Contacts of the helix formed by residues 355 - 371 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C HEA 3.6 26.2 - - - +
284C HIS* 5.0 0.4 - - + -
288C TYR* 3.8 21.3 - - + +
323C ILE* 4.0 14.6 - - + +
326C LEU* 3.6 32.5 - - + -
327C GLY 4.3 2.5 - - - +
330C VAL* 3.9 34.8 - - + -
351C ALA 4.4 2.2 - - - +
352C THR* 3.3 14.6 + - + +
353C MET 3.2 1.2 - - - -
354C VAL* 1.3 75.9 - - - +
356C ALA* 1.3 60.8 + - - +
357C VAL 3.0 1.7 + - - -
358C PRO* 3.4 9.0 - - - +
359C THR* 2.9 35.3 + - - +
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Residues in contact with ALA 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C HEA 3.9 42.9 - - + +
352C THR 4.4 1.0 + - - -
353C MET 3.2 15.7 + - - +
354C VAL 3.1 0.4 + - - -
355C ILE* 1.3 75.8 - - - +
357C VAL* 1.3 57.5 + - - +
359C THR* 4.0 1.2 - - - -
360C GLY* 3.0 25.7 + - - -
399C ILE* 3.7 21.7 - - + +
108D PRO* 5.1 2.5 - - - +
112D LEU* 3.8 13.5 - - + -
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Residues in contact with VAL 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C VAL* 2.9 20.7 + - + +
355C ILE 3.0 0.6 - - - -
356C ALA* 1.3 74.7 - - - +
358C PRO* 1.3 73.0 - - + +
359C THR 3.2 0.9 - - - -
360C GLY* 3.2 2.3 + - - -
361C ILE* 3.1 27.5 + - + +
14D TRD 5.5 0.9 - - + -
104D TRP 5.6 0.3 - - - +
105D THR* 4.1 26.0 - - + +
108D PRO* 4.9 8.0 - - + +
109D ILE* 3.6 40.4 - - + +
112D LEU* 3.9 22.0 - - + -
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Residues in contact with PRO 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C ALA* 3.5 24.7 - - + +
322C ALA* 4.2 15.5 - - + -
323C ILE* 3.6 19.7 - - + -
326C LEU* 4.3 9.6 - - + -
354C VAL* 3.3 15.0 - - + +
355C ILE* 3.4 14.4 - - - +
357C VAL* 1.3 91.1 - - + +
359C THR* 1.3 58.9 + - - +
361C ILE* 3.3 27.9 - - + +
362C MET* 3.3 13.3 + - - +
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Residues in contact with THR 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C HEA 3.6 26.6 + - + +
288C TYR* 5.7 0.9 - - - -
295C PHE* 4.6 9.1 - - + -
323C ILE* 3.0 18.9 - - - +
355C ILE* 2.9 24.0 + - - +
356C ALA 4.1 2.9 - - - -
357C VAL 3.2 0.6 - - - -
358C PRO* 1.3 78.0 - - - +
360C GLY* 1.3 60.2 + - - +
362C MET* 3.2 10.0 + - + +
363C ILE* 3.1 22.0 + - + +
366C TRP* 6.4 0.4 - - + -
391C PHE* 3.5 35.4 - - + -
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Residues in contact with GLY 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C HEA 3.5 32.9 - - - +
356C ALA 3.0 14.0 + - - -
357C VAL 3.2 1.5 + - - -
359C THR* 1.3 73.2 - - - +
361C ILE* 1.3 65.9 + - - +
363C ILE* 3.1 2.6 + - - +
364C PHE* 2.9 37.5 + - - -
104D TRP 5.3 0.4 - - - -
108D PRO* 5.8 1.8 - - - -
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Residues in contact with ILE 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C PRO* 4.3 25.1 - - + +
316C MET* 5.0 0.7 - - - +
319C ALA* 4.4 13.5 - - + -
357C VAL* 3.1 19.8 + - + +
358C PRO* 3.3 17.5 - - + +
360C GLY* 1.3 74.5 - - - +
362C MET* 1.3 55.1 + - + +
364C PHE* 3.8 2.1 - - - +
365C SER* 2.7 44.5 + - - +
104D TRP* 4.2 21.8 + - + +
105D THR* 3.7 32.1 - - + +
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Residues in contact with MET 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C PHE* 3.7 32.5 - - + -
299C SER* 5.3 0.4 - - - +
316C MET* 3.7 44.6 - - + +
319C ALA* 3.7 16.2 - - + -
320C MET* 3.6 35.7 - - + -
323C ILE* 5.1 3.6 - - - -
358C PRO 3.3 15.0 - - - +
359C THR* 3.2 7.6 + - + +
360C GLY 3.2 0.8 - - - -
361C ILE* 1.3 73.1 - - + +
363C ILE* 1.3 64.7 + - - +
365C SER* 3.4 1.4 + - - -
366C TRP* 3.0 48.7 + - + -
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Residues in contact with ILE 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C HEA 3.8 27.6 - - + -
359C THR* 3.1 16.6 + - + +
360C GLY 3.1 7.2 + - - +
362C MET* 1.3 76.3 - - - +
364C PHE* 1.3 65.8 + - + +
366C TRP* 3.3 27.0 + - + +
367C ILE* 3.1 36.9 + - + +
387C PHE* 5.3 0.4 - - + -
388C LEU* 4.3 16.9 - - + +
391C PHE* 4.0 19.7 - - + -
392C THR* 3.8 23.6 - - - +
72D VAL* 4.3 11.2 - - + -
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Residues in contact with PHE 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C HEA 4.3 22.0 - - + -
360C GLY* 2.9 33.1 + - - +
361C ILE 4.0 0.2 - - - +
363C ILE* 1.3 79.5 - - + +
365C SER* 1.3 54.0 + - - +
367C ILE* 3.0 15.0 + - + +
368C ALA* 2.8 35.5 + - - +
68D ILE* 6.1 1.1 - - + -
71D PHE* 4.7 18.4 - + - -
72D VAL* 4.3 20.4 - - + -
75D LEU* 5.3 4.7 - - + -
104D TRP* 3.4 64.0 - + + -
108D PRO* 4.3 11.4 - - + -
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Residues in contact with SER 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C ILE* 5.5 0.2 - - - -
311C PHE* 3.4 24.2 + - - +
312C GLY* 4.9 2.4 + - - -
315C PRO* 5.5 1.6 - - - +
316C MET* 3.5 27.6 - - - +
361C ILE* 2.7 31.2 + - - +
362C MET 3.7 0.2 - - - -
363C ILE 3.4 0.2 - - - -
364C PHE* 1.3 75.4 - - - +
366C TRP* 1.3 52.8 - - - +
368C ALA 3.4 0.2 + - - -
369C THR* 2.7 37.6 + - - -
104D TRP* 3.8 18.1 - - - -
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Residues in contact with TRP 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C PHE* 3.4 58.1 - + + -
298C VAL* 3.9 7.4 - - + -
299C SER* 2.8 29.6 + - - +
302C ILE* 3.8 17.9 - - + +
310C ILE* 3.8 13.5 - - + -
316C MET* 3.2 19.4 - - + +
359C THR* 6.4 0.2 - - + -
362C MET* 3.0 39.9 + - + +
363C ILE* 3.5 24.0 - - + +
364C PHE 3.2 0.2 - - - -
365C SER* 1.3 74.6 - - - +
367C ILE* 1.3 63.3 + - - +
369C THR* 3.5 6.6 + - - -
370C MET* 3.4 26.3 + - - +
387C PHE* 4.2 14.1 - + - -
388C LEU* 3.4 29.8 - - + -
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Residues in contact with ILE 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363C ILE* 3.1 20.5 + - + +
364C PHE* 3.0 16.8 + - + +
366C TRP* 1.3 75.8 - - - +
368C ALA* 1.3 56.9 + - - +
370C MET* 3.1 27.8 + - + +
371C TRP* 3.0 38.3 + - + +
388C LEU* 4.6 5.4 - - + -
72D VAL* 4.1 30.3 - - + +
75D LEU* 4.3 35.0 - - + +
76D ILE* 4.1 12.1 - - + -
79D ALA* 5.2 0.4 - - + +
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Residues in contact with ALA 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308C LYS* 3.0 19.4 + - - -
311C PHE* 3.6 35.4 - - + -
364C PHE 2.8 19.5 + - - +
365C SER 3.8 1.1 - - - +
367C ILE* 1.3 71.0 - - - +
369C THR* 1.3 62.1 + - - +
371C TRP* 3.3 18.0 + - + +
94D PHE* 3.8 5.8 - - + -
100D LEU* 5.2 4.5 - - + -
104D TRP* 4.1 12.6 - - + -
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Residues in contact with THR 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C ILE* 3.9 20.0 - - + +
303C ALA* 4.0 15.7 - - - +
306C ALA* 3.7 2.6 - - - +
308C LYS* 3.4 31.5 - - + +
309C PRO 3.8 16.8 - - - +
310C ILE* 3.6 18.3 - - + +
311C PHE* 2.8 21.4 + - - +
365C SER 2.7 21.5 + - - -
366C TRP* 3.6 8.3 - - - -
367C ILE 3.3 0.2 - - - -
368C ALA* 1.3 77.6 - - - +
370C MET* 1.3 59.9 + - - +
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Residues in contact with MET 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302C ILE* 3.9 15.0 - - + -
306C ALA* 3.9 8.5 - - - -
366C TRP 3.4 10.1 + - - +
367C ILE* 3.1 40.7 + - + +
369C THR* 1.3 75.3 - - - +
371C TRP* 1.3 64.2 + - - +
372C GLY 3.4 0.5 + - - -
373C GLY* 3.2 15.8 + - - -
375C ILE* 3.7 24.1 - - + +
381C MET* 4.4 11.2 - - + -
385C LEU* 3.3 30.7 - - - -
388C LEU* 4.2 5.6 - - + -
76D ILE* 4.0 26.0 - - + -
79D ALA* 4.4 11.4 - - + -
80D VAL* 4.9 2.9 - - - -
83D PHE* 4.2 3.1 - - - +
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Residues in contact with TRP 371 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C LYS* 2.9 28.8 + - - -
367C ILE* 3.0 21.0 + - + +
368C ALA* 3.5 15.9 - - + +
369C THR 3.3 0.8 - - - -
370C MET* 1.3 75.8 - - - +
372C GLY* 1.3 62.8 + - - +
373C GLY 3.2 0.4 + - - -
8D DMU 3.8 32.0 + - - +
75D LEU* 3.8 35.7 - - + -
78D TYR* 3.5 40.2 - + - -
79D ALA* 4.3 13.2 - - + -
83D PHE* 3.8 20.5 - + - -
94D PHE* 3.2 10.2 - + + -
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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