Contacts of the helix formed by residues 356 - 373 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B LEU* 3.5 24.9 - - + +
100B LEU* 3.9 15.0 - - + +
105B GLY* 5.2 0.7 - - - -
106B PRO* 3.7 25.4 - - + -
192B ALA* 4.5 2.0 - - + +
195B ILE* 3.5 25.1 - - + -
196B GLN* 2.9 52.8 + - + -
199B VAL* 4.5 10.3 - - + -
352B ILE* 2.5 15.2 + - + +
355B LEU* 1.3 75.2 - - - +
357B PRO* 1.3 68.6 - - - +
358B GLU* 3.4 22.4 - - + -
359B GLY* 3.1 29.4 + - - -
360B GLY 3.1 10.1 + - - -
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Residues in contact with PRO 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B GLN* 3.4 34.7 - - + +
354B ARG 4.7 2.0 - - - +
355B LEU* 3.8 4.0 - - - +
356B TYR* 1.3 85.7 - - - +
358B GLU* 1.3 83.3 + - + +
359B GLY 3.1 0.7 + - - -
360B GLY 3.2 9.2 + - - -
361B GLN* 3.2 15.8 + - - +
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Residues in contact with GLU 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 3.7 24.1 - - + +
104B ASP 5.2 2.1 - - - +
105B GLY* 4.6 6.1 - - - -
106B PRO* 4.4 9.9 - - - +
356B TYR* 3.8 20.5 - - + -
357B PRO* 1.3 103.8 - - + +
359B GLY* 1.3 59.9 + - - +
361B GLN* 4.0 4.3 - - - +
362B LEU* 3.5 22.7 + - - +
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Residues in contact with GLY 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 4.5 4.4 - - - +
99B LEU* 3.8 10.9 - - - +
352B ILE* 4.5 0.9 - - - -
356B TYR* 3.1 30.2 + - - -
358B GLU* 1.3 78.7 - - - +
360B GLY* 1.3 59.0 + - - +
362B LEU* 2.9 6.4 + - - +
363B LEU* 2.8 35.2 + - - +
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Residues in contact with GLY 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B TRP* 5.1 0.4 - - - -
349B TYR* 3.2 23.8 - - - -
352B ILE* 3.3 24.9 - - - +
353B GLN* 4.5 4.7 - - - -
356B TYR 3.1 11.1 + - - -
357B PRO 3.2 2.4 + - - -
359B GLY* 1.3 74.3 - - - +
361B GLN* 1.3 63.0 + - - +
363B LEU* 3.7 4.3 - - - +
364B ASP* 3.0 21.1 + - - +
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Residues in contact with GLN 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B TYR* 3.8 20.6 + - - -
353B GLN* 4.9 7.0 + - - +
357B PRO 3.2 15.6 + - - +
358B GLU* 4.0 5.8 - - - +
360B GLY* 1.3 75.1 - - - +
362B LEU* 1.3 64.8 + - + +
364B ASP* 3.9 2.4 - - - +
365B GLU* 2.5 68.4 + - - +
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Residues in contact with LEU 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B SER* 5.2 0.9 - - - +
95B ARG* 3.6 51.8 - - + +
96B LEU* 3.8 15.7 - - + +
99B LEU* 3.5 29.6 - - + -
358B GLU 3.5 10.8 - - - +
359B GLY 2.9 6.5 + - - +
361B GLN* 1.3 88.6 - - + +
363B LEU* 1.3 61.1 + - - +
365B GLU* 3.8 13.9 - - - +
366B LYS* 2.9 32.1 + - - +
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Residues in contact with LEU 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 3.8 24.7 - - + -
199B VAL* 3.7 29.6 - - + -
344B TRP* 4.0 13.7 - - + -
352B ILE* 3.8 25.1 - - + -
359B GLY 2.8 22.5 + - - +
360B GLY 3.7 3.4 - - - +
362B LEU* 1.3 72.9 - - - +
364B ASP* 1.3 57.2 + - - +
366B LYS* 3.2 12.0 + - - +
367B PHE* 3.0 40.9 + - + -
464B MET* 3.7 29.2 - - + -
468B LEU* 4.3 7.9 - - + -
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Residues in contact with ASP 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B TRP* 2.8 37.9 + - - +
345B GLU* 5.4 5.2 - - - +
349B TYR* 3.6 34.8 + - + -
360B GLY 3.0 17.5 + - - +
361B GLN* 3.9 2.3 + - - +
363B LEU* 1.3 76.8 - - - +
365B GLU* 1.3 64.1 + - - +
367B PHE* 3.9 3.4 - - - +
368B GLN* 3.3 27.2 + - - +
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Residues in contact with GLU 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B SER* 3.9 10.5 + - - +
95B ARG* 3.5 24.3 + - - -
361B GLN* 2.5 54.4 + - - +
362B LEU* 3.8 13.9 - - - +
363B LEU 3.3 0.2 - - - -
364B ASP* 1.3 78.0 - - - +
366B LYS* 1.3 53.1 + - - +
368B GLN* 3.4 5.6 + - - +
369B ALA* 2.8 35.2 + - - +
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Residues in contact with LYS 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TYR* 4.0 8.5 + - + +
92B SER* 3.6 33.1 + - - +
93B PHE* 3.8 22.7 - - + +
96B LEU* 3.3 33.7 - - + -
203B HIS* 4.7 5.6 + - + -
362B LEU 2.9 14.6 + - - +
363B LEU* 3.5 14.1 - - - +
365B GLU* 1.3 73.7 - - - +
367B PHE* 1.3 67.3 + - - +
369B ALA* 3.3 3.5 + - - +
370B ALA* 3.1 18.0 + - - +
460B LEU* 5.0 2.4 - - - +
461B GLU* 2.6 48.4 + - - +
464B MET* 3.7 19.2 - - - -
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Residues in contact with PHE 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B TRP* 3.6 46.7 - + + -
363B LEU* 3.0 25.2 + - + +
364B ASP 3.9 3.6 - - - +
365B GLU 3.4 0.2 - - - -
366B LYS* 1.3 77.6 - - - +
368B GLN* 1.3 61.2 + - - +
370B ALA* 3.0 5.4 + - - +
371B TYR* 2.9 29.9 + - - +
394B TRP* 4.9 7.2 - + + -
461B GLU* 3.0 39.3 - - + -
464B MET* 4.2 6.3 - - + -
465B GLN* 3.2 54.3 - - + +
468B LEU* 4.1 17.5 - - + -
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Residues in contact with GLN 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B GLU* 5.3 5.0 - - - +
364B ASP* 3.3 20.1 + - - +
365B GLU* 3.7 5.8 - - - +
366B LYS 3.2 0.2 - - - -
367B PHE* 1.3 79.5 - - - +
369B ALA* 1.3 65.9 + - - +
371B TYR* 4.6 15.8 - - - +
372B SER* 2.9 45.1 + - - +
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Residues in contact with ALA 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ASP* 3.9 17.8 - - - +
89B TYR* 4.3 8.9 - - + +
92B SER* 3.6 21.1 - - - +
365B GLU 2.8 17.5 + - - +
366B LYS 3.4 6.5 - - - +
367B PHE 3.2 0.4 - - - -
368B GLN* 1.3 76.1 - - - +
370B ALA* 1.3 57.3 + - - +
372B SER* 3.9 3.2 + - - -
373B LEU* 2.9 31.2 + - - +
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Residues in contact with ALA 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TYR* 3.7 17.7 - - + -
366B LYS 3.1 3.8 + - - +
367B PHE 3.0 6.2 + - - +
369B ALA* 1.3 74.4 - - - +
371B TYR* 1.3 68.6 + - - +
373B LEU* 3.6 14.0 + - - +
394B TRP* 5.2 0.2 - - + -
454B HIS* 4.3 0.2 - - - -
457B LEU* 4.3 14.1 - - + +
458B LEU* 3.3 22.2 - - - +
461B GLU* 3.7 34.1 - - + -
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Residues in contact with TYR 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B PHE 2.9 16.1 + - - +
368B GLN* 4.2 18.8 - - - +
370B ALA* 1.3 79.9 - - - +
372B SER* 1.3 66.1 + - - +
373B LEU 3.4 3.1 + - - +
387B SER* 6.4 1.8 - - - -
390B ARG* 3.5 30.2 + - + +
391B ARG* 3.8 44.3 + - - +
394B TRP* 3.6 56.7 - + + -
395B ASN* 4.7 1.3 + - - -
458B LEU* 4.5 8.8 - - + +
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Residues in contact with SER 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B GLN* 2.9 35.2 + - - +
369B ALA* 3.9 2.8 + - - -
371B TYR* 1.3 80.0 - - - +
373B LEU* 1.3 66.1 + - - +
374B THR* 3.0 15.9 + - - +
390B ARG* 4.1 8.1 + - - +
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Residues in contact with LEU 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B HIS* 3.9 20.2 - - + +
88B ASP* 4.5 20.2 - - + +
89B TYR* 4.3 8.7 - - + +
369B ALA 2.9 21.9 + - - +
370B ALA* 3.8 8.5 - - - +
371B TYR 3.3 1.8 - - - +
372B SER* 1.3 74.8 + - - +
374B THR* 1.3 63.0 + - - +
375B TYR* 3.9 31.6 - - + +
390B ARG* 3.4 11.6 - - - -
454B HIS* 3.1 34.2 + - + +
457B LEU* 3.8 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