Contacts of the helix formed by residues 394 - 413 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E SER* 4.1 2.4 + - - +
389E GLU 3.4 7.9 - - - -
390E ILE* 3.2 22.0 + - + +
393E GLY* 1.3 75.0 - - - +
395E SER* 1.3 54.2 + - - +
396E GLU* 3.5 5.6 + - - -
397E ILE* 2.9 21.1 + - - +
398E GLN* 2.7 33.0 + - - +
501E FAD 2.5 62.5 + - - +
365F GLN* 3.9 5.8 - - - +
368F GLY* 5.3 1.3 - - - -
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Residues in contact with SER 395 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349E LYS* 4.7 1.4 + - - +
350E LEU* 3.7 25.6 - - - +
353E SER* 4.4 2.3 + - - -
354E GLU* 4.0 8.4 + - - -
389E GLU* 3.1 34.1 + - - +
393E GLY 3.9 0.2 + - - -
394E THR* 1.3 74.2 - - - +
396E GLU* 1.3 60.0 + - - +
398E GLN* 3.4 7.1 + - - +
399E ARG* 3.1 44.1 + - - +
365F GLN* 3.7 10.1 + - - +
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Residues in contact with GLU 396 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394E THR* 3.0 1.1 + - - -
395E SER* 1.3 79.9 - - - +
397E ILE* 1.3 67.5 + - - +
399E ARG* 3.3 6.2 + - - -
400E LEU* 3.1 26.5 + - - +
501E FAD 3.0 52.4 + - - +
309F VAL* 4.5 2.0 - - + -
313F LYS* 2.8 41.9 + - - +
362F GLN* 5.4 0.2 + - - -
365F GLN* 2.9 32.1 + - - +
312G PHE* 3.5 27.9 - - + -
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Residues in contact with ILE 397 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161E SER* 3.8 24.9 - - - +
272E ARG* 4.3 20.4 - - - +
393E GLY* 4.4 5.4 - - - -
394E THR* 2.9 24.6 + - - +
396E GLU* 1.3 78.6 - - - +
398E GLN* 1.3 62.7 + - - +
400E LEU* 3.2 25.9 + - + +
401E VAL* 3.0 28.9 + - + +
501E FAD 3.9 28.7 - - + +
300F PHE* 4.7 8.1 - - + -
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Residues in contact with GLN 398 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E ARG* 3.3 22.6 + - - +
346E ALA* 3.2 34.8 - - - +
349E LYS* 3.8 20.5 - - + +
350E LEU* 4.2 19.5 - - + -
392E GLU 3.1 18.0 + - - -
393E GLY* 2.9 27.2 + - - +
394E THR 2.7 21.3 + - - +
395E SER* 3.5 10.8 - - - +
397E ILE* 1.3 72.9 - - - +
399E ARG* 1.3 56.7 + - - +
401E VAL* 3.2 6.2 + - - +
402E ILE* 2.9 34.2 + - - +
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Residues in contact with ARG 399 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350E LEU* 3.6 27.9 - - + +
354E GLU* 3.1 38.2 + - - -
395E SER* 3.1 21.4 + - - +
396E GLU* 3.3 10.8 + - - +
398E GLN* 1.3 70.5 - - - +
400E LEU* 1.3 59.8 + - - +
402E ILE* 4.3 2.7 - - - -
403E ALA* 2.8 31.6 + - - +
312G PHE* 3.6 41.2 - - + -
315G ALA* 3.4 18.1 - - + +
316G ASP* 2.9 36.1 + - - +
319G LEU* 5.4 1.8 - - - +
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Residues in contact with LEU 400 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396E GLU 3.1 15.6 + - - +
397E ILE* 3.4 22.4 - - + +
399E ARG* 1.3 74.1 - - - +
401E VAL* 1.3 58.4 + - + +
403E ALA* 3.4 3.8 + - - +
404E GLY* 3.0 26.5 + - - -
501E FAD 3.5 33.4 - - + +
300F PHE* 6.3 0.2 - - + -
308G GLN* 3.9 14.1 - - + +
311G GLN* 3.5 24.1 - - + +
312G PHE* 3.6 21.1 - - + -
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Residues in contact with VAL 401 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E ARG* 4.2 18.4 - - - +
342E ILE* 3.6 31.2 - - + +
343E LYS* 5.1 0.4 - - - -
346E ALA* 4.0 17.5 - - + -
397E ILE* 3.0 24.8 + - + +
398E GLN* 3.2 8.3 + - - +
400E LEU* 1.3 74.9 - - + +
402E ILE* 1.3 66.1 + - - +
404E GLY* 3.3 2.0 + - - -
405E HIS* 3.1 35.4 + - + +
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Residues in contact with ILE 402 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343E LYS* 4.1 14.4 - - + +
346E ALA* 3.9 15.3 - - + +
347E MET* 3.6 55.4 - - + +
350E LEU* 3.8 27.8 - - + -
398E GLN 2.9 23.6 + - - +
399E ARG* 3.8 5.4 - - - +
401E VAL* 1.3 75.6 - - - +
403E ALA* 1.3 64.7 + - - +
405E HIS* 3.4 1.4 + - - +
406E LEU* 3.0 21.4 + - + +
315G ALA* 3.9 22.9 - - + +
318G ALA* 4.6 4.9 - - + -
319G LEU* 5.0 2.9 - - + -
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Residues in contact with ALA 403 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399E ARG 2.8 22.6 + - - +
400E LEU* 3.7 5.2 - - - +
402E ILE* 1.3 74.2 - - - +
404E GLY* 1.3 62.3 + - - +
406E LEU* 3.2 7.3 + - - +
407E LEU* 2.9 32.3 + - + +
311G GLN* 3.5 47.6 - - + +
314G LEU* 5.5 1.8 - - + -
315G ALA* 4.0 5.8 - - - +
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Residues in contact with GLY 404 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400E LEU 3.0 15.0 + - - -
401E VAL* 3.3 3.3 + - - -
403E ALA* 1.3 75.8 - - - +
405E HIS* 1.3 57.0 - - - +
407E LEU* 3.4 6.2 + - - +
408E ARG* 3.0 49.9 + - - +
411E ARG* 5.3 0.7 + - - -
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Residues in contact with HIS 405 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342E ILE* 3.4 48.5 - - + +
343E LYS* 4.0 28.0 + - + -
401E VAL* 3.1 31.9 + - + +
402E ILE 4.1 0.9 - - - +
404E GLY* 1.3 72.6 - - - +
406E LEU* 1.3 66.9 + - - +
408E ARG* 3.5 31.4 + - + +
409E SER* 3.0 23.7 + - - -
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Residues in contact with LEU 406 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343E LYS* 4.7 11.1 - - + +
402E ILE* 3.0 19.4 + - + +
403E ALA* 3.2 5.8 + - - +
405E HIS* 1.3 75.3 - - - +
407E LEU* 1.3 64.9 + - + +
409E SER* 2.6 28.3 + - - +
410E TYR* 3.2 27.4 + - + -
287G LEU* 4.4 17.3 - - + -
291G VAL* 4.5 7.4 - - + -
314G LEU* 3.7 42.2 - - + +
315G ALA* 4.8 0.7 - - - +
318G ALA* 3.7 24.0 - - + -
322G GLU* 4.7 7.4 - - - +
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Residues in contact with LEU 407 (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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403E ALA* 2.9 21.5 + - + +
404E GLY* 3.8 5.8 - - - +
406E LEU* 1.3 76.1 - - + +
408E ARG* 1.3 65.6 + - - +
410E TYR* 3.0 7.2 + - - +
411E ARG* 3.0 48.9 + - - +
291G VAL* 4.0 27.8 - - + -
295G GLU* 4.2 7.4 - - - +
305G THR* 3.8 43.3 - - + +
311G GLN* 4.7 13.7 - - + +
314G LEU* 4.3 13.7 - - + -
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Residues in contact with ARG 408 (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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404E GLY* 3.0 41.3 + - - +
405E HIS* 3.6 39.5 + - + +
407E LEU* 1.3 75.3 - - - +
409E SER* 1.3 53.8 + - - +
411E ARG* 3.2 20.8 + - + +
412E SER* 2.8 38.0 + - - -
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Residues in contact with SER 409 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343E LYS* 6.4 0.4 - - - -
405E HIS 3.0 14.5 + - - -
406E LEU* 2.6 25.4 + - - +
408E ARG* 1.3 74.5 - - - +
410E TYR* 1.3 69.7 + - - +
412E SER* 3.3 15.7 + - - -
413E ALA* 3.4 16.3 + - - +
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Residues in contact with TYR 410 (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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406E LEU* 3.3 40.2 - - + -
407E LEU 3.0 8.3 + - - +
409E SER* 1.3 86.6 + - - +
411E ARG* 1.3 61.6 + - - +
413E ALA* 3.4 18.3 - - - +
284G GLN* 3.6 13.2 + - - -
287G LEU* 3.8 7.3 - - + +
288G ASP* 2.6 46.9 + - + -
291G VAL* 3.6 44.2 - - + -
292G ASN* 4.6 11.0 - - - +
295G GLU* 5.1 4.3 - - + +
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Residues in contact with ARG 411 (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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404E GLY 5.3 1.0 + - - -
407E LEU* 3.0 41.1 + - - +
408E ARG* 3.7 22.2 - - + +
410E TYR* 1.3 74.7 - - - +
412E SER* 1.3 65.9 + - - +
413E ALA 3.6 5.0 - - - +
295G GLU* 2.9 41.6 + - - +
305G THR* 4.1 4.4 + - - -
306G LYS* 4.1 17.5 - - - +
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Residues in contact with SER 412 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408E ARG* 2.8 23.4 + - - -
409E SER* 3.3 11.6 + - - -
411E ARG* 1.3 73.9 - - - +
413E ALA* 1.3 69.4 + - - +
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Residues in contact with ALA 413 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409E SER 3.4 14.5 + - - +
410E TYR* 3.4 15.5 - - - +
411E ARG 3.4 6.4 - - - +
412E SER* 1.3 85.5 + - - +
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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