Contacts of the helix formed by residues 276 - 292 (chain A) in PDB entry 3S3J
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 GLN 276 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A ARG 3.1 19.7 + - - +
241A TRP* 3.3 27.8 - - + +
245A TYR* 3.2 19.2 + - - -
251A PRO* 3.8 9.7 - - + +
252A MET* 4.7 6.1 - - - +
275A GLY* 1.3 78.2 - - - +
277A CYS* 1.3 67.8 + - - +
278A TRP* 3.2 28.9 - - + -
279A VAL* 2.9 19.9 + - - +
280A PHE* 2.9 20.8 + - - -
277B PHQ 3.7 1.3 + - - +
278B 02Y 2.8 36.4 + - - +
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Residues in contact with CYS 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A TRP* 4.2 1.6 - - - -
276A GLN* 1.3 69.8 - - - +
278A TRP* 1.3 73.7 + - - +
280A PHE* 3.1 5.1 + - - +
281A ALA* 3.0 24.1 + - - +
334A PHE* 3.9 12.6 - - - -
335A HIS* 3.6 14.6 - - + +
336A CYS* 3.6 19.8 - - - +
360A THR* 3.3 25.9 + - + +
278B 02Y 1.8 59.3 + - + +
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Residues in contact with TRP 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 3.7 26.6 - - + +
169A GLN* 3.2 27.1 - - - +
178A ILE* 4.3 10.2 - - + +
180A TRP* 4.2 15.4 - + - -
251A PRO* 3.4 29.5 + - + -
252A MET* 3.7 25.5 - - + +
254A TRP 5.6 0.2 + - - -
276A GLN* 3.2 38.8 - - + -
277A CYS* 1.3 83.0 - - - +
279A VAL* 1.3 75.9 + - + +
281A ALA* 3.8 1.7 - - - +
282A ALA* 2.8 30.7 + - - +
334A PHE* 3.9 20.2 - + + -
336A CYS* 3.7 18.6 - - - -
277B PHQ 4.1 8.1 - + - -
278B 02Y 3.7 12.6 - - + -
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Residues in contact with VAL 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A TRP* 4.1 8.5 - - + -
237A LEU* 3.8 16.8 - - + -
251A PRO* 3.5 15.5 - - + +
254A TRP* 4.1 13.5 - - + -
260A ILE* 3.8 28.5 - - + -
275A GLY* 4.2 1.3 - - - -
276A GLN 2.9 21.2 + - - +
278A TRP* 1.3 104.1 - - + +
280A PHE* 1.3 64.8 + - - +
282A ALA* 3.8 4.0 - - - +
283A VAL* 3.2 24.3 + - - +
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Residues in contact with PHE 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A VAL* 3.3 35.2 - - + +
229A ASN* 3.6 19.3 - - + -
237A LEU* 3.5 28.0 - - + -
239A GLY* 3.7 27.8 - - - -
241A TRP* 4.2 4.9 - + - -
275A GLY* 3.9 12.3 - - - -
276A GLN* 2.9 40.2 + - - -
277A CYS 3.6 5.8 - - - +
279A VAL* 1.3 77.0 - - - +
281A ALA* 1.3 62.6 + - - +
283A VAL 3.6 0.2 + - - -
284A ALA* 3.1 21.8 + - - +
359A PRO* 3.8 21.0 - - + +
360A THR* 3.9 13.0 - - - +
361A PRO* 3.8 18.4 - - + -
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Residues in contact with ALA 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A CYS 3.0 15.6 + - - +
278A TRP 3.8 4.3 - - - +
280A PHE* 1.3 75.5 - - - +
282A ALA* 1.3 63.9 + - - +
284A ALA 3.5 0.5 + - - -
285A CYS* 3.0 21.0 + - - +
297A VAL* 3.8 8.9 - - + +
336A CYS* 4.1 7.9 - - + +
337A TRP* 3.8 38.6 - - - +
338A VAL* 3.3 15.1 - - + +
359A PRO* 4.1 7.4 - - + +
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Residues in contact with ALA 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 3.5 11.9 - - + -
180A TRP* 3.2 40.6 - - + +
182A PHE* 3.6 9.9 - - - -
257A SER* 3.4 2.4 + - - -
278A TRP 2.8 18.6 + - - +
279A VAL 3.8 1.8 - - - +
280A PHE 3.3 0.2 - - - -
281A ALA* 1.3 77.8 - - - +
283A VAL* 1.3 63.4 + - - +
285A CYS* 3.2 5.0 + - - +
286A THR* 3.0 23.4 + - - -
297A VAL* 4.1 3.5 - - - +
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Residues in contact with VAL 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A VAL* 4.4 14.1 - - + -
236A VAL* 4.6 10.1 - - + -
237A LEU* 3.9 15.3 - - + -
257A SER* 3.6 16.8 - - - +
260A ILE* 4.2 24.0 - - + -
261A LEU* 3.7 30.3 - - + -
279A VAL* 3.2 17.3 + - + +
280A PHE 3.9 3.6 - - - +
282A ALA* 1.3 74.0 - - + +
284A ALA* 1.3 66.0 + - - +
286A THR* 3.0 4.9 + - - -
287A VAL* 2.9 24.9 + - + +
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Residues in contact with ALA 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A VAL* 4.1 12.8 - - + -
225A SER* 5.9 0.7 - - - -
228A VAL* 3.8 21.0 - - + +
280A PHE 3.1 15.1 + - - +
281A ALA 3.6 4.3 - - - +
283A VAL* 1.3 77.8 - - - +
285A CYS* 1.3 62.9 - - - +
287A VAL* 3.1 2.1 + - - +
288A LEU* 2.9 34.7 + - + +
338A VAL* 4.2 9.6 - - + -
359A PRO* 4.1 15.0 - - + -
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Residues in contact with CYS 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A PHE* 3.8 17.3 - - + -
281A ALA 3.0 14.9 + - - +
282A ALA 3.4 9.0 - - - +
283A VAL 3.2 0.2 - - - -
284A ALA* 1.3 75.4 - - - +
286A THR* 1.3 57.9 + - - +
288A LEU* 3.5 0.9 + - - +
289A ARG* 2.9 64.6 + - - +
295A THR* 3.8 31.4 - - + -
296A ARG* 4.2 2.2 - - - -
297A VAL* 3.8 17.3 - - + -
338A VAL* 4.2 0.9 - - + +
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Residues in contact with THR 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A PHE* 3.0 41.2 + - - +
184A GLN* 3.5 15.6 - - - +
189A ILE* 4.4 6.7 - - + -
257A SER* 2.8 25.3 + - - -
261A LEU* 3.8 24.0 - - + -
282A ALA 3.0 5.2 + - - -
283A VAL 3.0 9.4 + - - -
285A CYS* 1.3 78.3 - - - +
287A VAL* 1.3 61.6 + - - +
289A ARG* 3.4 1.1 + - - -
290A CYS* 3.0 23.0 + - - +
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Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A CYS* 3.8 32.1 - - + +
196A LEU* 4.6 19.1 - - + -
197A LEU* 5.8 0.2 - - + -
224A VAL* 3.8 30.7 - - + -
228A VAL* 5.6 0.7 - - + -
261A LEU* 4.3 14.4 - - + -
283A VAL* 2.9 29.6 + - + +
284A ALA* 3.1 6.9 + - - +
286A THR* 1.3 76.1 - - - +
288A LEU* 1.3 64.2 + - - +
290A CYS* 3.3 4.0 + - - +
291A LEU* 3.1 32.4 + - + +
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Residues in contact with LEU 288 (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 VAL* 4.7 2.2 - - + -
221A GLY* 4.0 16.8 - - - +
224A VAL* 3.9 34.3 - - + -
284A ALA* 2.9 22.5 + - + +
285A CYS 3.9 1.6 - - - +
287A VAL* 1.3 73.8 - - - +
289A ARG* 1.3 62.4 + - - +
291A LEU* 3.4 5.4 + - + +
292A GLY 3.0 4.3 + - - -
293A ILE* 2.9 47.5 + - + +
295A THR* 3.2 25.1 - - + +
338A VAL* 4.1 14.6 - - + -
340A SER* 3.5 19.7 - - - +
357A LEU* 4.1 7.4 - - + -
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Residues in contact with ARG 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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34A ARG* 5.2 0.3 + - - -
158A GLU* 3.2 27.7 + - - -
159A TYR* 3.1 29.1 + - - +
160A VAL* 3.9 18.8 - - - +
162A THR* 2.9 24.5 + - - +
164A GLN 4.8 2.8 + - - -
165A GLY* 5.9 0.2 - - - -
182A PHE* 3.9 21.9 - - - -
184A GLN* 3.7 26.2 - - - +
185A PHE* 4.5 3.5 - - - -
285A CYS* 2.9 33.4 + - - +
286A THR 3.9 3.1 - - - +
288A LEU* 1.3 71.7 - - - +
290A CYS* 1.3 60.6 + - - +
292A GLY* 2.8 24.1 + - - -
293A ILE 3.8 4.9 - - - +
295A THR* 2.9 31.9 + - - +
296A ARG* 4.1 10.7 - - - +
297A VAL 5.2 0.4 - - - +
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Residues in contact with CYS 290 (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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26A LEU* 4.6 4.4 - - - +
34A ARG* 5.1 0.5 + - - -
138A LEU* 3.4 19.8 - - - +
184A GLN* 3.3 31.1 - - + +
185A PHE* 4.4 9.9 - - - -
189A ILE* 4.3 1.1 - - + -
190A LEU* 3.6 41.5 - - - -
193A CYS* 3.9 15.9 - - - -
286A THR 3.0 14.8 + - - +
287A VAL 3.3 9.9 - - - +
289A ARG* 1.3 78.6 - - - +
291A LEU* 1.3 60.1 + - - +
292A GLY* 3.4 0.5 + - - -
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Residues in contact with LEU 291 (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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112A ILE* 4.0 20.9 - - + -
138A LEU* 3.5 14.7 - - + +
139A PHE* 3.1 36.0 + - + -
190A LEU* 4.2 20.6 - - + -
193A CYS* 4.3 12.8 - - + -
194A LEU* 4.4 12.3 - - + -
197A LEU* 4.2 18.2 - - + -
220A VAL* 3.9 24.7 - - + -
224A VAL* 4.7 1.1 - - + -
287A VAL* 3.1 31.8 + - + +
288A LEU* 4.0 5.6 - - - +
290A CYS* 1.3 75.1 - - - +
292A GLY* 1.3 58.1 + - - +
293A ILE* 3.5 2.7 - - + +
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Residues in contact with GLY 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ARG* 3.7 22.1 + - - -
139A PHE* 3.8 16.6 - - - +
141A ALA 4.5 3.5 + - - -
148A VAL* 4.1 4.0 - - - +
160A VAL* 4.3 12.0 - - - +
288A LEU 3.0 0.4 + - - -
289A ARG 2.8 16.5 + - - -
291A LEU* 1.3 80.6 - - - +
293A ILE* 1.3 61.2 + - - +
294A PRO* 3.3 11.3 - - - +
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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
------------------------------------------------------------
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