +
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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