Contacts of the helix formed by residues 356 - 372 (chain A) in PDB entry 6N0M
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 TYR 356 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LEU* 3.6 28.2 - - + +
100A LEU* 3.7 21.0 - - + +
104A ASP 5.0 0.3 + - - -
105A GLY* 5.0 0.4 - - - -
106A PRO* 3.8 20.9 - - + -
192A ALA* 4.7 1.6 - - + +
195A ILE* 3.4 22.9 - - + -
196A GLN* 3.1 50.0 + - + +
199A VAL* 4.4 16.8 - - + -
352A ILE* 2.6 16.3 + - + +
355A LEU* 1.3 75.6 - - - +
357A PRO* 1.3 66.9 - - - +
358A GLU* 3.3 21.3 - - + -
359A GLY* 3.2 20.0 + - - -
360A GLY* 2.9 15.9 + - - -
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Residues in contact with PRO 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A GLN* 3.2 33.4 - - + +
354A ARG 4.6 2.7 - - - +
355A LEU* 3.6 7.2 - - - +
356A TYR* 1.3 88.7 - - - +
358A GLU* 1.3 73.0 + - + +
359A GLY 2.9 6.8 + - - -
360A GLY* 2.9 10.7 + - - -
361A GLN* 3.5 11.6 + - - +
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Residues in contact with GLU 358 (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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99A LEU* 3.7 19.4 - - + +
104A ASP 4.6 2.1 - - - +
105A GLY* 3.9 18.0 - - - -
106A PRO* 4.3 2.6 - - - +
356A TYR* 3.9 28.0 - - + -
357A PRO* 1.3 96.6 - - + +
359A GLY* 1.3 56.2 + - - +
361A GLN* 4.9 2.4 + - - +
362A LEU* 3.7 21.0 + - - +
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Residues in contact with GLY 359 (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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96A LEU* 4.3 2.3 - - - +
99A LEU* 3.5 19.7 - - - +
356A TYR* 3.2 16.2 + - - -
357A PRO 3.0 0.2 - - - -
358A GLU* 1.3 82.5 - - - +
360A GLY* 1.3 63.2 + - - +
361A GLN 3.2 1.8 - - - -
362A LEU* 3.8 7.0 - - - +
363A LEU* 3.1 32.9 + - - +
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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
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344A TRP* 4.0 1.0 - - - -
349A TYR* 3.4 19.5 - - - -
352A ILE* 3.3 27.1 - - - +
353A GLN* 4.6 5.2 - - - -
356A TYR 2.9 7.8 + - - -
357A PRO 2.9 8.3 + - - -
359A GLY* 1.3 77.8 - - - +
361A GLN* 1.3 56.1 + - - +
363A LEU* 3.4 3.8 + - - +
364A ASP 3.1 21.8 + - - -
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Residues in contact with GLN 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A TYR* 3.6 24.9 + - - +
353A GLN* 5.3 1.9 - - + +
357A PRO 3.5 9.5 + - - +
358A GLU 5.3 2.2 - - - +
359A GLY 3.2 0.6 - - - -
360A GLY* 1.3 75.3 - - - +
362A LEU* 1.3 59.7 + - + +
364A ASP* 3.2 2.3 + - + +
365A GLU* 2.8 54.7 + - + +
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Residues in contact with LEU 362 (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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92A SER* 4.7 3.6 - - - +
95A ARG* 3.6 56.3 - - + +
96A LEU* 3.9 14.8 - - + +
99A LEU* 3.4 33.2 - - + -
358A GLU 3.7 12.3 - - - +
359A GLY* 3.5 7.3 + - - +
360A GLY 3.4 0.2 - - - -
361A GLN* 1.3 77.3 - - + +
363A LEU* 1.3 57.4 + - - +
365A GLU* 3.9 17.0 - - + +
366A LYS* 3.2 28.9 + - - +
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Residues in contact with LEU 363 (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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96A LEU* 3.8 27.8 - - + -
199A VAL* 3.7 32.5 - - + -
344A TRP* 3.8 11.2 - - + -
352A ILE* 4.1 18.6 - - + -
359A GLY 3.1 21.5 + - - +
360A GLY 3.6 5.8 - - - +
362A LEU* 1.3 74.1 - - - +
364A ASP* 1.3 66.2 + - - +
365A GLU 3.0 1.3 - - - -
366A LYS* 3.0 6.9 + - - +
367A PHE* 2.9 41.2 + - + -
464A MET* 3.9 25.6 - - + -
468A LEU* 4.2 6.7 - - + -
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Residues in contact with ASP 364 (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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344A TRP* 2.8 37.2 + - - +
345A GLU* 5.8 0.3 - - - -
349A TYR* 3.5 46.0 + - + +
360A GLY 3.1 4.8 + - - -
361A GLN* 3.2 4.8 + - + +
363A LEU* 1.3 78.6 - - - +
365A GLU* 1.3 62.3 + - - +
367A PHE* 4.1 1.7 - - - +
368A GLN* 3.2 27.4 + - - +
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Residues in contact with GLU 365 (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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92A SER* 4.0 11.3 + - - +
95A ARG* 3.9 21.0 + - - -
361A GLN* 2.8 55.1 + - + +
362A LEU* 4.1 16.5 - - + +
364A ASP* 1.3 74.1 - - + +
366A LYS* 1.3 53.4 + - - +
368A GLN* 3.4 6.4 + - - +
369A ALA* 2.8 34.3 + - - +
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Residues in contact with LYS 366 (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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89A TYR* 3.5 20.0 + - + +
92A SER* 3.4 39.7 - - - +
93A PHE* 4.0 9.6 - - - +
96A LEU* 3.5 32.7 - - + +
203A HIS* 3.9 16.4 + - - -
207A LEU* 5.6 0.6 - - - +
362A LEU 3.2 14.2 + - - +
363A LEU* 3.0 8.4 + - - +
365A GLU* 1.3 73.4 - - - +
367A PHE* 1.3 66.4 + - - +
369A ALA* 3.2 2.3 + - - +
370A ALA* 3.0 24.8 + - - +
460A LEU* 4.6 4.0 - - - +
461A GLU* 2.7 35.7 + - - +
464A MET* 3.9 10.6 - - - -
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Residues in contact with PHE 367 (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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344A TRP* 3.6 47.3 - + + +
363A LEU* 2.9 27.0 + - + +
364A ASP 4.1 2.9 - - - +
366A LYS* 1.3 75.7 - - - +
368A GLN* 1.3 64.7 + - - +
370A ALA* 3.1 1.6 + - - +
371A TYR* 3.0 25.8 + - - +
394A TRP* 4.9 6.6 - + + -
461A GLU* 3.1 50.3 - - + -
464A MET* 4.4 8.1 - - + -
465A GLN* 3.3 47.1 - - + +
468A LEU* 4.1 16.6 - - + -
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Residues in contact with GLN 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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364A ASP* 3.2 23.0 + - - +
365A GLU* 3.5 6.7 - - - +
366A LYS 3.2 0.2 - - - -
367A PHE* 1.3 79.2 - - - +
369A ALA* 1.3 52.7 + - - +
371A TYR* 4.9 4.1 - - - +
372A SER* 2.5 61.7 + - - +
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Residues in contact with ALA 369 (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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88A ASP* 4.0 19.1 - - - +
89A TYR* 4.6 8.2 - - + +
92A SER* 3.7 21.3 - - - +
365A GLU 2.8 20.6 + - - +
366A LYS 3.2 5.8 + - - +
368A GLN* 1.3 73.2 - - - +
370A ALA* 1.3 57.3 + - - +
372A SER* 4.2 3.4 - - - -
373A LEU* 3.1 27.3 + - - +
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Residues in contact with ALA 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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89A TYR* 4.0 13.5 - - + -
366A LYS 3.0 15.3 + - - +
367A PHE 3.8 2.5 - - - +
369A ALA* 1.3 74.3 - - - +
371A TYR* 1.3 72.4 + - - +
373A LEU* 3.6 16.5 + - - +
394A TRP* 5.0 0.7 - - + -
454A HIS* 4.3 2.3 - - - -
457A LEU* 4.4 13.1 - - + +
458A LEU* 3.7 18.1 - - + +
461A GLU* 3.6 29.4 - - + -
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Residues in contact with TYR 371 (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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367A PHE 3.0 15.9 + - - +
368A GLN* 4.1 5.8 - - - +
370A ALA* 1.3 83.1 - - - +
372A SER* 1.3 61.2 + - - +
373A LEU 3.1 3.1 + - - +
387A SER* 5.1 2.9 - - - -
390A ARG* 3.1 32.8 + - + -
391A ARG* 3.7 54.7 + - + +
394A TRP* 4.4 38.7 - + + -
395A ASN* 4.6 3.1 + - - -
458A LEU* 4.1 13.9 - - + +
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Residues in contact with SER 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A GLN* 2.5 44.2 + - - +
369A ALA* 4.2 2.9 - - - -
371A TYR* 1.3 74.3 - - - +
373A LEU* 1.3 58.4 + - - +
374A THR* 2.9 18.5 + - - +
390A ARG* 4.1 7.5 + - - +
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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
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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