Contacts of the helix formed by residues 394 - 411 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A GLN* 3.8 5.4 - - - +
368A GLY* 5.2 2.0 - - - -
161B SER* 4.1 2.7 + - - +
389B GLU 3.4 7.9 - - - -
390B ILE* 3.2 15.1 + - + +
393B GLY* 1.3 78.3 - - - +
395B SER* 1.3 64.9 + - - +
396B GLU* 3.4 6.3 + - - -
397B ILE* 3.0 21.8 + - - +
398B GLN* 3.0 17.7 + - - +
501B FAD 2.5 69.1 + - - +
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Residues in contact with SER 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A GLN* 3.6 9.1 + - - +
349B LYS* 4.6 1.2 + - - +
350B LEU* 3.7 23.8 - - - +
353B SER* 4.1 3.8 + - - -
354B GLU* 3.7 10.8 + - - -
389B GLU* 3.0 33.6 + - - +
394B THR* 1.3 73.0 - - - +
396B GLU* 1.3 60.6 + - - +
398B GLN* 3.3 8.9 + - - +
399B ARG* 3.0 43.7 + - - +
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Residues in contact with GLU 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A VAL* 4.3 2.5 - - + -
310A ILE* 5.5 0.2 - - + -
313A LYS* 2.6 41.9 + - - +
365A GLN* 3.0 30.3 + - - +
394B THR* 3.4 0.3 + - - -
395B SER* 1.3 79.3 - - - +
397B ILE* 1.3 67.4 + - - +
399B ARG* 3.4 6.3 + - - +
400B LEU* 3.1 21.1 + - - +
501B FAD 3.1 46.8 + - - +
312D PHE* 3.4 34.2 - - + -
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Residues in contact with ILE 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A PHE* 5.4 2.2 - - + -
161B SER* 3.9 20.0 - - - +
272B ARG* 4.1 13.9 - - - +
393B GLY* 4.2 6.5 - - - -
394B THR* 3.0 24.2 + - - +
396B GLU* 1.3 76.9 - - - +
398B GLN* 1.3 65.1 + - - +
400B LEU* 3.1 12.3 + - + +
401B VAL* 2.9 24.4 + - + +
501B FAD 3.8 40.4 - - + +
502B COS 3.7 45.8 - - + +
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Residues in contact with GLN 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ARG* 3.5 20.5 + - - +
346B ALA* 3.3 40.4 - - - +
349B LYS* 3.8 20.3 - - + +
350B LEU* 4.0 13.2 - - + -
392B GLU 3.1 17.6 + - - -
393B GLY* 2.8 28.3 + - - +
394B THR 3.0 14.9 + - - +
395B SER* 3.4 11.7 - - - +
397B ILE* 1.3 76.0 - - - +
399B ARG* 1.3 57.3 + - - +
401B VAL* 3.2 5.1 + - - +
402B ILE* 2.8 35.9 + - - +
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Residues in contact with ARG 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B LEU* 3.7 24.9 - - + +
354B GLU* 3.1 39.6 + - - -
395B SER* 3.0 24.7 + - - +
396B GLU* 3.6 13.9 + - - +
397B ILE 3.3 0.2 - - - -
398B GLN* 1.3 75.2 - - - +
400B LEU* 1.3 57.0 + - - +
402B ILE* 4.3 2.5 - - - -
403B ALA* 2.9 27.8 + - - +
311D GLN 4.7 0.3 - - - +
312D PHE* 3.6 41.5 - - + -
315D ALA* 3.4 18.7 - - + +
316D ASP* 2.9 36.2 + - - +
319D LEU* 5.7 1.4 - - - +
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Residues in contact with LEU 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A PHE* 6.2 0.4 - - + -
396B GLU 3.1 16.3 + - - +
397B ILE* 3.1 17.1 + - + +
399B ARG* 1.3 72.1 - - - +
401B VAL* 1.3 61.0 - - + +
403B ALA* 3.4 3.4 + - - +
404B GLY* 3.0 26.5 + - - -
501B FAD 3.9 28.3 - - + +
502B COS 5.5 7.2 - - - +
308D GLN* 3.8 17.3 - - + +
311D GLN* 3.4 25.4 - - + +
312D PHE* 3.5 21.5 - - + -
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Residues in contact with VAL 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ARG* 4.1 15.3 - - - +
342B ILE* 3.8 30.1 - - + +
343B LYS* 4.9 0.4 - - - -
346B ALA* 4.0 16.8 - - + -
397B ILE* 2.9 19.0 + - + +
398B GLN* 3.6 7.9 - - - +
400B LEU* 1.3 75.8 - - - +
402B ILE* 1.3 64.9 + - - +
404B GLY* 3.4 1.4 + - - -
405B HIS* 3.2 35.4 + - + +
502B COS 4.0 27.8 - - - +
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Residues in contact with ILE 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B LYS* 4.1 12.9 - - + +
346B ALA* 3.8 16.4 - - + -
347B MET* 3.8 53.8 - - + +
350B LEU* 3.7 28.3 - - + -
398B GLN 2.8 22.8 + - - +
399B ARG* 3.8 4.3 - - - +
401B VAL* 1.3 76.9 - - - +
403B ALA* 1.3 59.1 + - - +
405B HIS* 3.2 3.6 + - - +
406B LEU* 2.9 26.8 + - + +
315D ALA* 3.7 24.2 - - + +
318D ALA* 4.7 4.0 - - + -
319D LEU* 5.0 2.9 - - + -
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Residues in contact with ALA 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B ARG 2.9 16.2 + - - +
400B LEU* 3.8 4.3 - - - +
402B ILE* 1.3 75.3 - - - +
404B GLY* 1.3 65.2 + - - +
406B LEU* 3.6 8.1 - - - +
407B LEU* 3.0 32.8 + - + +
311D GLN* 3.3 49.6 - - + +
314D LEU* 5.5 1.8 - - + -
315D ALA* 3.9 5.6 - - + +
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Residues in contact with GLY 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B LEU 3.0 16.6 + - - -
401B VAL* 3.4 2.4 + - - -
402B ILE 3.3 0.2 - - - -
403B ALA* 1.3 75.5 - - - +
405B HIS* 1.3 61.2 + - - +
407B LEU* 3.5 6.4 + - - +
408B ARG* 3.1 43.0 + - - +
411B ARG* 5.4 0.5 + - - -
311D GLN* 6.2 0.4 - - - -
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Residues in contact with HIS 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ILE* 3.2 51.9 - - + +
343B LYS* 3.7 29.8 - - + +
401B VAL* 3.2 29.9 + - + +
402B ILE 3.8 1.6 - - - +
404B GLY* 1.3 72.8 - - - +
406B LEU* 1.3 67.0 + - - +
408B ARG* 3.3 31.5 + - + +
409B SER* 3.0 24.0 + - - -
502B COS 6.3 0.7 - - - -
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Residues in contact with LEU 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B LYS* 4.6 9.6 - - + +
402B ILE* 2.9 18.7 + - + +
403B ALA* 3.6 6.3 - - - +
405B HIS* 1.3 76.2 - - - +
407B LEU* 1.3 64.5 + - + +
409B SER* 2.6 30.4 + - - +
410B TYR* 3.3 30.6 + - + -
287D LEU* 4.6 10.3 - - + -
291D VAL* 4.5 13.7 - - + -
314D LEU* 3.6 43.7 - - + +
315D ALA* 4.7 0.9 - - - +
318D ALA* 3.8 22.2 - - + -
322D GLU* 4.8 7.4 - - - +
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Residues in contact with LEU 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B ALA* 3.0 24.8 + - + +
404B GLY* 4.0 4.9 - - - +
406B LEU* 1.3 76.9 - - + +
408B ARG* 1.3 58.1 + - - +
410B TYR* 3.0 9.0 + - - +
411B ARG* 3.0 52.8 + - - +
291D VAL* 3.9 23.6 - - + -
295D GLU* 4.1 7.5 - - - +
305D THR* 3.8 47.6 - - + +
311D GLN* 4.6 12.1 - - + +
314D LEU* 4.2 13.7 - - + -
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Residues in contact with ARG 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B GLY* 3.1 29.5 + - - +
405B HIS* 3.3 50.9 + - + +
406B LEU 3.3 0.2 - - - -
407B LEU* 1.3 72.1 - - - +
409B SER* 1.3 65.0 + - - +
411B ARG* 3.1 41.3 + - - +
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Residues in contact with SER 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B HIS 3.0 12.9 + - - -
406B LEU* 2.6 24.6 + - - +
408B ARG* 1.3 77.2 - - - +
410B TYR* 1.3 69.3 + - - +
411B ARG 4.3 3.1 - - - -
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Residues in contact with TYR 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406B LEU* 3.3 41.7 - - + -
407B LEU 3.0 8.9 + - - +
409B SER* 1.3 84.4 + - - +
411B ARG* 1.3 60.6 + - + +
284D GLN* 3.5 12.5 + - - -
287D LEU* 3.8 9.0 - - - +
288D ASP* 2.6 49.9 + - + -
291D VAL* 3.6 40.4 - - + -
292D ASN* 4.3 15.8 - - - +
295D GLU* 5.5 2.7 - - + +
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Residues in contact with ARG 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B GLY 5.4 0.2 + - - -
407B LEU* 3.0 35.0 + - - +
408B ARG* 3.1 33.4 + - - +
409B SER 4.3 3.4 - - - -
410B TYR* 1.3 81.3 - - - +
295D GLU* 2.8 39.1 + - - +
305D THR* 4.3 4.8 + - - -
306D LYS* 6.1 3.6 - - - +
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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
------------------------------------------------------------
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