Contacts of the helix formed by residues 274 - 294 (chain A) in PDB entry 4FRA
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 VAL 274 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A PHE* 3.8 14.8 - - + +
201A LEU* 3.6 32.3 - - + -
204A VAL* 3.4 44.4 - - + +
205A ASP 3.4 11.6 + - - +
206A TYR 4.4 0.2 - - - +
207A LEU* 4.2 16.6 - - + -
272A GLY 3.8 0.6 + - - -
273A SER* 1.3 73.1 - - - +
275A GLN* 1.3 64.5 + - - +
277A VAL* 3.3 0.9 + - - +
278A GLN* 2.9 47.6 + - + +
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Residues in contact with GLN 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LEU* 4.5 11.0 - - + +
273A SER* 3.2 7.8 + - - +
274A VAL* 1.3 79.8 - - - +
276A GLU* 1.4 62.0 + - - +
278A GLN* 3.4 5.2 + - - +
279A ARG* 3.0 68.9 + - - +
282A ARG* 5.2 0.3 + - - -
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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
----------------------------------------------------------
227A PRO* 3.1 37.9 - - + +
228A LEU* 4.4 22.2 - - + +
273A SER* 3.1 14.6 + - - +
275A GLN* 1.4 78.9 + - + +
277A VAL* 1.3 61.5 + - - +
279A ARG* 2.7 40.6 + - - +
280A LEU* 3.0 28.4 + - - +
309A TYR* 4.6 8.5 + - - -
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Residues in contact with VAL 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ILE* 4.2 4.0 - - + -
207A LEU* 3.9 26.2 - - + +
209A CYS* 4.1 19.5 - - - -
228A LEU* 5.4 1.6 - - + -
270A PHE* 4.4 7.0 - - + -
271A GLY* 3.5 13.0 - - - +
272A GLY* 3.3 30.7 - - - +
273A SER 2.9 19.1 + - - +
274A VAL 3.9 2.7 - - - +
276A GLU* 1.3 76.3 - - - +
278A GLN* 1.3 60.7 + - - +
280A LEU* 3.3 5.1 + - - +
281A THR* 2.9 41.9 + - + +
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Residues in contact with GLN 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ILE* 2.8 37.8 + - - +
193A SER* 3.1 18.3 - - - +
197A GLU* 2.8 58.5 + - + +
200A PHE* 3.7 12.1 - - - -
201A LEU* 5.5 2.7 - - + -
207A LEU* 4.8 2.9 - - + -
274A VAL* 2.9 33.5 + - + +
275A GLN* 3.9 5.4 - - - +
277A VAL* 1.3 76.3 - - - +
279A ARG* 1.3 61.0 + - - +
281A THR* 3.3 2.1 + - - -
282A ARG* 2.9 33.6 + - - +
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Residues in contact with ARG 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A GLN* 3.0 48.7 + - + +
276A GLU* 2.7 46.7 + - - +
277A VAL 3.2 0.2 - - - -
278A GLN* 1.3 76.4 - - - +
280A LEU* 1.3 62.0 + - - +
282A ARG* 3.8 29.5 + - - +
283A ALA* 3.0 25.6 + - - +
309A TYR* 3.7 14.4 - - + +
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Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A MET* 3.9 27.6 - - + -
228A LEU* 3.8 21.1 - - + -
270A PHE* 4.0 18.2 - - + -
276A GLU 3.0 16.6 + - - +
277A VAL* 3.7 5.2 - - - +
279A ARG* 1.3 76.5 - - - +
281A THR* 1.3 68.7 + - + +
283A ALA* 3.3 2.3 + - - +
284A CYS* 2.9 37.2 + - - -
306A LEU* 3.6 24.7 - - + -
309A TYR* 3.7 38.7 + - + -
310A LEU* 4.1 4.7 - - + -
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Residues in contact with THR 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A MET* 3.5 41.2 - - - +
192A ILE* 3.8 23.2 - - + +
193A SER* 3.1 25.0 + - - -
270A PHE* 4.2 12.6 - - + -
277A VAL* 2.9 22.9 + - + +
278A GLN* 3.3 4.9 + - - -
280A LEU* 1.3 82.1 - - + +
282A ARG* 1.3 60.1 + - - +
284A CYS 3.4 0.3 + - - -
285A HIS* 2.9 31.4 + - - +
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Residues in contact with ARG 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A SER* 3.8 14.5 - - - -
197A GLU* 3.9 22.6 + - - -
275A GLN 5.2 0.2 + - - -
278A GLN* 2.9 20.2 + - - +
279A ARG* 3.8 41.7 + - - +
281A THR* 1.3 76.7 + - - +
283A ALA* 1.3 61.4 + - - +
285A HIS* 3.3 5.8 + - + +
286A GLN* 2.9 51.0 + - + +
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Residues in contact with ALA 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ARG 3.0 18.5 + - - +
280A LEU 3.7 0.2 - - - +
282A ARG* 1.3 76.8 - - - +
284A CYS* 1.3 58.7 + - - +
286A GLN* 3.4 8.0 + - - +
287A ALA* 2.9 29.1 + - - +
309A TYR* 3.6 29.2 - - + -
313A HIS* 5.8 0.4 - - + -
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Residues in contact with CYS 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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189A MET* 4.0 20.9 - - + -
280A LEU* 2.9 32.6 + - - +
281A THR 3.9 2.9 - - - +
283A ALA* 1.3 74.0 - - - +
285A HIS* 1.3 66.0 + - - +
287A ALA* 3.3 6.3 + - - +
288A MET* 2.9 31.1 + - + +
305A HIS* 3.7 39.9 - - + -
306A LEU* 3.7 11.0 - - - -
309A TYR* 4.2 9.6 - - - -
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Residues in contact with HIS 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ARG 6.1 0.4 + - - -
189A MET* 4.3 0.7 - - + -
190A GLU* 3.5 54.5 + - + +
193A SER* 4.6 7.0 - - - +
281A THR 2.9 18.2 + - - +
282A ARG* 3.6 6.3 - - + +
284A CYS* 1.3 76.6 - - - +
286A GLN* 1.3 65.2 + - + +
288A MET* 3.3 16.2 + - - +
289A MET* 3.0 55.1 + - + +
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Residues in contact with GLN 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ARG* 2.9 44.2 + - + +
283A ALA* 3.8 7.2 - - - +
285A HIS* 1.3 78.2 - - + +
287A ALA* 1.3 60.6 + - - +
289A MET* 3.2 24.2 + - + +
290A VAL* 3.0 28.8 + - + +
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Residues in contact with ALA 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A GLN* 3.7 26.5 - - + +
283A ALA 2.9 18.2 + - - +
284A CYS* 3.7 2.9 - - - +
286A GLN* 1.3 76.3 - - - +
288A MET* 1.3 60.9 + - - +
290A VAL* 3.3 5.2 + - - +
291A ASP* 3.0 22.7 + - - +
305A HIS* 3.5 23.8 - - + -
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Residues in contact with MET 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ARG 5.3 10.5 - - - +
189A MET* 3.5 30.3 - - + +
190A GLU 5.3 0.2 - - - +
284A CYS* 2.9 25.5 + - + +
285A HIS* 3.4 22.2 - - + +
287A ALA* 1.3 74.8 - - - +
289A MET* 1.3 58.4 + - - +
291A ASP* 3.4 4.1 + - - +
292A GLN* 2.9 37.3 + - - +
297A GLU* 6.2 0.9 - - - +
301A HIS 4.9 0.7 - - - -
302A ASP* 4.0 29.4 - - - -
305A HIS* 3.4 28.3 - - + +
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Residues in contact with MET 289 (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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285A HIS* 3.0 46.5 + - + +
286A GLN* 3.2 33.8 + - + +
288A MET* 1.3 75.0 - - + +
290A VAL* 1.3 64.9 + - + +
292A GLN* 3.3 15.5 + - - +
293A ALA* 3.0 24.4 + - - +
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Residues in contact with VAL 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A GLN* 3.6 34.1 - - + +
286A GLN* 3.0 17.0 + - + +
287A ALA* 3.6 7.9 - - - +
289A MET* 1.3 73.2 - - + +
291A ASP* 1.3 66.7 + - - +
293A ALA* 3.1 8.8 + - + +
294A ASN* 3.0 34.6 + - - +
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Residues in contact with ASP 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A GLN 4.2 2.1 - - - +
252A SER* 2.8 26.5 + - - -
253A GLN* 2.8 28.9 + - - +
287A ALA 3.0 14.0 + - - +
288A MET* 3.6 10.3 - - - +
290A VAL* 1.3 75.2 - - - +
292A GLN* 1.3 62.4 + - - +
294A ASN* 3.1 10.3 + - - +
295A GLY 3.1 0.2 + - - -
296A ILE* 2.9 50.9 + - - +
297A GLU* 5.3 1.3 - - - +
298A ALA 4.3 5.0 + - - -
305A HIS* 3.4 17.2 + - + +
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Residues in contact with GLN 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ARG* 4.2 19.4 - - - +
288A MET* 2.9 23.2 + - + +
289A MET* 3.4 17.8 - - - +
290A VAL 3.3 0.2 - - - -
291A ASP* 1.3 74.8 - - - +
293A ALA* 1.3 63.6 + - - +
295A GLY* 3.0 14.4 + - - -
296A ILE 3.8 4.4 + - - +
297A GLU* 5.1 11.5 + - - +
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Residues in contact with ALA 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A MET 3.0 10.0 + - - +
290A VAL* 3.1 11.2 + - + +
292A GLN* 1.3 80.8 - - - +
294A ASN* 1.3 63.8 + - - +
295A GLY 3.3 0.9 + - - -
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Residues in contact with ASN 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A GLN 4.8 9.8 - - - +
253A GLN* 4.8 2.6 + - - -
290A VAL* 3.0 34.6 + - - +
291A ASP* 3.1 8.1 + - - +
293A ALA* 1.3 82.6 + - - +
295A GLY* 1.3 60.7 + - - +
296A ILE* 3.4 10.5 + - + +
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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) + - + + + + + -
------------------------------------------------------------
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