Contacts of the helix formed by residues 355 - 371 (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 ILE 355 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A HEA 3.6 26.0 - - - +
284A HIS* 4.7 0.7 - - + -
288A TYR* 3.6 28.3 - - + +
323A ILE* 4.6 11.2 - - + +
326A LEU* 3.7 44.2 - - + +
327A GLY 4.3 2.0 - - - +
330A VAL* 4.1 17.5 - - + -
351A ALA 4.1 5.4 - - - +
352A THR* 3.5 16.4 - - + +
353A MET 3.2 0.6 - - - -
354A VAL* 1.3 76.9 - - - +
356A ALA* 1.3 59.5 + - - +
357A VAL 3.1 1.0 + - - -
358A PRO* 3.4 12.2 - - - +
359A THR* 2.8 29.5 + - - +
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Residues in contact with ALA 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A HEA 3.9 44.2 - - + +
352A THR 4.3 1.0 + - - -
353A MET 3.1 15.1 + - - +
355A ILE* 1.3 77.6 - - - +
357A VAL* 1.3 57.1 + - - +
359A THR* 3.8 0.7 - - - -
360A GLY* 2.9 27.2 + - - -
399A ILE* 3.8 20.7 - - + +
108B PRO* 5.4 1.5 - - - +
112B LEU* 4.0 11.9 - - + -
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Residues in contact with VAL 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A VAL* 2.9 19.9 + - + +
356A ALA* 1.3 73.8 - - - +
358A PRO* 1.4 73.5 - - + +
360A GLY* 3.2 2.9 + - - -
361A ILE* 3.0 25.3 + - + +
104B TRP 5.6 0.9 - - - +
105B THR* 4.1 33.7 - - + +
108B PRO* 4.6 9.6 - - + +
109B ILE* 3.8 28.3 - - + +
112B LEU* 3.9 20.9 - - + -
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Residues in contact with PRO 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ALA* 3.5 31.2 - - + +
322A ALA* 4.2 15.9 - - + -
323A ILE* 3.8 13.2 - - + -
326A LEU* 4.4 11.2 - - + -
354A VAL* 3.2 18.6 - - + +
355A ILE 3.4 9.2 - - - +
357A VAL* 1.4 87.2 - - + +
359A THR* 1.3 61.4 + - - +
361A ILE* 3.2 19.0 + - + +
362A MET* 3.2 24.3 + - - +
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Residues in contact with THR 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A HEA 3.6 25.0 + - + +
288A TYR* 5.7 0.9 - - - -
295A PHE* 4.6 9.4 - - + -
323A ILE* 3.5 19.7 - - + +
355A ILE* 2.8 25.3 + - - +
356A ALA 3.9 3.1 - - - -
357A VAL 3.2 0.4 - - - -
358A PRO* 1.3 73.7 - - - +
360A GLY* 1.3 63.7 + - - +
362A MET* 3.1 7.9 + - + +
363A ILE* 3.0 22.8 + - + +
366A TRP* 6.4 0.7 - - + -
391A PHE* 3.5 35.2 - - + -
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Residues in contact with GLY 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A HEA 3.5 33.1 - - - +
356A ALA 2.9 14.1 + - - -
357A VAL* 3.2 2.2 + - - -
359A THR* 1.3 74.5 - - - +
361A ILE* 1.3 63.4 + - - +
363A ILE* 3.3 2.1 + - - +
364A PHE* 3.0 36.9 + - - -
104B TRP 5.3 1.1 - - - -
108B PRO* 5.7 2.2 - - - -
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Residues in contact with ILE 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A PRO* 4.2 32.5 - - + +
316A MET* 5.5 0.7 - - - -
319A ALA* 4.4 4.7 - - + -
357A VAL* 3.0 21.9 + - + +
358A PRO* 3.3 18.4 - - + +
360A GLY* 1.3 76.5 - - - +
362A MET* 1.3 58.1 + - + +
364A PHE* 3.6 1.4 + - - +
365A SER* 2.8 40.9 + - - +
104B TRP* 4.1 22.7 + - + +
105B THR* 3.9 30.1 - - + +
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Residues in contact with MET 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A PHE* 4.1 21.8 - - + +
299A SER* 5.1 2.2 - - - +
316A MET* 3.7 34.5 - - + +
319A ALA* 3.7 18.4 - - + -
320A MET* 3.7 33.9 - - + -
323A ILE* 4.2 11.7 - - - -
358A PRO 3.3 13.2 - - - +
359A THR* 3.1 8.7 + - + +
361A ILE* 1.3 73.8 - - - +
363A ILE* 1.3 64.9 + - - +
365A SER* 3.6 1.6 - - - -
366A TRP* 3.0 59.1 + - + -
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Residues in contact with ILE 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A HEA 3.9 29.6 - - + -
359A THR* 3.0 19.1 + - + +
360A GLY 3.3 6.2 + - - +
362A MET* 1.3 74.9 - - - +
364A PHE* 1.3 60.3 + - + +
366A TRP* 3.4 28.6 + - + +
367A ILE* 3.1 43.1 + - + +
387A PHE* 5.1 0.7 - - + -
388A LEU* 4.2 19.4 - - + +
391A PHE* 4.2 18.2 - - + -
392A THR* 3.8 22.0 - - - +
72B VAL* 4.2 11.2 - - + -
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Residues in contact with PHE 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A HEA 4.3 27.6 - - + -
360A GLY 3.0 27.1 + - - +
363A ILE* 1.3 77.4 - - + +
365A SER* 1.3 55.6 + - - +
367A ILE* 3.3 12.2 + - + +
368A ALA* 2.8 34.7 + - - +
3B DMU 3.7 31.0 - - + +
68B ILE* 5.8 1.6 - - + -
71B PHE* 4.5 10.1 - + - -
72B VAL* 4.0 24.0 - - + -
75B LEU* 5.0 0.4 - - + -
104B TRP* 3.5 58.1 - + + -
108B PRO* 4.6 8.3 - - + -
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Residues in contact with SER 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A PHE* 3.5 21.0 + - - +
312A GLY* 4.8 2.9 + - - -
315A PRO* 5.4 1.2 - - - +
316A MET* 3.7 26.0 - - - +
361A ILE* 2.8 28.4 + - - +
362A MET 3.6 4.7 - - - -
363A ILE 3.3 0.2 - - - -
364A PHE* 1.3 75.4 - - - +
366A TRP* 1.3 54.4 + - - +
368A ALA* 3.2 2.4 + - - -
369A THR* 2.7 37.7 + - - -
104B TRP* 3.8 17.2 - - - -
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Residues in contact with TRP 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A PHE* 3.5 53.4 - + + -
298A VAL* 3.8 12.8 - - + -
299A SER* 2.9 28.7 + - - +
302A ILE* 3.9 14.9 - - + +
310A ILE* 4.0 11.7 - - + -
316A MET* 3.3 16.1 - - + +
359A THR* 6.4 0.9 - - + -
362A MET* 3.0 48.6 + - + +
363A ILE* 3.6 21.5 - - + +
365A SER* 1.3 75.2 - - - +
367A ILE* 1.3 61.8 - - - +
369A THR* 3.4 6.6 + - - -
370A MET* 3.3 25.3 + - - +
387A PHE* 4.0 13.7 - + - -
388A LEU* 3.4 32.8 - - + -
391A PHE* 6.0 0.2 - + - -
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Residues in contact with ILE 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ILE* 3.1 22.1 + - + +
364A PHE* 3.3 14.8 + - + +
365A SER 3.3 0.2 - - - -
366A TRP* 1.3 74.6 - - - +
368A ALA* 1.3 58.7 + - - +
370A MET* 3.3 21.0 + - + +
371A TRP* 3.0 31.7 + - + +
388A LEU* 4.6 5.8 - - + -
3B DMU 3.9 18.8 - - + -
72B VAL* 4.1 35.2 - - + +
75B LEU* 4.1 30.5 - - + -
76B ILE* 4.1 14.6 - - + -
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Residues in contact with ALA 368 (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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308A LYS* 2.9 19.6 + - - -
311A PHE* 3.4 36.8 - - + -
364A PHE 2.8 19.9 + - - +
365A SER 3.2 1.8 + - - +
367A ILE* 1.3 70.9 - - - +
369A THR* 1.3 62.5 + - - +
371A TRP* 3.3 18.0 + - - +
3B DMU 4.1 19.2 - - + +
94B PHE* 3.8 3.8 - - - -
104B TRP* 4.2 4.7 - - + -
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Residues in contact with THR 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ILE* 4.0 19.5 - - + +
303A ALA* 4.1 5.2 - - - -
306A ALA* 3.8 2.2 - - + +
308A LYS* 3.1 41.9 + - - +
309A PRO 3.5 20.4 - - - +
310A ILE* 3.6 21.0 - - + +
311A PHE* 3.0 18.5 + - - +
365A SER 2.7 20.0 + - - -
366A TRP* 3.5 8.7 - - - -
367A ILE 3.2 0.2 - - - -
368A ALA* 1.3 74.1 - - - +
370A MET* 1.3 63.7 + - - +
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Residues in contact with MET 370 (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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302A ILE* 4.0 13.7 - - + -
306A ALA* 3.9 9.6 - - - -
366A TRP 3.4 11.4 - - - +
367A ILE* 3.3 23.3 + - + +
369A THR* 1.3 74.4 - - - +
371A TRP* 1.3 60.2 + - - +
372A GLY 3.3 0.7 + - - -
373A GLY* 2.9 23.4 + - - -
375A ILE* 3.6 21.9 - - + +
381A MET* 4.5 8.3 - - + -
385A LEU* 3.3 31.9 - - - -
388A LEU* 4.6 3.8 - - + -
76B ILE* 3.8 35.4 - - + +
79B ALA* 3.9 15.3 - - + -
80B VAL* 4.8 7.4 - - - -
83B PHE* 4.2 1.2 - - - +
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Residues in contact with TRP 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LYS* 2.9 31.2 + - - -
367A ILE* 3.0 13.8 + - + +
368A ALA 3.4 11.4 - - - +
369A THR 3.2 0.4 - - - -
370A MET* 1.3 74.6 - - - +
372A GLY* 1.3 62.9 + - - +
3B DMU 3.6 61.3 + - + +
75B LEU* 4.1 29.6 - - + -
78B TYR* 3.6 39.0 - + - -
79B ALA* 4.0 20.4 - - + -
83B PHE* 3.8 20.2 - + - -
94B PHE* 3.3 8.2 - + + -
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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