Contacts of the helix formed by residues 258 - 278 (chain A) in PDB entry 2V4R
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 ASN 258 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A SER* 2.8 10.6 + - - +
257A ARG* 1.3 76.5 - - - +
259A LEU* 1.3 62.0 + - - +
260A GLU* 2.4 44.0 + - - +
261A GLU* 2.7 31.6 + - + +
262A ILE* 3.1 19.1 + - - +
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Residues in contact with LEU 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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257A ARG 3.5 4.4 + - - -
258A ASN* 1.3 73.1 + - - +
260A GLU* 1.3 62.3 + - + +
262A ILE* 3.4 4.0 + - - +
263A LYS* 2.8 54.1 + - + +
317A VAL* 4.1 10.5 - - + -
320A LEU* 3.9 25.6 - - + -
321A GLN* 3.4 46.0 - - + +
324A LEU* 4.4 13.7 - - + -
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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
----------------------------------------------------------
258A ASN* 2.4 26.0 + - - +
259A LEU* 1.3 76.9 - - + +
261A GLU* 1.3 58.8 + - - -
263A LYS* 2.5 46.4 + - - +
264A PRO* 3.4 18.7 - - - +
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Residues in contact with GLU 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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252A MET* 4.7 2.2 - - - +
254A ARG* 3.1 39.5 + - - +
255A ASN 3.9 2.4 - - - +
256A SER* 2.9 35.0 + - - +
258A ASN* 2.7 34.2 + - + +
260A GLU* 1.3 73.5 - - - +
262A ILE* 1.3 62.3 + - - +
264A PRO* 3.8 6.3 - - - +
265A TYR* 3.7 19.9 - - + -
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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
----------------------------------------------------------
252A MET* 3.8 23.1 - - + -
256A SER* 4.1 13.2 - - - +
257A ARG 4.0 13.7 - - - -
258A ASN 3.1 23.5 + - - +
259A LEU* 4.0 2.9 - - - +
260A GLU 3.3 0.2 - - - -
261A GLU* 1.3 80.6 - - - +
263A LYS* 1.3 65.8 + - - +
264A PRO 3.4 0.9 - - - -
265A TYR* 3.0 14.3 + - - +
266A LEU* 3.1 7.7 + - + -
320A LEU* 3.7 20.0 - - + -
324A LEU* 4.3 8.7 - - + -
331A ILE* 4.1 24.0 - - + -
334A ILE* 3.8 31.6 - - + -
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Residues in contact with LYS 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A LEU* 2.8 48.3 + - + +
260A GLU* 2.5 44.2 + - - +
262A ILE* 1.3 74.3 - - - +
264A PRO* 1.3 61.7 - - + +
266A LEU* 3.0 9.3 + - + +
267A PHE* 2.7 65.6 + - + -
317A VAL* 4.5 17.2 - - + +
320A LEU* 4.8 4.2 - - + +
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Residues in contact with PRO 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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260A GLU 3.4 17.5 - - - +
261A GLU 3.8 7.0 - - - +
262A ILE 3.5 3.1 - - - -
263A LYS* 1.3 95.6 - - + +
265A TYR* 1.3 61.4 + - + +
267A PHE* 4.0 9.3 - - + +
268A ARG* 3.1 45.8 + - - +
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Residues in contact with TYR 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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250A VAL* 3.7 23.1 - - + +
251A THR 3.8 14.1 - - - -
252A MET* 3.3 26.7 - - + -
253A LYS* 3.0 43.7 + - + +
261A GLU* 3.7 21.3 - - + -
262A ILE 3.0 7.0 + - - +
264A PRO* 1.3 80.3 - - + +
266A LEU* 1.3 60.4 + - - +
268A ARG* 3.2 25.7 + - - +
269A ALA* 2.9 28.2 + - - +
334A ILE* 3.6 19.5 - - + -
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Residues in contact with LEU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ILE 3.1 8.3 + - - +
263A LYS* 3.0 10.0 + - - +
265A TYR* 1.3 77.9 - - - +
267A PHE* 1.3 66.3 + - + +
269A ALA* 3.2 6.6 + - - +
270A ILE* 3.0 27.1 + - + +
287A VAL* 4.2 7.0 - - + -
316A SER* 3.7 36.1 - - - +
317A VAL* 4.4 5.6 - - + +
320A LEU* 3.6 30.7 - - + -
334A ILE* 3.9 20.3 - - + +
335A GLY 4.2 11.4 - - - +
336A VAL* 3.5 32.3 - - + -
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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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263A LYS* 2.7 49.0 + - + +
264A PRO* 4.0 8.3 - - + +
266A LEU* 1.3 75.7 - - + +
268A ARG* 1.3 64.3 + - - +
270A ILE* 3.4 10.6 + - + +
271A GLU* 3.2 27.0 + - - +
313A TYR* 3.4 42.0 + + + +
316A SER* 3.9 9.4 - - - -
317A VAL* 3.7 31.0 - - + -
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Residues in contact with ARG 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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250A VAL* 5.5 8.4 - - + +
264A PRO* 3.1 37.3 + - - +
265A TYR* 3.2 40.2 + - - +
267A PHE* 1.3 76.0 - - - +
269A ALA* 1.3 65.0 + - - +
271A GLU* 3.0 20.1 + - + +
272A GLU* 3.2 31.4 + - - +
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Residues in contact with ALA 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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248A ARG* 3.5 30.1 - - - +
250A VAL* 4.7 10.0 - - + +
265A TYR 2.9 13.9 + - - +
266A LEU* 3.3 10.3 - - - +
268A ARG* 1.3 77.1 - - - +
270A ILE* 1.3 53.5 + - - +
272A GLU* 3.8 5.5 + - - +
273A SER* 2.4 34.4 + - - -
334A ILE 4.5 3.4 - - - +
335A GLY* 4.0 15.9 - - - -
336A VAL* 3.8 3.8 - - + -
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Residues in contact with ILE 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 LEU* 3.0 19.5 + - + +
267A PHE* 3.6 20.0 - - + +
268A ARG 3.1 0.2 - - - -
269A ALA* 1.3 75.0 - - - +
271A GLU* 1.3 60.8 + - - +
273A SER* 3.0 4.1 + - - -
274A TYR* 2.8 50.7 + - + -
285A ILE* 5.5 0.2 - - + -
309A LYS* 4.8 0.4 - - + -
312A ALA* 3.9 11.9 - - + +
313A TYR* 4.0 25.8 - - + -
316A SER* 3.4 35.9 - - - +
336A VAL* 3.7 25.1 - - + -
338A PHE* 4.4 2.9 - - + -
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Residues in contact with GLU 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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267A PHE 3.2 9.1 + - - +
268A ARG* 3.0 12.7 + - + +
270A ILE* 1.3 79.1 - - - +
272A GLU* 1.3 57.9 + - + +
274A TYR* 3.2 5.9 + - - +
275A TYR* 2.9 30.1 + - - +
309A LYS* 3.6 26.6 + - - +
313A TYR* 2.4 32.7 + - - +
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Residues in contact with GLU 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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248A ARG* 4.2 30.6 + - + +
250A VAL* 5.2 9.1 - - - +
268A ARG* 3.2 33.9 + - + +
269A ALA* 4.1 5.4 - - - +
271A GLU* 1.3 79.5 - - + +
273A SER* 1.3 63.6 + - - +
275A TYR* 3.3 8.9 + - + -
276A LYS* 2.9 38.7 + - + +
6T G 5.5 0.3 + - - -
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Residues in contact with SER 273 (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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246A ILE* 3.7 7.3 - - - +
247A GLY* 3.8 4.8 - - - -
248A ARG* 3.6 18.3 + - - +
269A ALA 2.4 22.7 + - - -
270A ILE 3.0 9.4 + - - -
272A GLU* 1.3 77.7 - - - +
274A TYR* 1.3 58.5 + - - +
276A LYS* 3.3 7.4 + - - +
277A LEU* 2.9 29.8 + - - +
336A VAL* 3.2 13.2 - - - +
338A PHE* 3.4 27.1 - - - -
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Residues in contact with TYR 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ILE* 2.8 26.9 + - + +
271A GLU 3.6 4.3 - - - +
273A SER* 1.3 73.6 - - - +
275A TYR* 1.3 66.6 - - - +
276A LYS 2.9 2.7 + - - -
277A LEU* 3.1 34.3 + - + +
278A ASP* 3.4 9.5 + - - -
282A PRO* 4.5 2.1 - - + +
307A ILE* 2.9 29.7 + - - +
308A SER* 3.0 10.1 + - - -
309A LYS* 3.7 51.1 - - + +
312A ALA* 3.6 12.7 - - + +
338A PHE* 3.2 33.5 - + - -
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Residues in contact with TYR 275 (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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271A GLU 2.9 15.9 + - - +
272A GLU* 3.7 10.1 - - + +
274A TYR* 1.3 76.6 - - - +
276A LYS* 1.3 83.8 + - + +
278A ASP* 4.0 11.8 - - - +
309A LYS* 5.8 0.4 - - - +
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Residues in contact with LYS 276 (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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80A GLU* 3.3 35.6 + - - +
246A ILE* 3.8 15.7 - - + -
248A ARG* 3.1 39.5 - - - +
272A GLU* 2.9 32.6 + - - +
273A SER* 3.5 5.2 - - - +
274A TYR 2.9 0.6 - - - -
275A TYR* 1.3 102.6 - - + +
277A LEU* 1.3 68.7 + - - +
278A ASP* 3.1 8.6 + - - +
280A ARG* 3.7 10.0 + - - -
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ILE* 3.8 19.0 - - + +
273A SER 2.9 17.4 + - - +
274A TYR* 3.1 39.9 + - + +
276A LYS* 1.3 76.8 - - - +
278A ASP* 1.3 71.3 + - - +
279A LYS 3.8 0.7 - - - +
280A ARG* 3.1 43.9 + - + +
282A PRO* 3.6 28.5 - - + -
338A PHE* 4.4 9.2 - - + -
341A PHE* 3.5 32.3 - - + -
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Residues in contact with ASP 278 (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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274A TYR 3.4 8.1 + - - -
275A TYR 4.0 10.6 - - - +
276A LYS 3.1 9.1 - - - +
277A LEU* 1.3 87.8 - - - +
279A LYS* 1.3 90.2 + - - +
280A ARG* 3.1 6.4 + - - +
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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
------------------------------------------------------------
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