Contacts of the helix formed by residues 294 - 314 (chain A) in PDB entry 1O7F
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 LEU 294 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ILE* 3.8 8.1 - - + -
192A LEU* 3.7 29.4 - - + -
195A ALA* 4.0 24.7 - - + -
199A ARG* 4.0 29.2 - - - +
226A TRP* 4.9 5.6 - - + -
230A GLN* 5.3 6.5 - - + +
231A THR* 5.0 11.0 - - - +
290A CYS* 3.0 20.4 - - - +
291A ASP 3.9 5.4 - - - +
292A GLU 3.1 1.6 + - - -
293A GLU* 1.3 72.5 - - - +
295A GLN* 1.3 70.8 + - - +
296A ASP 3.4 2.3 - - - +
297A THR* 3.2 10.2 + - - -
298A MET* 3.1 30.6 + - + +
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Residues in contact with GLN 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A THR* 2.8 49.5 - - - +
232A SER* 5.7 1.1 - - - -
291A ASP 4.8 1.5 + - - +
292A GLU 4.0 10.4 + - - +
294A LEU* 1.3 83.7 - - - +
296A ASP* 1.3 68.5 + - - +
298A MET* 3.2 13.3 + - - +
299A LEU* 3.3 12.4 + - + +
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Residues in contact with ASP 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A GLU 4.9 6.6 - - - +
293A GLU* 5.3 6.7 - - + +
294A LEU 3.4 2.3 - - - +
295A GLN* 1.3 79.1 - - - +
297A THR* 1.3 55.0 + - - +
299A LEU* 3.0 17.5 + - + +
300A LEU* 2.7 35.9 + - - +
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Residues in contact with THR 297 (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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188A ALA* 3.5 38.1 - - + -
191A ILE* 3.9 11.4 - - + +
192A LEU* 4.0 17.0 - - + -
293A GLU* 3.6 12.6 + - - +
294A LEU* 3.2 25.7 + - - -
296A ASP* 1.3 78.5 - - - +
298A MET* 1.3 61.2 + - - +
300A LEU* 3.2 9.1 + - + +
301A LEU* 3.0 33.0 + - + +
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Residues in contact with MET 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LEU* 4.5 17.7 - - - -
226A TRP* 5.1 7.0 - - - -
227A MET* 3.3 60.8 - - + +
230A GLN* 5.2 5.6 - - + -
231A THR* 4.6 14.6 - - - +
232A SER* 6.2 2.0 - - - -
234A VAL* 4.1 10.1 - - + -
243A MET* 3.4 16.3 - - + +
294A LEU* 3.1 23.2 + - + +
295A GLN* 3.6 13.7 - - - +
296A ASP 3.2 0.4 - - - -
297A THR* 1.3 75.6 - - - +
299A LEU* 1.3 58.4 + - - +
301A LEU* 3.3 2.9 + - - -
302A SER* 2.8 30.1 + - - -
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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
----------------------------------------------------------
295A GLN* 3.3 10.1 + - + +
296A ASP* 3.0 19.5 + - - +
298A MET* 1.3 79.8 - - - +
300A LEU* 1.3 60.9 + - - +
302A SER* 3.2 13.3 - - - +
303A GLN* 3.0 43.9 + - + +
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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
----------------------------------------------------------
184A LYS* 4.0 31.9 - - + +
185A ILE* 6.2 1.3 - - + -
188A ALA* 5.4 3.4 - - + -
296A ASP 2.7 15.7 + - - +
297A THR* 3.3 13.9 - - + +
298A MET 3.2 0.2 - - - -
299A LEU* 1.3 71.1 - - - +
301A LEU* 1.3 73.6 + - + +
303A GLN* 3.1 20.9 + - + +
304A MET* 2.9 47.7 + - + +
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Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ILE* 6.2 1.8 - - + -
188A ALA* 4.0 24.2 - - + -
192A LEU* 4.1 26.2 - - + -
227A MET* 4.6 9.6 - - + -
243A MET* 3.5 39.6 - - + +
246A VAL* 4.6 9.4 - - + +
247A LEU* 4.6 15.7 - - + -
297A THR* 3.0 21.9 + - + +
298A MET* 4.8 1.8 - - - -
300A LEU* 1.3 85.4 - - + +
302A SER* 1.3 57.1 + - - +
304A MET* 4.4 7.6 - - - +
305A GLY* 2.7 34.4 + - - -
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Residues in contact with SER 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A GLN* 3.4 21.5 + - - +
243A MET* 3.7 17.4 - - - +
298A MET 2.8 15.5 + - - -
299A LEU* 3.2 22.9 - - - +
300A LEU 3.1 0.2 - - - -
301A LEU* 1.3 78.4 - - - +
303A GLN* 1.3 57.4 + - - +
305A GLY* 4.2 0.2 - - - -
306A PRO* 3.1 24.8 - - - +
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Residues in contact with GLN 303 (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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299A LEU* 3.0 39.9 + - + +
300A LEU* 3.1 18.8 + - + +
302A SER* 1.3 78.7 - - - +
304A MET* 1.3 63.3 + - + +
305A GLY 3.2 1.1 + - - -
306A PRO* 3.4 13.0 - - - +
307A ASP* 5.0 1.2 + - - +
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Residues in contact with MET 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A LYS* 6.3 1.6 - - - -
185A ILE* 3.6 34.1 - - + -
246A VAL* 3.4 28.2 - - + +
249A GLU* 6.1 0.9 - - - +
300A LEU* 2.9 44.2 + - + +
301A LEU* 4.2 4.5 - - - +
303A GLN* 1.3 75.7 - - + +
305A GLY* 1.3 64.0 + - - +
306A PRO 3.7 0.2 - - - -
307A ASP* 3.8 9.7 + - - +
308A ALA* 3.6 11.1 + - - +
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Residues in contact with GLY 305 (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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239A GLN 5.9 0.2 - - - -
242A GLY* 4.0 15.1 - - - +
243A MET* 4.3 3.4 - - - -
246A VAL* 3.9 9.6 - - - -
301A LEU 2.7 22.8 + - - -
302A SER 4.2 0.4 - - - -
304A MET* 1.3 72.6 - - - +
306A PRO* 1.3 73.4 - - - +
307A ASP 3.0 0.9 + - - -
308A ALA* 3.2 4.2 + - - +
309A HIS* 2.9 24.7 + - - +
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Residues in contact with PRO 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A GLN* 6.3 3.4 - - + -
243A MET* 6.0 0.2 - - + -
302A SER 3.1 18.6 - - - +
303A GLN 3.4 10.3 - - - +
305A GLY* 1.3 88.0 - - - +
307A ASP* 1.3 61.4 + - - +
309A HIS* 3.4 8.5 + - + +
310A MET* 3.0 23.7 + - - +
328A ILE* 4.4 6.8 - - + +
331A ASP* 6.5 0.2 - - + -
332A GLU* 3.1 31.3 - - + +
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Residues in contact with ASP 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A GLN 5.0 1.1 + - - +
304A MET* 3.8 11.2 + - - +
305A GLY 3.2 0.8 - - - -
306A PRO* 1.3 75.1 - - - +
308A ALA* 1.3 66.7 + - - +
310A MET* 2.8 24.5 + - - +
311A ARG* 2.9 52.7 + - - +
332A GLU* 4.2 14.4 - - - +
380A LEU* 6.0 0.5 - - - +
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Residues in contact with ALA 308 (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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242A GLY 4.1 2.0 - - - +
245A GLN* 4.1 20.8 + - + +
246A VAL* 3.7 26.7 - - + +
249A GLU* 4.0 9.0 - - - +
304A MET 3.6 1.9 + - - +
305A GLY 3.2 7.5 + - - +
307A ASP* 1.3 79.4 + - - +
309A HIS* 1.3 63.1 + - - +
311A ARG* 3.3 25.4 + - - +
312A MET* 3.2 22.7 + - - +
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Residues in contact with HIS 309 (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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238A THR* 3.2 31.5 + - + -
239A GLN* 5.0 2.7 - - - -
241A VAL* 3.9 12.0 - - + +
242A GLY* 3.7 15.6 - - - -
305A GLY 2.9 13.7 + - - +
306A PRO* 3.4 11.9 - - + +
308A ALA* 1.3 77.3 - - - +
310A MET* 1.3 58.6 + - - +
312A MET* 3.0 33.7 + - + +
313A ILE* 2.9 48.0 + - + +
325A ASP* 5.3 0.7 - - - -
328A ILE* 3.3 34.0 - - + +
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Residues in contact with MET 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A PRO 3.0 13.0 + - - +
307A ASP* 2.8 21.1 + - - +
309A HIS* 1.3 72.0 - - - +
311A ARG* 1.3 66.9 + - + +
313A ILE* 3.2 7.4 + - - +
314A LEU* 2.9 54.8 + - + +
328A ILE* 4.4 7.4 - - - +
329A ILE* 4.3 19.3 - - + +
332A GLU* 3.6 31.2 - - + +
333A LEU* 4.6 13.7 - - - -
336A ILE* 5.0 6.1 - - + -
380A LEU* 4.4 25.8 - - + -
428A LEU* 4.7 3.1 - - + -
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Residues in contact with ARG 311 (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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249A GLU* 2.9 40.6 + - - -
307A ASP* 2.9 45.1 + - - +
308A ALA* 3.3 16.7 + - - +
310A MET* 1.3 85.8 - - + +
312A MET* 1.3 57.4 + - - +
314A LEU* 4.2 5.6 - - - +
315A ARG* 3.1 36.6 + - - +
356A PHE* 3.9 26.9 - - + -
380A LEU* 4.6 9.2 - - + -
426A HIS* 4.0 33.4 + - - -
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Residues in contact with MET 312 (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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241A VAL* 3.8 17.3 - - + -
245A GLN* 3.3 32.8 - - + +
261A HIS* 3.3 43.4 + - + +
262A PHE 3.8 8.7 - - - +
308A ALA 3.2 11.7 + - - +
309A HIS* 3.0 40.5 + - + +
311A ARG* 1.3 78.2 - - - +
313A ILE* 1.3 70.7 + - + +
315A ARG* 3.5 22.3 - - - +
316A LYS* 4.4 6.2 - - - +
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Residues in contact with ILE 313 (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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309A HIS* 2.9 44.1 + - + +
310A MET* 3.7 7.9 - - - +
312A MET* 1.3 78.8 - - + +
314A LEU* 1.3 51.8 + - - +
315A ARG 2.9 4.7 - - - -
316A LYS* 2.7 48.8 + - + +
321A ARG* 4.3 6.9 + - + -
325A ASP* 3.2 50.7 - - + +
328A ILE* 4.8 8.3 - - + -
329A ILE* 3.8 19.1 - - + -
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Residues in contact with LEU 314 (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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310A MET* 2.9 45.2 + - + +
311A ARG 4.7 1.3 - - - +
312A MET 3.5 0.2 - - - -
313A ILE* 1.3 72.2 - - - +
315A ARG* 1.3 56.7 + - - +
316A LYS 3.0 6.2 + - - +
321A ARG* 3.4 30.5 + - - +
329A ILE* 3.5 35.0 - - + -
354A LEU* 4.2 16.8 - - + +
356A PHE* 3.5 38.1 + - + +
428A LEU* 3.7 29.2 - - + -
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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