Contacts of the helix formed by residues 292 - 307 (chain A) in PDB entry 1ISR
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 GLU 292 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLN* 4.8 1.7 - - - +
110A TRP* 3.8 36.0 + - + -
164A SER* 4.2 9.9 + - - -
232A THR* 2.9 26.1 + - + +
233A GLU 5.0 2.3 - - - +
236A TYR* 4.3 19.4 - - + +
263A SER* 2.9 24.1 + - - +
291A CYS* 1.3 76.4 - - - +
293A GLY* 1.3 66.8 + - - +
294A MET* 3.4 5.9 - - + +
295A THR* 3.3 12.9 + - - +
296A VAL* 3.2 14.9 + - - +
319A GLY* 4.0 7.6 - - - -
1001A GLU* 5.3 5.7 - - + +
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Residues in contact with GLY 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A GLU* 1.3 73.6 - - - +
294A MET* 1.3 61.4 + - - +
295A THR 3.1 0.2 - - - -
296A VAL* 3.0 5.3 + - - -
297A ARG* 2.9 24.6 + - - +
319A GLY* 3.3 23.1 + - - -
320A TRP 4.9 0.2 - - - -
323A ARG* 3.7 15.5 - - - +
326A VAL* 3.3 25.8 - - - +
1001A GLU* 5.2 0.6 + - - -
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Residues in contact with MET 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A HIS* 4.2 29.2 - - + +
71A ARG* 5.1 7.2 - - - +
263A SER* 4.2 29.6 - - - +
270A PHE* 4.7 1.4 - - - -
292A GLU* 3.4 4.1 - - - +
293A GLY* 1.3 79.7 - - - +
295A THR* 1.3 56.7 + - - +
297A ARG* 3.8 30.6 - - + +
298A GLY* 3.2 20.6 + - - -
323A ARG* 4.5 8.0 - - - +
325A GLU* 4.3 28.0 - - + +
326A VAL* 4.8 3.4 - - - -
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Residues in contact with THR 295 (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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230A VAL* 5.6 1.6 - - + -
231A HIS 5.2 0.2 - - - -
232A THR* 2.8 28.7 + - - +
261A ILE* 4.0 30.1 - - + +
262A TYR 4.6 2.2 - - - +
263A SER* 2.8 28.5 + - - +
270A PHE* 3.6 10.3 - - + -
273A LEU* 5.9 1.5 - - + +
289A CYS* 5.1 1.8 - - - -
291A CYS* 3.9 14.8 - - + -
292A GLU* 3.3 9.1 + - - +
293A GLY 3.1 0.6 - - - -
294A MET* 1.3 76.3 - - - +
296A VAL* 1.3 65.6 + - - +
298A GLY 3.5 0.9 + - - -
299A LEU* 3.2 20.3 + - - +
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Residues in contact with VAL 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A CYS* 4.5 10.1 - - + +
291A CYS* 4.0 19.1 - - + +
292A GLU 3.2 17.3 - - - +
293A GLY* 3.0 6.9 + - - +
295A THR* 1.3 75.6 - - - +
297A ARG* 1.3 65.5 + - - +
299A LEU* 3.4 10.4 + - + +
300A LEU* 3.1 32.3 + - + +
314A LEU* 5.1 3.8 - - + -
316A GLY* 6.0 0.2 - - - -
320A TRP* 3.5 56.1 - - + -
326A VAL* 4.1 6.1 - - + -
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Residues in contact with ARG 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A GLY 2.9 15.5 + - - +
294A MET* 3.8 33.4 - - + +
295A THR 3.2 0.2 - - - -
296A VAL* 1.3 75.1 - - - +
298A GLY* 1.3 59.8 + - - +
300A LEU* 3.2 7.3 + - - +
301A SER* 2.8 29.6 + - - -
325A GLU 3.6 12.6 + - - -
326A VAL* 3.2 28.9 + - + +
328A GLU* 3.1 36.1 + - - -
330A TYR* 4.1 24.3 + - + -
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Residues in contact with GLY 298 (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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270A PHE* 3.4 33.2 - - - +
294A MET 3.2 11.0 + - - -
295A THR 3.5 0.2 + - - -
296A VAL 3.3 0.4 - - - -
297A ARG* 1.3 78.8 - - - +
299A LEU* 1.3 61.5 + - - +
301A SER* 3.2 10.1 + - - -
302A ALA* 3.0 19.8 + - - +
305A ARG* 4.7 0.9 + - - -
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Residues in contact with LEU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A VAL* 6.2 3.6 - - + -
270A PHE* 3.5 8.4 - - + +
273A LEU* 4.5 17.7 - - + -
274A LEU* 3.9 30.1 - - + +
277A LEU* 4.2 20.9 - - + -
287A VAL* 5.6 2.2 - - + -
289A CYS* 5.1 14.1 - - - -
295A THR 3.2 13.7 + - - +
296A VAL* 3.6 11.4 - - + +
297A ARG 3.2 0.4 - - - -
298A GLY* 1.3 74.7 - - - +
300A LEU* 1.3 64.5 + - + +
302A ALA* 3.1 6.7 + - - +
303A MET* 3.0 31.5 + - + +
312A PHE* 6.3 2.0 - - + -
314A LEU* 4.2 31.2 - - + -
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Residues in contact with LEU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A VAL* 3.1 31.4 + - + +
297A ARG* 3.7 4.3 - - - +
299A LEU* 1.3 76.8 - - + +
301A SER* 1.3 60.6 + - - +
303A MET* 3.4 19.5 + - - +
304A ARG 3.3 15.6 + - - -
314A LEU* 4.2 16.2 - - + -
320A TRP* 4.9 1.6 - - + -
326A VAL 4.5 10.5 - - - +
327A ILE* 4.1 15.5 - - + -
330A TYR* 3.4 30.8 - - + -
333A GLU* 3.2 33.1 - - + +
334A ALA* 3.7 23.1 - - + -
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Residues in contact with SER 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A GLU* 4.9 4.3 + - - +
297A ARG* 2.8 15.3 + - - -
298A GLY* 3.2 17.0 - - - -
299A LEU 3.1 0.2 - - - -
300A LEU* 1.3 80.0 - - - +
302A ALA* 1.3 56.3 + - - +
304A ARG* 3.5 4.0 + - - +
305A ARG* 2.8 52.0 + - - +
330A TYR* 3.5 28.5 + - - -
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Residues in contact with ALA 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A PHE* 3.8 21.5 - - + +
271A ASP* 4.3 5.9 - - - +
274A LEU* 3.2 23.7 - - + +
298A GLY 3.0 10.4 + - - +
299A LEU* 3.1 9.6 + - - +
301A SER* 1.3 72.8 - - - +
303A MET* 1.3 62.8 + - - +
304A ARG 3.0 5.2 - - - -
305A ARG* 3.4 25.4 + - - +
306A LEU* 3.2 19.6 + - - +
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Residues in contact with MET 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LEU* 3.7 14.6 - - + -
299A LEU* 3.0 25.6 + - - +
300A LEU* 3.5 34.3 - - - +
301A SER 3.3 0.2 - - - -
302A ALA* 1.3 77.7 - - - +
304A ARG* 1.3 57.1 + - - +
307A GLY* 3.2 4.2 + - - -
308A VAL* 3.1 59.9 + - + +
309A VAL* 5.5 0.3 - - - +
310A GLY 5.2 3.8 - - - +
311A GLU* 5.1 7.0 - - + +
312A PHE* 3.7 38.1 - - + +
314A LEU* 4.8 7.9 - - + -
333A GLU* 3.8 19.5 - - + +
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Residues in contact with ARG 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A LEU 3.3 3.4 + - - +
301A SER 3.5 10.3 - - - +
302A ALA 3.0 0.2 - - - -
303A MET* 1.3 77.9 - - - +
305A ARG* 1.3 66.7 + - + +
306A LEU 3.0 5.7 + - - -
307A GLY* 3.2 11.8 + - - -
329A GLY 3.2 22.4 + - - -
330A TYR* 3.8 25.9 - - + +
332A VAL* 5.2 6.7 - - - +
333A GLU* 2.9 41.1 + - - +
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Residues in contact with ARG 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A GLU* 3.2 65.2 + - - +
270A PHE* 4.2 3.4 - - - +
271A ASP* 3.2 22.5 + - - +
298A GLY 4.7 0.6 + - - -
301A SER* 2.8 50.1 + - - +
302A ALA* 3.4 20.6 + - - +
304A ARG* 1.3 78.2 - - + +
306A LEU* 1.3 57.8 + - - +
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Residues in contact with LEU 306 (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 ASP* 6.0 1.3 - - - +
274A LEU* 4.0 13.5 - - + -
275A ARG* 5.8 3.4 - - + +
278A ARG* 3.5 36.3 - - - +
302A ALA 3.2 15.2 + - - +
304A ARG 3.0 0.8 - - - -
305A ARG* 1.3 81.1 - - - +
307A GLY* 1.3 59.6 + - - +
308A VAL* 3.7 16.7 - - + +
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Residues in contact with GLY 307 (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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303A MET 3.2 4.2 + - - -
304A ARG* 3.2 12.0 + - - -
306A LEU* 1.3 81.0 - - - +
308A VAL* 1.3 64.6 + - - +
309A VAL* 4.2 5.8 + - - +
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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