Contacts of the helix formed by residues 360 - 370 (chain B) in PDB entry 2VM8
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 GLU 360 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B THR* 3.9 3.1 - - + -
333B HIS* 6.0 0.3 - - - -
356B ASN* 3.9 11.1 + - - +
357B GLY* 3.2 7.9 + - - +
359B GLU* 1.3 103.6 + - + +
361B ARG* 1.3 59.8 + - - +
362B MET 3.6 1.3 - - - -
363B SER* 3.8 7.5 - - - -
364B VAL* 2.8 47.7 + - + +
420B ILE* 3.5 32.1 - - + +
425B HIS* 4.1 5.9 + - - +
432B ASN* 3.0 24.5 - - - +
434B PHE* 4.0 17.0 - - + -
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Residues in contact with ARG 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLY* 3.4 5.7 - - - -
70B ILE 3.1 40.5 + - - +
71B ASP* 3.4 13.0 + - - +
101B THR* 2.8 27.6 + - - +
280B THR* 3.4 25.5 - - - +
283B LEU* 6.0 0.2 - - + -
329B THR* 3.2 34.1 + - - +
330B GLY* 3.8 19.5 - - - +
331B SER 4.4 0.2 - - - +
357B GLY 3.4 7.1 + - - +
358B THR* 4.1 7.8 + - - +
359B GLU 3.5 2.6 - - - -
360B GLU* 1.3 79.1 - - - +
362B MET* 1.3 69.3 + - + +
364B VAL* 3.7 1.7 - - - +
365B ILE* 3.2 38.0 + - + +
384B THR* 2.9 26.1 + - - +
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Residues in contact with MET 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ILE* 3.9 20.4 - - + -
67B PRO 4.7 2.5 - - - +
69B GLY* 3.7 19.5 - - - +
99B GLY 4.1 8.1 + - - +
100B GLY* 3.1 35.4 - - - +
101B THR* 3.8 5.8 - - - +
360B GLU 3.6 0.2 - - - -
361B ARG* 1.3 88.3 - - - +
363B SER* 1.3 59.6 + - - +
365B ILE* 4.1 7.0 - - - -
366B TRP 3.4 3.1 + - - -
380B PHE* 3.3 34.0 - - + -
384B THR* 3.7 33.2 - - + +
412B TRP* 3.2 22.7 - - + -
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Residues in contact with SER 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B GLY* 4.9 3.4 + - - -
359B GLU 5.0 3.0 + - - -
360B GLU* 3.4 14.0 + - - -
361B ARG 3.2 1.0 - - - -
362B MET* 1.3 76.1 - - - +
364B VAL* 1.3 56.8 + - - +
366B TRP* 3.1 5.9 + - - +
367B ASP* 2.9 31.2 + - - +
412B TRP* 3.6 14.3 - - - -
420B ILE* 5.5 2.5 - - - -
439B CYS* 3.9 13.5 - - - -
440B ARG 3.7 5.4 - - - +
441B GLY 2.8 22.9 + - - -
442B SER* 3.9 6.6 - - - -
443B PRO* 4.4 4.5 - - - +
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Residues in contact with VAL 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B THR* 4.0 14.1 - - + +
283B LEU* 4.0 7.2 - - + +
284B GLY* 3.6 33.7 - - - +
360B GLU* 2.8 40.4 + - + +
361B ARG 3.7 3.6 - - - +
363B SER* 1.3 78.5 - - - +
365B ILE* 1.3 55.3 + - + +
367B ASP* 3.4 0.9 + - - +
368B LYS* 2.8 45.5 + - + +
420B ILE* 4.3 14.1 - - + -
434B PHE* 4.7 5.4 - - + -
437B MET* 4.3 10.8 - - - -
439B CYS* 3.9 7.8 - - - -
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Residues in contact with ILE 365 (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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280B THR* 6.4 0.4 - - - -
283B LEU* 4.0 21.1 - - + -
318B ASN* 4.4 7.2 - - - +
321B LEU* 4.1 19.1 - - + -
329B THR* 3.5 33.9 - - + +
361B ARG* 3.2 31.0 + - + +
364B VAL* 1.3 74.7 - - + +
366B TRP* 1.3 58.9 + - - +
369B ALA* 2.7 38.9 + - + +
370B VAL 3.7 1.0 + - - -
375B MET* 4.6 2.7 - - + -
380B PHE* 4.1 19.7 - - + -
383B VAL* 4.5 7.9 - - + -
384B THR* 3.9 14.4 - - + -
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Residues in contact with TRP 366 (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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64B MET* 3.6 21.8 - - + -
362B MET 3.4 13.8 + - - +
363B SER 3.1 10.4 + - - +
365B ILE* 1.3 79.4 - - - +
367B ASP* 1.3 61.7 + - - +
370B VAL* 3.3 32.6 + - + -
371B VAL* 3.0 41.5 + - + +
377B GLU* 3.7 22.9 - - + -
380B PHE* 3.4 48.4 - + - -
412B TRP* 3.4 17.7 - - + -
414B PRO* 3.4 37.2 + - + +
440B ARG 3.5 12.3 - - - +
441B GLY* 3.9 8.7 - - - -
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Residues in contact with ASP 367 (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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363B SER 2.9 15.6 + - - +
364B VAL 3.8 4.0 - - - +
366B TRP* 1.3 74.9 - - - +
368B LYS* 1.3 71.1 + - + +
371B VAL* 3.5 16.7 - - - +
372B THR* 3.4 18.7 - - - +
437B MET* 5.2 4.6 - - - +
438B GLU 3.8 8.8 - - - +
439B CYS* 3.8 17.4 - - - -
440B ARG* 2.8 42.8 + - - +
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Residues in contact with LYS 368 (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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283B LEU 3.2 21.2 + - - +
284B GLY* 4.3 11.7 + - - +
314B PRO* 3.2 29.7 - - - +
315B ASP* 4.8 2.8 - - - +
318B ASN* 3.5 25.8 + - - +
364B VAL* 2.8 32.5 + - + +
365B ILE 4.1 0.2 - - - +
367B ASP* 1.3 89.0 - - + +
369B ALA* 1.3 56.6 + - - +
372B THR* 2.9 23.0 + - + +
374B LYS* 3.7 11.6 - - - +
437B MET* 5.4 7.4 - - + -
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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
----------------------------------------------------------
318B ASN* 3.6 19.7 - - + +
322B SER* 4.1 6.7 - - - +
365B ILE* 2.7 21.4 + - + +
368B LYS* 1.3 75.5 - - - +
370B VAL* 1.3 55.5 + - - +
372B THR* 3.3 8.1 - - - -
374B LYS* 2.7 32.8 + - + +
375B MET* 2.8 38.2 + - + -
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Residues in contact with VAL 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A ALA* 4.3 8.5 - - - +
365B ILE 3.7 1.1 + - - +
366B TRP* 3.3 58.0 + - + +
369B ALA* 1.3 76.3 - - - +
371B VAL* 1.3 63.5 + - + +
372B THR 3.0 1.3 - - - -
373B GLY* 2.8 21.8 + - - -
375B MET* 3.4 37.5 - - + +
376B ASP* 3.9 9.9 - - - +
377B GLU 4.7 5.2 - - - +
380B PHE* 4.0 9.4 - - + -
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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