Contacts of the helix formed by residues 394 - 413 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365G GLN* 3.9 3.6 - - - +
368G GLY* 5.2 1.8 - - - -
161H SER* 4.2 1.1 - - - +
389H GLU 3.3 9.6 - - - -
390H ILE* 3.1 24.0 + - + +
393H GLY* 1.3 76.5 - - - +
395H SER* 1.3 59.7 + - - +
396H GLU* 3.4 6.9 + - - +
397H ILE* 3.0 22.1 + - - +
398H GLN* 2.8 24.7 + - - +
501H FAD 2.6 61.8 + - - +
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Residues in contact with SER 395 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365G GLN* 4.0 9.4 - - - -
349H LYS* 4.6 1.0 + - - +
350H LEU* 3.6 26.7 - - - +
353H SER* 4.1 5.0 + - - -
354H GLU* 3.8 7.7 + - - -
389H GLU* 3.1 30.2 + - - +
393H GLY 3.8 0.4 + - - -
394H THR* 1.3 71.8 - - - +
396H GLU* 1.3 56.2 + - - +
398H GLN* 3.1 8.0 + - - +
399H ARG* 2.8 49.4 + - - +
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Residues in contact with GLU 396 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312F PHE* 3.5 18.9 - - + -
309G VAL* 4.0 14.8 - - + -
313G LYS* 2.8 41.3 + - - +
365G GLN* 2.9 31.6 + - - +
394H THR* 3.4 1.2 - - - -
395H SER* 1.3 80.5 - - - +
397H ILE* 1.3 64.6 + - - +
399H ARG* 3.3 5.2 + - - +
400H LEU* 3.0 27.7 + - - +
501H FAD 3.0 46.6 + - - +
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Residues in contact with ILE 397 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300G PHE* 5.0 6.5 - - + -
161H SER* 3.9 24.0 - - - +
272H ARG* 4.2 17.5 - - - +
393H GLY* 4.3 6.3 - - - -
394H THR* 3.0 25.2 + - - +
396H GLU* 1.3 76.7 - - - +
398H GLN* 1.3 61.6 + - - +
400H LEU* 3.3 23.1 + - + +
401H VAL* 2.9 40.6 + - + +
501H FAD 4.0 28.0 - - + +
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Residues in contact with GLN 398 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272H ARG* 3.6 17.8 + - - +
346H ALA* 3.2 31.4 - - - +
349H LYS* 3.7 18.5 - - + +
350H LEU* 3.9 26.0 - - + -
392H GLU 3.1 17.4 + - - -
393H GLY* 2.7 30.5 + - - +
394H THR 2.8 14.6 + - - +
395H SER* 3.1 12.1 + - - +
397H ILE* 1.3 76.8 - - - +
399H ARG* 1.3 58.0 + - - +
401H VAL* 3.2 5.3 + - - +
402H ILE* 2.8 34.5 + - - +
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Residues in contact with ARG 399 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312F PHE* 3.7 41.5 - - + -
315F ALA* 3.4 18.8 - - + +
316F ASP* 2.9 33.6 + - - +
350H LEU* 3.6 27.3 - - + +
354H GLU* 3.1 40.4 + - - -
395H SER* 2.8 28.1 + - - +
396H GLU* 3.3 12.8 + - - +
398H GLN* 1.3 72.4 - - - +
400H LEU* 1.3 56.6 + - - +
402H ILE* 3.3 3.2 + - - -
403H ALA* 2.8 32.3 + - - +
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Residues in contact with LEU 400 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308F GLN* 4.1 14.4 - - + +
311F GLN* 3.3 25.4 - - - +
312F PHE* 3.6 20.2 - - + -
396H GLU 3.0 18.5 + - - +
397H ILE* 3.5 18.4 - - + +
399H ARG* 1.3 76.3 - - - +
401H VAL* 1.3 59.2 + - + +
403H ALA* 3.8 3.7 - - - +
404H GLY* 3.0 26.5 + - - -
501H FAD 3.4 38.4 - - + +
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Residues in contact with VAL 401 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272H ARG* 4.0 19.5 - - - +
342H ILE* 3.9 30.3 - - + +
343H LYS* 5.0 0.4 - - - -
346H ALA* 3.9 17.9 - - + -
397H ILE* 2.9 32.4 + - + +
398H GLN* 3.5 5.6 - - - +
400H LEU* 1.3 76.2 - - + +
402H ILE* 1.3 64.1 + - - +
404H GLY* 3.5 0.9 + - - -
405H HIS* 3.1 36.4 + - + +
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Residues in contact with ILE 402 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315F ALA* 4.0 23.6 - - + +
318F ALA* 4.5 4.7 - - + -
319F LEU* 4.5 2.9 - - + -
343H LYS* 4.2 13.3 - - + +
346H ALA* 3.9 15.5 - - + -
347H MET* 3.7 56.1 - - + +
350H LEU* 3.8 28.3 - - + -
398H GLN 2.8 25.4 + - - +
399H ARG* 3.8 4.7 - - - +
401H VAL* 1.3 72.0 - - - +
403H ALA* 1.3 57.4 + - - +
405H HIS* 3.2 2.6 + - - +
406H LEU* 2.9 27.6 + - + +
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Residues in contact with ALA 403 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311F GLN* 3.3 50.3 - - + +
314F LEU* 5.5 1.6 - - + -
315F ALA* 4.0 4.9 - - + +
399H ARG 2.8 19.3 + - - +
400H LEU* 3.8 5.4 - - - +
402H ILE* 1.3 72.5 - - - +
404H GLY* 1.3 63.2 + - - +
406H LEU* 3.7 7.3 - - - +
407H LEU* 3.0 32.8 + - + +
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Residues in contact with GLY 404 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311F GLN* 5.7 0.6 + - - -
400H LEU 3.0 17.1 + - - -
401H VAL* 3.9 1.6 - - - -
402H ILE 3.3 0.2 - - - -
403H ALA* 1.3 76.0 - - - +
405H HIS* 1.3 57.0 + - - +
407H LEU* 3.7 5.7 + - - +
408H ARG* 3.1 44.7 + - - +
411H ARG* 5.4 1.2 + - - -
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Residues in contact with HIS 405 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342H ILE* 3.3 50.5 - - + +
343H LYS* 3.8 29.2 - - + -
401H VAL* 3.1 31.9 + - + +
402H ILE 4.0 0.9 - - - +
404H GLY* 1.3 73.1 - - - +
406H LEU* 1.3 67.0 + - - +
408H ARG* 3.4 29.9 + - - +
409H SER* 3.0 23.6 + - - -
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Residues in contact with LEU 406 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287F LEU* 4.6 15.9 - - + -
291F VAL* 4.7 6.5 - - + -
314F LEU* 3.6 41.7 - - + +
315F ALA* 4.7 1.3 - - - +
318F ALA* 3.7 23.3 - - + -
322F GLU* 4.6 9.4 - - - +
343H LYS* 4.6 10.4 - - + +
402H ILE* 2.9 18.4 + - + +
403H ALA* 3.7 5.6 - - - +
405H HIS* 1.3 76.3 - - - +
407H LEU* 1.3 62.4 + - + +
409H SER* 2.6 26.7 + - - +
410H TYR* 3.2 29.0 + - + -
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Residues in contact with LEU 407 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291F VAL* 4.0 20.9 - - + -
295F GLU* 3.8 12.7 - - - +
305F THR* 3.8 46.4 - - + +
311F GLN* 4.7 10.8 - - + +
314F LEU* 4.4 13.0 - - + -
403H ALA* 3.0 25.0 + - + +
404H GLY* 4.1 5.2 - - - +
406H LEU* 1.3 74.8 - - + +
408H ARG* 1.3 65.8 + - - +
410H TYR* 3.2 5.4 + - - +
411H ARG* 3.0 49.0 + - - +
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Residues in contact with ARG 408 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404H GLY* 3.1 30.6 + - - +
405H HIS* 3.5 45.6 + - - +
406H LEU 3.3 0.2 - - - -
407H LEU* 1.3 75.4 - - - +
409H SER* 1.3 57.0 + - - +
411H ARG* 3.4 17.7 + - + +
412H SER* 2.8 30.3 + - - -
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Residues in contact with SER 409 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405H HIS 3.0 13.0 + - - -
406H LEU* 2.6 26.0 + - - +
408H ARG* 1.3 75.3 - - - +
410H TYR* 1.3 66.7 + - - +
412H SER* 4.0 6.0 - - - -
413H ALA* 3.1 28.2 + - - +
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Residues in contact with TYR 410 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284F GLN* 3.6 11.3 + - - -
287F LEU* 3.9 8.3 - - - +
288F ASP* 2.6 45.9 + - + -
291F VAL* 3.5 43.7 - - + -
292F ASN* 5.5 2.7 - - + -
295F GLU* 5.6 2.7 - - + +
406H LEU* 3.2 41.2 + - + -
407H LEU* 3.2 6.7 + - + +
409H SER* 1.3 85.6 + - - +
411H ARG* 1.3 62.1 + - + +
413H ALA* 3.2 23.2 - - + +
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Residues in contact with ARG 411 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295F GLU* 2.8 40.6 + - - +
305F THR* 4.3 4.9 + - - -
306F LYS* 4.8 16.3 - - - +
404H GLY 5.4 1.4 + - - -
407H LEU* 3.0 42.1 + - - +
408H ARG* 3.8 16.7 - - + +
410H TYR* 1.3 74.6 - - + +
412H SER* 1.3 64.0 + - - +
413H ALA 3.5 6.8 + - - +
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Residues in contact with SER 412 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408H ARG* 2.8 23.0 + - - -
409H SER* 4.0 6.7 - - - -
411H ARG* 1.3 73.9 - - - +
413H ALA* 1.3 60.1 + - - +
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Residues in contact with ALA 413 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409H SER 3.1 19.8 + - - +
410H TYR* 3.2 18.1 - - + +
411H ARG 3.5 5.4 - - - +
412H SER* 1.3 80.4 - - - +
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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
------------------------------------------------------------
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