Contacts of the helix formed by residues 394 - 411 (chain G) in PDB entry 2VIG
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 THR 394 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161G SER* 4.1 2.7 - - - +
389G GLU 3.4 9.6 - - - -
390G ILE* 3.5 15.7 - - + +
393G GLY* 1.3 75.6 - - - +
395G SER* 1.3 65.6 + - - +
396G GLU* 3.5 5.1 + - - -
397G ILE* 2.9 23.4 + - - +
398G GLN* 2.9 20.5 + - - +
501G FAD 2.7 68.6 + - - +
365H GLN* 4.1 3.1 - - - +
368H GLY* 5.3 1.8 - - - -
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Residues in contact with SER 395 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349G LYS* 4.6 1.7 - - - +
350G LEU* 3.6 25.9 - - - +
353G SER* 4.3 3.0 + - - -
354G GLU* 4.0 8.2 + - - +
389G GLU* 3.1 34.6 + - - +
393G GLY 3.8 0.4 + - - -
394G THR* 1.3 71.8 - - - +
396G GLU* 1.3 64.8 + - - +
398G GLN* 3.3 6.6 + - - +
399G ARG* 3.1 42.0 + - - +
365H GLN* 3.9 10.0 + - - +
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Residues in contact with GLU 396 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312E PHE* 3.4 23.5 - - + -
394G THR* 3.1 0.9 + - - -
395G SER* 1.3 76.9 - - - +
397G ILE* 1.3 67.8 + - - +
399G ARG* 3.4 7.6 + - - +
400G LEU* 3.2 20.6 + - - +
501G FAD 3.1 43.9 + - - +
309H VAL* 4.0 14.8 - - + -
310H ILE* 5.6 0.2 - - + -
313H LYS* 2.7 42.0 + - - -
365H GLN* 2.8 37.1 + - - +
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Residues in contact with ILE 397 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161G SER* 3.9 31.4 - - - +
272G ARG* 4.2 14.4 - - - +
393G GLY* 4.2 6.5 - - - -
394G THR* 2.9 25.7 + - - +
396G GLU* 1.3 78.6 - - - +
398G GLN* 1.3 63.2 + - - +
400G LEU* 3.2 24.3 + - + +
401G VAL* 3.0 22.3 + - + +
501G FAD 4.2 14.8 - - + +
502G COS 4.0 46.0 - - + +
300H PHE* 4.6 0.7 - - + -
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Residues in contact with GLN 398 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272G ARG* 3.7 18.3 + - - +
346G ALA* 3.3 41.5 - - + +
349G LYS* 3.7 18.4 - - + +
350G LEU* 4.0 17.3 - - + -
392G GLU 3.2 16.6 + - - -
393G GLY* 2.8 31.4 + - - +
394G THR 2.9 14.5 + - - +
395G SER* 3.3 10.1 + - - +
397G ILE* 1.3 75.4 - - - +
399G ARG* 1.3 63.1 + - - +
401G VAL* 3.2 5.1 + - - +
402G ILE* 2.9 28.5 + - + +
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Residues in contact with ARG 399 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312E PHE* 3.7 39.0 - - + -
315E ALA* 3.4 16.1 - - + +
316E ASP* 2.8 37.0 + - - +
319E LEU* 5.7 1.6 - - - +
350G LEU* 3.7 19.0 - - + +
354G GLU* 3.3 38.0 + - - -
395G SER* 3.1 29.2 + - - +
396G GLU* 3.6 13.8 + - - +
398G GLN* 1.3 75.7 - - - +
400G LEU* 1.3 51.5 + - - +
402G ILE* 3.3 3.3 + - - -
403G ALA* 2.8 36.3 + - - +
313H LYS* 6.0 0.4 - - - +
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Residues in contact with LEU 400 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308E GLN* 4.1 12.3 - - + +
311E GLN* 3.3 26.6 - - + +
312E PHE* 3.8 19.1 - - + -
396G GLU 3.2 13.1 + - - +
397G ILE* 3.2 23.3 + - + +
399G ARG* 1.3 71.6 - - - +
401G VAL* 1.3 67.1 + - + +
403G ALA* 3.5 4.3 + - - +
404G GLY* 3.1 20.1 + - - -
501G FAD 3.6 37.0 - - + +
502G COS 6.1 2.2 - - + +
300H PHE* 6.1 0.4 - - + -
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Residues in contact with VAL 401 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272G ARG* 4.2 18.2 - - - +
342G ILE* 3.6 31.4 - - + +
343G LYS 4.9 0.2 - - - +
346G ALA* 4.0 17.9 - - + -
397G ILE* 3.0 20.7 + - + +
398G GLN* 3.6 7.9 - - - +
400G LEU* 1.3 75.8 - - + +
402G ILE* 1.3 61.5 + - - +
404G GLY* 3.4 2.0 + - - -
405G HIS* 3.1 35.2 + - + +
408G ARG* 4.7 0.8 + - - +
502G COS 3.7 23.1 - - - +
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Residues in contact with ILE 402 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315E ALA* 3.9 26.0 - - + +
318E ALA* 4.7 4.7 - - + -
319E LEU* 5.2 2.2 - - + -
343G LYS* 4.0 13.3 - - + +
346G ALA* 3.8 15.0 - - + -
347G MET* 3.8 54.5 - - + +
350G LEU* 3.8 26.9 - - + -
398G GLN 2.9 23.0 + - - +
399G ARG* 3.7 4.7 - - - +
401G VAL* 1.3 73.1 - - - +
403G ALA* 1.3 60.2 + - - +
404G GLY 3.2 0.2 + - - -
405G HIS* 3.3 2.8 + - - +
406G LEU* 2.8 29.2 + - + +
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Residues in contact with ALA 403 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311E GLN* 3.5 47.6 - - + +
314E LEU* 5.6 0.9 - - + -
315E ALA* 3.9 6.5 - - - +
399G ARG 2.8 21.2 + - - +
400G LEU* 3.7 7.0 - - - +
402G ILE* 1.3 72.1 - - - +
404G GLY* 1.3 57.4 + - - +
406G LEU* 3.4 7.7 + - - +
407G LEU* 3.0 37.9 + - + +
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Residues in contact with GLY 404 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400G LEU 3.1 16.8 + - - -
401G VAL 3.8 1.8 - - - -
402G ILE 3.2 0.2 - - - -
403G ALA* 1.3 75.3 - - - +
405G HIS* 1.3 57.9 + - - +
407G LEU* 3.6 5.9 + - - +
408G ARG* 3.1 51.3 + - - +
411G ARG* 5.6 0.5 + - - -
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Residues in contact with HIS 405 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342G ILE* 3.4 47.6 - - + +
343G LYS* 3.8 29.5 + - + +
401G VAL* 3.1 31.1 + - + +
402G ILE 3.9 1.1 - - - +
404G GLY* 1.3 72.4 - - - +
406G LEU* 1.3 66.5 + - - +
408G ARG* 3.4 30.8 + - + +
409G SER* 3.0 24.4 + - - -
502G COS 6.1 1.6 - - - -
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Residues in contact with LEU 406 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287E LEU* 4.4 16.8 - - + -
291E VAL* 4.6 5.4 - - + -
314E LEU* 3.6 42.6 - - + +
315E ALA* 4.6 1.8 - - - +
318E ALA* 3.8 24.7 - - + -
322E GLU* 5.1 6.1 - - - +
343G LYS* 4.7 9.5 - - + +
402G ILE* 2.8 19.3 + - + +
403G ALA* 3.4 6.0 + - - +
405G HIS* 1.3 76.5 - - - +
407G LEU* 1.3 63.6 + - + +
409G SER* 2.7 26.4 + - - +
410G TYR* 3.1 35.6 - - + -
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Residues in contact with LEU 407 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291E VAL* 4.0 27.1 - - + -
295E GLU* 4.3 6.0 - - - +
305E THR* 3.7 45.1 - - + +
311E GLN* 4.8 8.5 - - + -
314E LEU* 4.3 14.4 - - + -
403G ALA* 3.0 23.0 + - + +
404G GLY* 4.0 5.8 - - - +
406G LEU* 1.3 76.2 - - + +
408G ARG* 1.3 66.4 + - - +
410G TYR* 3.2 6.2 + - - +
411G ARG* 3.1 50.0 + - - +
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Residues in contact with ARG 408 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401G VAL* 4.7 1.0 + - - +
404G GLY* 3.1 41.2 + - - +
405G HIS* 3.5 41.7 + - + +
406G LEU 3.4 0.2 - - - -
407G LEU* 1.3 76.0 - - - +
409G SER* 1.3 61.3 + - - +
411G ARG* 3.0 39.3 + - - +
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Residues in contact with SER 409 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405G HIS 3.0 13.2 + - - -
406G LEU* 2.7 23.5 + - - +
407G LEU 3.3 0.2 - - - -
408G ARG* 1.3 76.7 - - - +
410G TYR* 1.3 70.4 + - - +
411G ARG 4.3 2.8 - - - -
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Residues in contact with TYR 410 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284E GLN* 3.6 11.8 + - - -
287E LEU* 3.9 13.3 - - - +
288E ASP* 2.7 42.0 + - + -
291E VAL* 3.6 39.7 - - + -
292E ASN* 5.6 1.3 - - + -
295E GLU* 5.7 2.9 - - + +
406G LEU* 3.1 42.8 - - + +
407G LEU* 3.2 8.1 + - - +
409G SER* 1.3 86.2 + - - +
411G ARG* 1.3 63.7 + - + +
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Residues in contact with ARG 411 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295E GLU* 2.9 41.8 + - - +
305E THR* 4.2 3.8 + - - -
306E LYS* 4.5 14.9 - - - +
404G GLY 5.6 0.2 + - - -
407G LEU* 3.1 39.0 + - - +
408G ARG* 3.0 32.1 + - - +
409G SER 4.3 2.7 - - - -
410G TYR* 1.3 80.8 - - - +
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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