Contacts of the helix formed by residues 267 - 285 (chain A) in PDB entry 1VJZ
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 PRO 267 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A TYR* 5.5 0.9 - - + -
221A PRO* 4.1 17.9 - - + +
265A LYS 4.0 4.9 - - - +
266A THR* 1.3 90.5 - - + +
268A HIS* 1.3 66.8 - - - +
269A ASP* 3.7 17.5 - - - +
270A VAL* 3.0 23.2 + - + +
271A VAL* 3.1 10.2 + - - +
307A ASP* 3.4 11.0 - - - +
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Residues in contact with HIS 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A THR 3.4 2.8 + - - -
267A PRO* 1.3 72.9 - - - +
269A ASP* 1.3 63.4 + - - +
271A VAL* 3.3 5.2 + - + +
272A LEU* 3.0 61.2 + - + +
305A ARG* 4.0 13.9 - - - +
307A ASP* 2.8 31.3 + - - +
308A VAL* 3.6 26.2 - - + +
319A ASP* 2.7 38.7 + - - -
321A LYS* 4.2 18.0 - - + -
322A MSE 4.8 3.1 - - + -
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Residues in contact with ASP 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A PRO* 3.2 16.9 - - - +
268A HIS* 1.3 78.9 - - - +
270A VAL* 1.3 76.1 + - - +
272A LEU* 4.3 4.6 - - - +
273A LYS* 3.0 29.5 + - - +
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Residues in contact with VAL 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A VAL* 3.8 28.5 - - + -
221A PRO* 4.1 18.8 - - + +
222A GLU* 4.0 17.0 - - - -
223A TRP* 4.1 7.0 - - + +
266A THR* 3.9 13.7 - - + -
267A PRO* 3.0 21.3 + - + +
269A ASP* 1.3 91.1 - - - +
271A VAL* 1.3 66.9 + - - +
273A LYS* 3.9 3.7 - - - +
274A TRP* 2.9 24.0 + - - +
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Residues in contact with VAL 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A VAL* 4.7 7.2 - - - -
262A ALA* 4.0 24.0 - - + +
266A THR* 3.7 19.5 - - + -
267A PRO 3.1 14.1 + - - +
268A HIS* 3.7 9.0 - - + +
270A VAL* 1.3 77.4 - - - +
272A LEU* 1.3 55.2 + - + +
274A TRP* 3.6 4.0 - - + -
275A LEU* 2.7 44.0 + - + +
305A ARG* 3.7 24.7 - - - +
322A MSE 3.6 31.0 - - + -
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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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268A HIS* 3.0 49.3 + - + +
269A ASP* 4.3 4.9 - - - +
271A VAL* 1.3 72.8 - - + +
273A LYS* 1.3 66.3 + - - +
275A LEU* 4.3 1.3 - - + -
276A GLU* 3.0 26.9 + - - +
321A LYS* 4.0 25.4 - - + +
322A MSE 3.9 36.8 - - + -
325A LEU* 3.6 25.7 - - + +
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Residues in contact with LYS 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A TRP* 3.6 35.8 + - + +
224A PRO* 3.6 16.7 - - - +
269A ASP* 3.0 21.7 + - - +
270A VAL* 3.9 4.5 - - - +
272A LEU* 1.3 78.4 - - - +
274A TRP* 1.3 62.3 + - - +
276A GLU* 3.8 4.5 - - - +
277A ASP* 3.2 27.3 + - - +
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Residues in contact with TRP 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A GLY 3.3 26.9 - - - -
201A ILE 2.8 24.3 + - - -
202A PRO* 3.4 16.7 - - + +
205A VAL* 3.9 19.7 - - + -
206A THR* 3.6 19.7 - - + -
223A TRP* 3.5 39.1 - + + +
238A LEU* 4.4 7.9 - - + +
261A GLY* 3.7 26.9 - - - -
262A ALA* 4.1 8.1 - - + -
270A VAL 2.9 17.4 + - - +
271A VAL* 3.7 9.6 - - + -
273A LYS* 1.3 76.0 - - - +
275A LEU* 1.3 92.6 + - + +
276A GLU 3.2 0.2 + - - -
277A ASP* 3.2 4.5 + - - +
278A LEU* 3.0 39.4 + - + +
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Residues in contact with LEU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A MSE 4.2 25.8 - - + -
261A GLY* 5.3 0.9 - - - -
271A VAL* 2.7 24.6 + - + +
272A LEU* 3.9 5.2 - - + +
274A TRP* 1.3 96.0 - - + +
276A GLU* 1.3 57.8 + - - +
278A LEU* 3.2 4.2 + - + +
279A LEU* 2.8 53.3 + - + +
291A LEU* 5.0 7.0 - - + -
322A MSE 3.9 37.5 - - + -
325A LEU* 4.0 13.0 - - + -
326A LEU* 4.5 11.9 - - + -
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Residues in contact with GLU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LEU 3.0 18.1 + - - +
273A LYS* 3.8 4.6 - - - +
275A LEU* 1.3 73.1 - - - +
277A ASP* 1.3 64.4 + - - +
279A LEU* 3.8 2.9 - - - +
280A GLU* 2.9 34.2 + - + +
325A LEU* 3.7 23.7 - - + +
328A LYS* 3.2 18.4 + - - -
329A TYR* 2.6 33.7 + - + +
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Residues in contact with ASP 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A TRP* 2.7 36.8 + - + +
224A PRO* 5.5 1.7 - - - +
235A ARG* 3.8 30.8 + - + +
238A LEU* 5.0 1.3 - - + -
273A LYS* 3.2 12.0 + - - +
274A TRP 3.6 7.6 - - - +
276A GLU* 1.3 81.7 - - - +
278A LEU* 1.3 63.3 + - - +
280A GLU* 3.3 5.9 + - - +
281A ILE* 3.2 28.4 + - - +
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Residues in contact with LEU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A GLY* 4.0 15.7 - - - -
201A ILE 5.5 0.7 - - - +
238A LEU* 4.4 17.6 - - + +
242A TYR* 3.4 35.2 - - + +
260A MSE 3.9 24.5 - - + -
274A TRP* 3.0 43.6 + - + +
275A LEU* 3.6 9.4 - - + +
277A ASP* 1.3 77.6 - - - +
279A LEU* 1.3 57.4 + - - +
281A ILE* 3.2 8.1 + - + +
282A PHE* 3.0 43.9 + - + -
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Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A MSE 3.8 31.9 - - + -
275A LEU* 2.8 31.7 + - + +
276A GLU 3.8 3.4 - - - +
278A LEU* 1.3 73.3 - - - +
280A GLU* 1.3 57.8 + - - +
282A PHE* 3.3 6.8 + - + +
283A LYS* 2.9 29.6 + - - +
289A PHE* 3.9 25.1 - - + -
325A LEU* 3.8 37.9 - - + +
326A LEU* 3.8 21.3 - - + -
329A TYR* 3.9 19.7 - - + +
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Residues in contact with GLU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ARG* 2.8 34.0 + - - +
276A GLU* 2.9 20.4 + - + +
277A ASP* 3.6 6.7 - - - +
279A LEU* 1.3 74.3 - - - +
281A ILE* 1.3 58.4 + - - +
283A LYS* 3.4 2.9 + - + +
284A THR* 2.9 36.3 + - - +
329A TYR* 3.6 31.6 - - + +
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Residues in contact with ILE 281 (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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235A ARG* 3.6 35.7 - - + +
238A LEU* 3.6 20.9 - - + -
239A LEU* 3.6 39.7 - - + +
242A TYR* 4.3 17.3 - - + -
277A ASP 3.2 16.1 + - - +
278A LEU* 3.5 6.7 - - - +
280A GLU* 1.3 75.5 - - - +
282A PHE* 1.3 56.8 + - + +
284A THR* 3.3 5.0 + - - -
285A LEU* 2.7 62.6 + - + +
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Residues in contact with PHE 282 (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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7A ARG* 3.8 4.0 + - - +
242A TYR* 3.7 35.4 - + - -
257A CYS* 3.6 38.4 - - + -
260A MSE 4.0 13.5 - - - -
278A LEU* 3.0 46.9 + - + +
279A LEU* 3.6 9.9 - - - +
280A GLU 3.3 0.4 - - - -
281A ILE* 1.3 79.9 - - + +
283A LYS* 1.3 51.7 + - - +
286A ASN* 2.7 12.8 + - - -
287A ILE* 2.6 64.5 + - + +
289A PHE* 4.0 20.2 - + + -
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Residues in contact with LYS 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ARG* 3.8 23.0 + - - +
279A LEU 2.9 16.6 + - - +
280A GLU* 3.8 4.3 - - + +
282A PHE* 1.3 73.6 - - - +
284A THR* 1.3 67.7 + - - +
286A ASN* 3.1 13.7 + - - +
328A LYS 4.4 12.6 + - - -
329A TYR* 3.8 37.1 - - + +
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Residues in contact with THR 284 (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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235A ARG* 4.8 5.1 + - - +
239A LEU* 5.7 3.1 - - + -
280A GLU* 2.9 31.8 + - - +
281A ILE* 3.5 6.5 - - - -
283A LYS* 1.3 79.5 - - - +
285A LEU* 1.3 74.2 + - + +
286A ASN* 3.4 1.6 + - - +
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LEU* 4.2 10.3 - - + -
242A TYR* 3.8 33.7 - - + +
243A LEU* 3.8 26.7 - - + +
246A ILE* 4.2 13.0 - - + -
249A ARG* 2.9 30.4 + - - +
281A ILE* 2.7 43.3 + - + +
284A THR* 1.3 84.2 - - + +
286A ASN* 1.3 64.6 + - - +
287A ILE* 3.3 14.1 - - + -
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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
------------------------------------------------------------
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