Contacts of the helix formed by residues 356 - 373 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99E LEU* 3.5 20.5 - - + +
100E LEU* 3.5 21.8 - - + +
105E GLY* 5.8 0.7 - - - -
106E PRO* 4.5 10.8 - - + -
192E ALA 4.9 2.7 - - - -
195E ILE* 3.5 22.4 - - + -
196E GLN* 3.3 45.2 + - + -
199E VAL* 4.1 28.7 - - + -
352E ILE* 2.5 17.5 + - + +
355E LEU* 1.3 76.3 - - - +
357E PRO* 1.3 67.3 - - + +
358E GLU* 3.4 5.6 - - + -
359E GLY* 3.3 29.6 + - - -
360E GLY* 2.9 26.9 + - - -
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Residues in contact with PRO 357 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353E GLN* 3.6 28.8 - - + +
354E ARG 5.0 2.2 - - - +
355E LEU 3.9 4.7 - - - +
356E TYR* 1.3 91.5 - - + +
358E GLU* 1.3 71.1 + - + +
360E GLY* 3.3 9.4 + - - -
361E GLN* 3.5 12.0 + - - +
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Residues in contact with GLU 358 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E LEU* 3.2 35.5 - - + +
103E THR* 4.7 8.5 - - - +
104E ASP 6.0 0.4 - - - +
356E TYR* 3.4 5.8 - - + +
357E PRO* 1.3 86.3 - - + +
359E GLY* 1.3 61.1 + - - +
361E GLN* 3.7 11.2 + - - +
362E LEU* 3.7 23.4 + - - +
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Residues in contact with GLY 359 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E LEU* 4.7 1.9 - - - +
99E LEU* 3.4 22.8 - - - +
356E TYR* 3.3 27.3 + - - -
358E GLU* 1.3 77.6 - - - +
360E GLY* 1.3 63.5 + - - +
361E GLN 3.4 0.2 - - - -
362E LEU* 3.9 4.0 - - - +
363E LEU* 3.1 30.9 + - - +
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Residues in contact with GLY 360 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344E TRP* 4.1 0.3 - - - -
349E TYR* 3.6 15.6 - - - -
352E ILE* 3.3 28.0 - - - +
353E GLN* 4.6 6.3 - - - -
356E TYR 2.9 11.7 + - - -
357E PRO 3.3 3.2 + - - -
359E GLY* 1.3 74.2 - - - +
361E GLN* 1.3 66.1 + - - +
363E LEU* 3.2 7.3 + - - +
364E ASP 3.1 17.2 + - - -
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Residues in contact with GLN 361 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349E TYR* 3.9 21.8 + - - +
353E GLN* 5.0 2.2 + - - +
357E PRO 3.5 9.3 + - - +
358E GLU* 3.8 10.0 - - - +
360E GLY* 1.3 74.0 - - - +
362E LEU* 1.3 56.5 + - + +
364E ASP* 3.0 5.9 + - - +
365E GLU* 2.8 57.3 + - + +
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Residues in contact with LEU 362 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E SER* 4.9 3.0 + - - +
95E ARG* 3.5 58.3 - - + +
96E LEU* 4.0 15.2 - - + +
99E LEU* 3.5 31.4 - - + -
358E GLU* 3.7 19.7 + - - +
359E GLY 3.6 6.7 + - - +
360E GLY 3.3 0.6 - - - -
361E GLN* 1.3 82.7 - - + +
363E LEU* 1.3 61.7 + - - +
365E GLU* 3.6 14.8 + - + +
366E LYS* 3.1 25.3 + - - +
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Residues in contact with LEU 363 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E LEU* 4.2 12.6 - - + -
199E VAL* 3.8 31.9 - - + -
344E TRP* 3.8 16.4 - - + -
352E ILE* 4.5 9.0 - - + -
359E GLY 3.1 24.1 + - - +
360E GLY 3.2 6.3 + - - +
362E LEU* 1.3 73.2 - - - +
364E ASP* 1.3 61.3 + - - +
366E LYS* 3.0 19.7 + - - +
367E PHE* 2.8 46.0 + - + -
464E MET* 3.8 29.4 - - + -
468E LEU* 4.1 12.8 - - + -
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Residues in contact with ASP 364 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344E TRP* 3.1 32.0 + - - +
345E GLU* 5.9 2.6 - - - +
349E TYR* 3.4 41.3 + - + +
360E GLY 3.1 2.2 + - - -
361E GLN 3.0 5.6 + - - +
363E LEU* 1.3 77.1 - - - +
365E GLU* 1.3 64.3 + - - +
367E PHE* 4.2 1.6 - - - +
368E GLN* 2.9 39.5 + - - +
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Residues in contact with GLU 365 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E SER* 3.6 11.6 + - - +
95E ARG* 4.3 18.0 + - - -
361E GLN* 2.8 50.0 + - + +
362E LEU* 3.9 20.7 - - + +
364E ASP* 1.3 73.6 - - - +
366E LYS* 1.3 51.3 + - - +
368E GLN* 3.5 5.5 - - - +
369E ALA* 2.8 34.7 + - - +
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Residues in contact with LYS 366 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E TYR* 3.6 18.8 - - + +
92E SER* 3.8 22.0 - - - +
93E PHE* 3.9 23.8 - - + +
96E LEU* 3.3 33.0 - - - +
203E HIS* 5.0 6.1 - - - -
362E LEU 3.1 14.8 + - - +
363E LEU* 3.0 13.6 + - - +
365E GLU* 1.3 73.9 - - - +
367E PHE* 1.3 66.3 + - - +
369E ALA* 3.4 1.4 + - - +
370E ALA* 3.1 23.9 + - - +
460E LEU* 5.9 0.7 - - - -
461E GLU* 2.8 43.5 + - - +
464E MET* 4.0 16.8 - - - -
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Residues in contact with PHE 367 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344E TRP* 3.7 40.6 - + + +
363E LEU* 2.8 40.5 + - + +
364E ASP* 3.9 4.0 - - - +
366E LYS* 1.3 70.2 - - - +
368E GLN* 1.3 63.5 + - - +
370E ALA* 3.1 4.7 + - - +
371E TYR* 3.0 26.9 + - - +
394E TRP* 4.5 9.2 - + + -
461E GLU* 3.2 38.0 + - + -
464E MET* 4.2 14.1 - - + -
465E GLN* 3.5 57.2 - - + +
468E LEU* 4.3 9.6 - - + -
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Residues in contact with GLN 368 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364E ASP* 2.9 29.5 + - - +
365E GLU* 3.5 6.5 - - - +
367E PHE* 1.3 76.4 - - - +
369E ALA* 1.3 55.0 + - - +
371E TYR* 3.6 11.0 + - - +
372E SER* 2.5 50.1 + - - +
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Residues in contact with ALA 369 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E ASP* 4.0 19.0 - - + +
89E TYR* 4.9 5.4 - - + -
92E SER* 3.8 17.9 - - - +
365E GLU 2.8 22.1 + - - +
366E LYS 3.7 4.9 - - - +
367E PHE 3.2 0.2 - - - -
368E GLN* 1.3 73.0 - - - +
370E ALA* 1.3 58.3 + - - +
372E SER* 3.4 4.8 + - - -
373E LEU* 2.8 31.3 + - - +
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Residues in contact with ALA 370 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E TYR* 3.9 16.6 - - + -
366E LYS 3.1 17.0 + - - +
367E PHE 3.7 1.8 - - - +
369E ALA* 1.3 74.6 - - - +
371E TYR* 1.3 67.9 + - - +
372E SER 3.4 0.2 + - - -
373E LEU* 3.6 19.2 + - - +
394E TRP* 5.0 0.9 - - + -
454E HIS* 4.5 2.1 - - - -
457E LEU* 4.5 12.0 - - + +
458E LEU* 3.4 18.0 - - - +
461E GLU* 3.6 28.5 - - + -
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Residues in contact with TYR 371 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367E PHE 3.0 17.0 + - - +
368E GLN* 4.1 11.0 - - - +
370E ALA* 1.3 76.5 - - - +
372E SER* 1.3 52.9 + - - +
387E SER 5.5 1.1 - - - -
390E ARG* 2.5 34.1 + - + -
391E ARG* 3.3 50.3 - - + +
394E TRP* 4.3 42.7 - + + -
395E ASN* 5.1 0.7 + - - -
458E LEU* 4.2 10.3 - - + +
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Residues in contact with SER 372 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368E GLN* 2.5 39.1 + - - +
369E ALA* 3.4 6.8 + - - -
371E TYR* 1.3 78.1 - - - +
373E LEU* 1.3 63.4 + - - +
374E THR* 2.9 17.5 + - - +
390E ARG* 3.6 5.6 + - - +
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Residues in contact with LEU 373 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E HIS* 3.6 24.0 - - + +
88E ASP* 4.5 18.4 - - + +
89E TYR* 4.4 8.5 - - + +
369E ALA 2.8 22.4 + - - +
370E ALA* 3.6 8.4 + - - +
372E SER* 1.3 68.3 - - - +
374E THR* 1.3 53.6 + - - +
375E TYR* 3.4 39.7 - - + +
390E ARG* 2.9 19.4 + - - -
454E HIS* 2.9 40.5 + - + +
457E LEU* 3.7 22.2 - - + -
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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
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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