Contacts of the helix formed by residues 394 - 413 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365C GLN* 4.0 5.8 - - - +
368C GLY* 5.4 0.7 - - - -
161D SER* 4.0 2.6 + - - +
389D GLU 3.4 3.8 - - - -
390D ILE* 3.2 26.7 + - + +
393D GLY* 1.3 74.8 - - - +
395D SER* 1.3 55.0 + - - +
396D GLU* 3.5 5.8 - - - +
397D ILE* 3.0 23.1 + - - +
398D GLN* 2.8 31.4 + - - +
501D FAD 2.7 63.3 + - - +
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Residues in contact with SER 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C GLN* 3.8 5.6 - - - +
349D LYS* 4.7 1.1 + - - +
350D LEU* 3.6 26.4 - - - +
353D SER* 4.1 4.0 + - - -
354D GLU* 3.9 7.7 + - - -
389D GLU* 3.1 32.8 + - - +
393D GLY 3.7 0.2 + - - -
394D THR* 1.3 72.3 - - - +
396D GLU* 1.3 65.5 + - - +
398D GLN* 3.3 8.0 + - - +
399D ARG* 3.0 43.0 + - - +
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Residues in contact with GLU 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B PHE* 3.7 27.1 - - + -
309C VAL* 4.7 1.6 - - + -
313C LYS* 3.0 40.7 + - - +
365C GLN* 2.9 31.5 + - - +
394D THR* 3.1 0.9 - - - -
395D SER* 1.3 79.4 - - - +
397D ILE* 1.3 67.1 + - - +
399D ARG* 3.2 9.8 + - - +
400D LEU* 3.1 27.1 + - - +
501D FAD 2.9 49.1 + - - +
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Residues in contact with ILE 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C PHE* 5.4 2.7 - - + -
161D SER* 3.8 22.4 - - - +
272D ARG* 3.7 26.9 - - - +
393D GLY* 3.9 6.7 - - - -
394D THR* 3.0 21.8 + - - +
396D GLU* 1.3 77.9 - - - +
398D GLN* 1.3 62.9 + - - +
400D LEU* 3.3 11.1 + - + +
401D VAL* 3.0 27.9 + - + +
501D FAD 3.8 35.9 - - + +
502D COS 3.8 25.4 - - + +
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Residues in contact with GLN 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272D ARG* 3.4 20.6 + - - +
346D ALA* 3.2 34.5 - - - +
349D LYS* 3.8 20.7 - - + +
350D LEU* 4.1 20.6 - - + -
392D GLU 3.2 17.8 + - - -
393D GLY* 2.8 30.0 + - - +
394D THR 2.8 18.3 + - - +
395D SER* 3.4 13.5 - - - +
397D ILE* 1.3 73.0 - - - +
399D ARG* 1.3 57.6 + - - +
401D VAL* 3.3 4.7 + - - +
402D ILE* 2.9 34.1 + - - +
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Residues in contact with ARG 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B PHE* 3.6 40.6 - - + -
315B ALA* 3.4 16.4 - - + +
316B ASP* 2.9 36.7 + - - +
319B LEU* 5.5 2.0 - - - +
350D LEU* 3.7 26.5 - - + +
354D GLU* 3.0 39.8 + - - -
395D SER* 3.0 23.4 + - - +
396D GLU* 3.2 12.7 + - - +
398D GLN* 1.3 74.6 - - - +
400D LEU* 1.3 58.0 + - - +
402D ILE* 3.3 2.8 + - - -
403D ALA* 2.8 31.9 + - - +
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Residues in contact with LEU 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B GLN* 3.9 17.7 - - + +
311B GLN* 3.3 26.3 - - + +
312B PHE* 3.6 21.3 - - + -
396D GLU 3.1 16.3 + - - +
397D ILE* 3.6 12.8 - - + +
399D ARG* 1.3 76.5 - - - +
401D VAL* 1.3 58.7 - - + +
403D ALA* 3.8 3.7 - - - +
404D GLY* 3.0 25.3 + - - -
501D FAD 3.6 38.1 - - + +
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Residues in contact with VAL 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D ARG* 4.1 19.3 - - - +
342D ILE* 3.8 29.2 - - + +
343D LYS* 4.9 0.4 - - - -
346D ALA* 3.8 21.5 - - + -
397D ILE* 3.0 25.5 + - + +
398D GLN 3.6 7.9 - - - +
400D LEU* 1.3 74.6 - - + +
402D ILE* 1.3 66.2 + - - +
404D GLY* 3.4 1.9 + - - -
405D HIS* 3.1 35.1 + - + +
502D COS 6.0 1.3 - - - -
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Residues in contact with ILE 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B ALA* 4.0 23.3 - - + +
318B ALA* 4.7 3.8 - - + -
319B LEU* 5.1 2.7 - - + -
343D LYS* 4.0 14.0 - - + +
346D ALA* 3.8 15.0 - - + -
347D MET* 3.7 55.4 - - + +
350D LEU* 3.7 28.5 - - + -
398D GLN 2.9 25.2 + - - +
399D ARG* 3.7 5.4 - - - +
401D VAL* 1.3 75.9 - - - +
403D ALA* 1.3 58.3 + - - +
405D HIS* 3.3 1.9 + - - +
406D LEU* 2.8 29.0 + - + +
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Residues in contact with ALA 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B GLN* 3.4 47.1 - - + +
314B LEU* 5.4 2.0 - - + -
315B ALA* 4.1 5.4 - - + +
399D ARG 2.8 17.9 + - - +
400D LEU* 3.8 5.6 - - - +
402D ILE* 1.3 78.6 - - - +
404D GLY* 1.3 61.7 + - - +
406D LEU* 3.2 8.4 + - - +
407D LEU* 3.1 32.1 + - + +
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Residues in contact with GLY 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B GLN* 5.5 1.7 + - - -
400D LEU 3.0 17.1 + - - -
401D VAL* 3.4 2.0 + - - -
403D ALA* 1.3 76.5 - - - +
405D HIS* 1.3 59.3 + - - +
407D LEU* 3.6 6.4 + - - +
408D ARG* 3.2 40.5 + - - +
411D ARG* 5.6 0.3 + - - -
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Residues in contact with HIS 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342D ILE* 3.4 49.7 - - + +
343D LYS* 3.8 28.8 - - + +
401D VAL* 3.1 29.5 + - + +
402D ILE 4.0 0.2 - - - +
404D GLY* 1.3 74.7 - - - +
406D LEU* 1.3 67.0 + - - +
408D ARG* 3.5 37.2 + - + +
409D SER* 3.1 21.7 + - - -
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Residues in contact with LEU 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B LEU* 4.5 10.1 - - + -
291B VAL* 4.4 13.7 - - + -
314B LEU* 3.7 42.8 - - + +
315B ALA* 5.1 0.4 - - - -
318B ALA* 4.0 22.7 - - + -
322B GLU* 5.0 5.6 - - - +
343D LYS* 4.8 9.3 - - + +
402D ILE* 2.8 17.5 + - + +
403D ALA* 3.2 7.8 + - - +
405D HIS* 1.3 76.7 - - - +
407D LEU* 1.3 59.6 + - + +
409D SER* 2.5 32.1 + - - +
410D TYR* 3.3 31.9 + - + -
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Residues in contact with LEU 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B VAL* 3.9 27.8 - - + -
295B GLU* 4.2 6.4 - - - +
305B THR* 3.9 44.0 - - + +
311B GLN* 5.0 9.6 - - + -
314B LEU* 4.2 13.5 - - + -
403D ALA* 3.1 19.4 + - + +
404D GLY* 3.9 5.8 - - - +
406D LEU* 1.3 80.5 - - + +
408D ARG* 1.3 59.8 + - - +
410D TYR* 3.2 5.6 + - - +
411D ARG* 2.9 58.1 + - - +
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Residues in contact with ARG 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404D GLY* 3.2 26.2 + - - +
405D HIS* 3.8 37.1 + - + +
406D LEU 3.4 0.2 - - - -
407D LEU* 1.3 75.4 - - - +
409D SER* 1.3 52.3 + - - +
411D ARG* 3.2 17.9 + - - +
412D SER* 2.5 38.1 + - - -
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Residues in contact with SER 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343D LYS* 6.3 1.1 - - - -
405D HIS 3.1 11.1 + - - -
406D LEU* 2.5 28.9 + - - +
408D ARG* 1.3 78.0 - - - +
410D TYR* 1.3 67.4 + - - +
412D SER* 3.6 7.2 + - - -
413D ALA* 3.4 21.1 + - - +
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Residues in contact with TYR 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B GLN* 3.6 12.0 + - - -
287B LEU* 3.9 8.3 - - - +
288B ASP* 2.7 47.0 + - + -
291B VAL* 3.6 40.2 - - + -
292B ASN* 4.8 8.7 - - - -
295B GLU* 5.1 3.8 - - + +
406D LEU* 3.3 44.8 + - + -
407D LEU 3.2 7.4 + - - +
409D SER* 1.3 84.6 + - - +
411D ARG* 1.3 63.5 + - - +
413D ALA* 3.4 22.3 + - + +
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Residues in contact with ARG 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B GLU* 3.0 39.4 + - - +
305B THR* 4.4 3.2 + - - -
306B LYS* 4.2 23.4 - - - +
404D GLY 5.6 0.4 + - - -
407D LEU* 2.9 42.0 + - - +
408D ARG* 3.2 16.0 + - - +
410D TYR* 1.3 77.8 - - - +
412D SER* 1.3 60.8 + - - +
413D ALA 3.7 5.2 - - - +
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Residues in contact with SER 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408D ARG 2.5 25.7 + - - -
409D SER* 3.6 9.6 + - - -
410D TYR 3.3 0.2 - - - -
411D ARG* 1.3 75.0 - - - +
413D ALA* 1.3 62.8 + - - +
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Residues in contact with ALA 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409D SER 3.4 17.6 + - - +
410D TYR* 3.6 19.7 - - + +
411D ARG 3.4 6.7 - - - +
412D SER* 1.3 82.6 - - - +
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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