Contacts of the helix formed by residues 312 - 327 (chain A) in PDB entry 3OMA
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 GLY 312 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A ILE 3.7 1.2 + - - -
311A PHE* 1.3 82.0 - - - +
313A TYR* 1.3 64.7 + - - +
314A LEU 3.2 3.5 + - - -
315A PRO* 3.2 20.1 - - - +
316A MET* 3.0 26.3 + - - +
365A SER* 4.8 1.9 + - - -
95B THR* 2.9 21.9 + - - -
96B HIS* 5.3 5.8 - - - -
101B GLU* 5.3 1.1 - - - -
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Residues in contact with TYR 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A MET 3.4 9.4 + - - -
223A HIS* 3.5 26.0 - - + -
224A LYS 4.9 0.9 - - - -
225A VAL 2.5 30.1 + - - -
226A PRO* 4.8 1.3 - - + -
227A LEU* 4.0 29.2 - - + -
230A TRP* 3.1 15.6 + - - -
310A ILE* 4.1 21.3 + - + +
311A PHE 3.5 2.0 - - - -
312A GLY* 1.3 75.0 - - - +
314A LEU* 1.3 78.7 + - + +
316A MET* 3.3 9.9 + - - +
317A VAL* 3.2 35.2 + - + +
95B THR* 5.7 0.8 - - - -
96B HIS* 5.9 1.4 - - - -
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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
----------------------------------------------------------
223A HIS* 5.1 12.3 - - + -
313A TYR* 1.3 97.8 - - + +
315A PRO* 1.4 73.7 - - + +
317A VAL* 3.3 11.0 + - + +
318A TYR* 3.1 59.7 + - + +
96B HIS* 6.5 1.1 - - + -
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Residues in contact with PRO 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A GLY* 3.2 20.9 - - - +
314A LEU* 1.4 95.3 - - + +
316A MET* 1.3 51.3 + - - +
318A TYR* 3.9 8.2 - - + +
319A ALA* 2.8 36.8 + - - +
361A ILE* 4.2 22.2 - - + +
365A SER* 5.4 1.8 - - - +
96B HIS* 5.9 5.2 - - + +
101B GLU* 4.1 19.5 - - - +
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Residues in contact with MET 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LEU* 3.9 21.5 - - + -
299A SER* 3.9 8.1 - - - +
310A ILE* 4.1 13.5 - - + -
311A PHE 3.9 5.6 - - - +
312A GLY 3.0 25.0 + - - +
313A TYR 3.3 8.1 - - - +
314A LEU 3.2 0.2 - - - -
315A PRO* 1.3 71.9 - - - +
317A VAL* 1.3 67.1 + - - +
319A ALA* 3.4 4.4 + - - +
320A MET* 3.0 30.2 + - - +
361A ILE* 5.2 0.7 - - - -
362A MET* 3.7 30.1 - - + +
365A SER* 3.7 28.3 - - - -
366A TRP* 3.3 40.6 - - + +
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Residues in contact with VAL 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LEU* 3.8 17.3 - - + -
230A TRP* 3.6 55.2 - - + +
234A VAL* 5.2 0.3 - - - +
313A TYR* 3.2 30.4 + - + +
314A LEU* 3.3 11.4 + - + +
316A MET* 1.3 76.6 - - - +
318A TYR* 1.3 67.4 + - + +
320A MET* 3.4 11.1 + - + +
321A VAL* 3.0 31.7 + - + +
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Residues in contact with TYR 318 (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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314A LEU* 3.1 52.0 + - + +
315A PRO* 3.9 6.1 - - + +
317A VAL* 1.3 83.8 - - + +
319A ALA* 1.3 54.8 + - - +
321A VAL* 3.2 10.8 + - + +
322A ALA* 2.8 35.4 + - - +
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Residues in contact with ALA 319 (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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315A PRO 2.8 23.7 + - - +
316A MET 3.8 1.3 - - - +
318A TYR* 1.3 71.5 - - - +
320A MET* 1.3 58.2 + - - +
322A ALA* 3.4 1.3 + - - -
323A ILE* 2.9 37.1 + - - +
358A PRO* 3.5 37.6 - - + +
361A ILE* 4.4 8.5 - - + -
362A MET* 3.7 15.9 - - + -
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Residues in contact with MET 320 (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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227A LEU* 3.8 39.9 - - + +
230A TRP* 3.9 12.6 - - + -
231A SER* 3.7 32.3 - - - +
234A VAL* 3.7 19.3 - - + +
292A LEU* 4.0 22.5 - - + +
295A PHE* 4.5 6.7 - - - -
296A GLY* 5.0 1.6 - - - -
316A MET 3.0 18.7 + - - +
317A VAL* 3.6 7.2 - - + +
319A ALA* 1.3 73.8 - - - +
321A VAL* 1.3 60.8 + - - +
323A ILE* 3.7 6.3 + - - +
324A GLY* 3.0 21.8 + - - -
362A MET* 3.7 25.4 - - + -
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Residues in contact with VAL 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A TRP* 5.3 4.9 - - + -
234A VAL* 4.1 22.8 - - + +
317A VAL* 3.0 27.9 + - + +
318A TYR* 3.2 14.5 + - + +
320A MET* 1.3 73.2 - - - +
322A ALA* 1.3 60.6 + - - +
324A GLY* 3.2 1.9 + - - -
325A VAL* 2.9 41.4 + - + +
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Residues in contact with ALA 322 (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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318A TYR 2.8 22.1 + - - +
319A ALA* 3.6 5.2 - - - +
321A VAL* 1.3 74.0 - - - +
323A ILE* 1.3 56.9 + - - +
325A VAL* 3.3 5.8 + - - +
326A LEU* 2.9 41.7 + - + +
358A PRO* 4.2 17.3 - - + -
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Residues in contact with ILE 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A TYR* 3.5 38.0 - - + -
292A LEU* 4.6 10.5 - - + -
295A PHE* 4.3 13.5 - - + -
319A ALA 2.9 20.9 + - - +
320A MET* 3.9 6.1 - - - +
322A ALA* 1.3 72.5 - - - +
324A GLY* 1.3 68.9 + - - +
326A LEU* 3.9 5.2 - - - +
327A GLY* 3.0 22.3 + - - -
355A ILE* 4.6 7.8 - - + +
358A PRO* 3.8 16.2 - - + -
359A THR* 3.5 36.1 - - - +
362A MET* 4.2 17.9 - - - -
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Residues in contact with GLY 324 (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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234A VAL* 4.5 4.3 - - - -
238A LEU* 3.4 44.5 - - - +
288A TYR* 5.5 0.4 - - - -
292A LEU* 4.9 0.9 - - - -
320A MET 3.0 16.0 + - - -
321A VAL 3.6 4.0 - - - -
323A ILE* 1.3 79.4 - - - +
325A VAL* 1.3 61.8 + - - +
327A GLY* 3.6 5.0 + - - -
328A PHE* 3.5 11.1 - - - -
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Residues in contact with VAL 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A VAL* 2.9 32.1 + - + +
322A ALA* 3.8 5.6 - - - +
324A GLY* 1.3 74.6 - - - +
326A LEU* 1.3 71.3 + - + +
327A GLY 3.1 1.6 - - - -
328A PHE* 3.1 21.9 + - - +
329A VAL* 4.3 8.5 + - + +
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Residues in contact with LEU 326 (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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322A ALA* 2.9 31.4 + - + +
323A ILE 4.1 2.0 - - - +
325A VAL* 1.3 71.1 - - + +
327A GLY* 1.3 56.6 + - - +
328A PHE 3.0 11.7 + - - -
329A VAL* 3.2 28.3 + - + +
330A VAL* 3.4 17.2 - - - +
351A ALA* 4.7 5.6 - - + +
354A VAL* 3.6 36.1 - - + -
355A ILE* 3.7 31.4 - - + -
358A PRO* 4.4 10.3 - - + -
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Residues in contact with GLY 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A HIS* 3.7 24.4 - - - +
285A PRO* 3.2 30.2 - - - +
288A TYR* 4.3 8.3 - - - -
323A ILE 3.0 16.9 + - - -
324A GLY 3.6 4.0 + - - -
325A VAL 3.1 1.4 - - - -
326A LEU* 1.3 74.6 - - - +
328A PHE* 1.3 61.2 + - - +
329A VAL 3.6 0.4 - - - -
330A VAL* 4.0 5.5 + - - +
331A TRP* 5.4 0.7 + - - +
355A ILE* 4.3 1.5 - - - +
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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
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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