Contacts of the helix formed by residues 394 - 412 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A SER* 4.1 1.7 + - - +
389A GLU 3.4 4.5 - - - -
390A ILE* 3.1 27.9 + - + +
393A GLY* 1.3 76.3 - - - +
395A SER* 1.3 66.3 + - - +
396A GLU* 3.4 10.3 + - - -
397A ILE* 3.0 22.3 + - - +
398A GLN* 2.9 20.5 + - - +
501A FAD 2.8 56.3 + - - +
365B GLN* 3.9 5.4 - - - +
368B GLY* 5.3 1.8 - - - -
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Residues in contact with SER 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LYS* 4.7 1.1 - - - +
350A LEU* 3.8 15.3 - - - +
353A SER* 4.4 3.1 + - - -
354A GLU* 3.9 9.7 + - - -
389A GLU* 3.2 32.8 + - - +
394A THR* 1.3 73.7 - - - +
396A GLU* 1.3 72.0 + - - +
398A GLN* 3.3 7.0 + - - +
399A ARG* 3.1 46.4 + - - +
365B GLN* 3.9 3.9 + - - -
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Residues in contact with GLU 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A THR* 3.4 1.4 - - - -
395A SER* 1.3 83.7 - - - +
397A ILE* 1.3 64.0 + - - +
399A ARG* 3.3 5.8 + - - +
400A LEU* 3.1 26.4 + - - +
501A FAD 2.9 42.8 + - - +
309B VAL* 4.0 12.8 - - + -
313B LYS* 2.8 41.2 + - - +
365B GLN* 2.9 31.7 + - - +
312C PHE* 3.7 19.8 - - + -
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Residues in contact with ILE 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A SER* 3.8 32.1 - - - +
272A ARG* 3.9 24.9 - - - +
393A GLY* 4.1 7.0 - - - -
394A THR* 3.0 25.8 + - - +
396A GLU* 1.3 77.7 - - - +
398A GLN* 1.3 57.7 + - - +
400A LEU* 3.2 12.0 + - + +
401A VAL* 2.9 37.1 + - + +
501A FAD 3.9 32.8 - - + +
300B PHE* 5.4 2.7 - - + -
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Residues in contact with GLN 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ARG* 3.4 19.4 + - - +
346A ALA* 3.3 31.2 - - - +
349A LYS* 3.6 23.2 - - + +
350A LEU* 4.0 21.3 - - + +
392A GLU 3.2 17.0 + - - -
393A GLY* 2.6 28.7 + - - +
394A THR 2.9 18.2 + - - +
395A SER* 3.5 9.9 - - - +
397A ILE* 1.3 75.9 - - - +
399A ARG* 1.3 57.1 + - - +
401A VAL* 3.1 5.7 + - - +
402A ILE* 2.9 35.2 + - + +
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Residues in contact with ARG 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A LEU* 3.6 30.8 - - + +
354A GLU* 3.1 40.8 + - - -
395A SER* 3.1 20.1 + - - +
396A GLU* 3.7 11.1 + - - +
397A ILE 3.3 0.2 - - - -
398A GLN* 1.3 74.9 - - - +
400A LEU* 1.3 56.8 - - - +
402A ILE* 3.4 2.2 + - - -
403A ALA* 2.9 32.4 + - - +
312C PHE* 3.8 42.5 - - + -
315C ALA* 3.4 16.3 - - + +
316C ASP* 2.8 36.3 + - - +
319C LEU* 5.7 1.8 - - - +
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Residues in contact with LEU 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A GLU 3.1 18.4 + - - +
397A ILE* 3.5 16.2 - - + +
399A ARG* 1.3 75.5 - - - +
401A VAL* 1.3 64.1 + - + +
403A ALA* 3.6 3.7 + - - +
404A GLY* 3.1 20.6 + - - -
501A FAD 3.7 35.9 - - + +
308C GLN* 4.2 15.5 - - + +
311C GLN* 3.3 26.2 - - + +
312C PHE* 3.8 20.4 - - + -
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Residues in contact with VAL 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ARG* 4.1 15.9 - - - +
342A ILE* 3.7 31.0 - - + +
346A ALA* 3.9 18.6 - - + -
397A ILE* 2.9 33.1 + - + +
398A GLN* 3.4 8.3 - - - +
400A LEU* 1.3 78.5 - - + +
402A ILE* 1.3 64.0 + - - +
404A GLY* 3.3 3.0 + - - -
405A HIS* 3.2 33.4 + - + +
408A ARG* 4.8 0.3 + - - -
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Residues in contact with ILE 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A LYS* 4.0 13.1 - - + +
346A ALA* 3.8 16.4 - - + -
347A MET* 3.7 55.4 - - + +
350A LEU* 3.8 26.9 - - + -
398A GLN 2.9 23.0 + - - +
399A ARG* 3.7 4.9 - - - +
401A VAL* 1.3 76.5 - - - +
403A ALA* 1.3 58.6 + - - +
405A HIS* 3.2 2.3 + - - +
406A LEU* 2.9 28.0 + - + +
315C ALA* 3.6 26.0 - - + +
318C ALA* 4.6 4.5 - - + -
319C LEU* 5.4 2.0 - - + -
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Residues in contact with ALA 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ARG 2.9 19.9 + - - +
400A LEU 4.0 3.6 - - - +
402A ILE* 1.3 73.8 - - - +
404A GLY* 1.3 62.3 + - - +
406A LEU* 3.3 9.1 + - - +
407A LEU* 3.0 34.0 + - + +
311C GLN* 3.3 50.3 - - + +
314C LEU* 5.3 2.2 - - + -
315C ALA* 4.1 4.7 - - + +
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Residues in contact with GLY 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A LEU 3.1 15.1 + - - -
401A VAL 3.3 4.0 + - - -
402A ILE 3.2 0.2 - - - -
403A ALA* 1.3 77.9 - - - +
405A HIS* 1.3 55.5 + - - +
407A LEU* 3.9 7.0 - - - +
408A ARG* 3.1 51.3 + - - +
411A ARG* 5.4 0.3 + - - -
311C GLN* 6.2 0.4 - - - -
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Residues in contact with HIS 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ILE* 3.3 51.2 - - + +
343A LYS* 3.9 27.8 + - + -
401A VAL* 3.2 29.7 + - + +
402A ILE 4.0 0.9 - - - +
404A GLY* 1.3 72.6 - - - +
406A LEU* 1.3 66.7 + - - +
408A ARG* 3.4 31.5 + - + +
409A SER* 3.0 26.8 + - - -
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Residues in contact with LEU 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A LYS* 4.5 11.1 - - + +
402A ILE* 2.9 19.8 + - + +
403A ALA* 3.5 5.8 - - - +
405A HIS* 1.3 75.5 - - - +
407A LEU* 1.3 63.7 + - + +
409A SER* 3.1 16.6 + - - -
410A TYR* 3.2 41.7 + - + +
287C LEU* 4.6 11.2 - - + -
291C VAL* 4.6 12.1 - - + -
314C LEU* 3.6 43.3 - - + +
315C ALA* 4.7 2.0 - - - +
318C ALA* 3.8 23.3 - - + -
322C GLU* 4.7 7.6 - - - +
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Residues in contact with LEU 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A ALA* 3.0 24.3 + - + +
404A GLY* 3.9 7.4 - - - +
406A LEU* 1.3 78.1 - - + +
408A ARG* 1.3 62.8 + - - +
410A TYR* 3.2 6.8 + - - +
411A ARG* 3.1 49.4 + - - +
291C VAL* 4.2 20.6 - - + -
295C GLU* 4.2 6.8 - - - +
305C THR* 4.0 45.8 - - + +
311C GLN* 4.8 9.4 - - + -
314C LEU* 4.1 17.9 - - + -
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Residues in contact with ARG 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A VAL 4.8 0.2 + - - -
404A GLY* 3.1 33.4 + - - +
405A HIS* 3.4 48.8 + - + +
406A LEU 3.3 0.2 - - - -
407A LEU* 1.3 78.4 - - - +
409A SER* 1.3 55.9 + - - +
411A ARG* 3.3 22.9 + - - +
412A SER* 3.0 30.0 + - - -
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Residues in contact with SER 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A LYS* 5.4 6.4 + - - +
405A HIS 3.0 16.0 + - - -
406A LEU* 3.1 11.8 + - - -
408A ARG* 1.3 77.5 - - - +
410A TYR* 1.3 65.9 + - - +
412A SER* 3.2 24.2 + - - -
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Residues in contact with TYR 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A LEU* 3.2 43.6 + - + +
407A LEU* 3.2 7.2 + - - +
409A SER* 1.3 81.8 - - - +
411A ARG* 1.3 61.4 + - + +
412A SER 3.6 3.5 + - - -
284C GLN* 3.5 12.2 + - - -
287C LEU* 3.8 13.7 - - - +
288C ASP* 2.7 42.0 + - + -
291C VAL* 3.4 43.1 - - + -
292C ASN* 5.4 6.5 - - - -
295C GLU* 5.5 2.2 - - + +
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Residues in contact with ARG 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A GLY 5.4 0.2 + - - -
407A LEU* 3.1 38.2 + - - +
408A ARG* 3.7 25.9 - - - +
409A SER 3.3 0.2 - - - -
410A TYR* 1.3 77.5 - - - +
412A SER* 1.3 60.8 + - - +
295C GLU* 2.9 39.4 + - - +
305C THR* 4.3 3.0 + - - -
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Residues in contact with SER 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ARG 3.0 13.5 + - - -
409A SER* 3.2 23.4 + - - -
410A TYR 4.3 3.1 - - - -
411A ARG* 1.3 80.5 - - - +
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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