Contacts of the helix formed by residues 394 - 413 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365E GLN* 3.8 6.5 - - - +
368E GLY* 5.3 2.0 - - - -
161F SER* 4.2 2.6 + - - +
389F GLU 3.5 3.8 - - - -
390F ILE* 3.3 24.6 + - + +
393F GLY* 1.3 74.7 - - - +
395F SER* 1.3 66.4 + - - +
396F GLU* 3.4 6.0 + - - -
397F ILE* 2.9 20.4 + - - +
398F GLN* 2.9 20.1 + - - +
501F FAD 2.5 63.5 + - - +
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Residues in contact with SER 395 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365E GLN* 3.7 5.4 - - - +
349F LYS* 4.7 1.4 + - - +
350F LEU* 3.7 22.0 - - - +
353F SER* 4.1 4.7 + - - -
354F GLU* 3.7 10.5 + - - -
389F GLU* 3.1 29.9 + - - +
393F GLY 3.9 0.2 + - - -
394F THR* 1.3 75.4 - - - +
396F GLU* 1.3 66.6 + - - +
398F GLN* 3.2 7.8 + - - +
399F ARG* 2.9 44.7 + - - +
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Residues in contact with GLU 396 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309E VAL* 4.8 2.2 - - + -
313E LYS* 3.0 37.2 + - - +
362E GLN* 5.4 0.2 + - - -
365E GLN* 2.8 39.1 + - - +
394F THR* 3.4 0.9 + - - -
395F SER* 1.3 78.7 - - - +
397F ILE* 1.3 66.3 + - - +
399F ARG* 3.3 8.5 + - - +
400F LEU* 3.1 26.2 + - - +
501F FAD 3.0 42.9 + - - +
312H PHE* 3.7 27.9 - - + -
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Residues in contact with ILE 397 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300E PHE* 5.3 3.1 - - + -
161F SER* 4.0 23.1 - - - +
272F ARG* 4.0 23.6 - - - +
393F GLY* 4.0 10.5 - - - -
394F THR* 2.9 22.2 + - - +
396F GLU* 1.3 79.5 - - - +
398F GLN* 1.3 64.6 + - - +
400F LEU* 3.1 13.2 + - + +
401F VAL* 2.9 29.8 + - + +
501F FAD 3.7 42.6 - - + +
502F COS 4.2 15.7 - - + +
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Residues in contact with GLN 398 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272F ARG* 3.2 19.7 + - - +
346F ALA* 3.3 33.0 - - - +
349F LYS* 3.7 22.3 - - + +
350F LEU* 4.0 19.3 - - + -
392F GLU 3.1 18.0 + - - -
393F GLY* 2.8 28.0 + - - +
394F THR 2.9 18.0 + - - +
395F SER* 3.2 10.3 + - - +
397F ILE* 1.3 76.1 - - - +
399F ARG* 1.3 56.7 + - - +
401F VAL* 3.2 6.0 + - - +
402F ILE* 2.8 35.4 + - - +
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Residues in contact with ARG 399 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350F LEU* 3.7 25.7 - - + +
354F GLU* 3.0 40.0 + - - -
395F SER* 2.9 23.3 + - - +
396F GLU* 3.6 12.8 + - - +
398F GLN* 1.3 75.2 - - - +
400F LEU* 1.3 57.3 - - - +
402F ILE* 4.3 2.2 - - - -
403F ALA* 3.0 30.7 + - - +
311H GLN 4.7 0.2 - - - +
312H PHE* 3.7 41.9 - - + -
315H ALA* 3.4 17.6 - - + +
316H ASP* 2.9 36.6 + - - +
319H LEU* 5.7 1.4 - - - +
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Residues in contact with LEU 400 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396F GLU 3.1 17.6 + - - +
397F ILE* 3.1 18.7 + - + +
399F ARG* 1.3 74.2 - - - +
401F VAL* 1.3 61.6 + - + +
403F ALA* 3.7 3.8 - - - +
404F GLY* 3.0 25.1 + - - -
501F FAD 3.7 34.8 - - + +
308H GLN* 4.2 16.4 - - + +
311H GLN* 3.4 25.6 - - + +
312H PHE* 3.8 21.3 - - + -
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Residues in contact with VAL 401 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272F ARG* 4.1 18.4 - - - +
342F ILE* 3.7 31.4 - - + +
343F LYS* 5.0 0.4 - - - -
346F ALA* 3.9 17.7 - - + -
397F ILE* 2.9 26.0 + - + +
398F GLN* 3.6 6.7 - - - +
400F LEU* 1.3 74.1 - - + +
402F ILE* 1.3 67.0 + - - +
404F GLY* 3.3 1.8 + - - -
405F HIS* 3.1 36.5 + - + +
502F COS 6.3 0.7 - - - -
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Residues in contact with ILE 402 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343F LYS* 4.1 13.0 - - + +
346F ALA* 3.9 13.0 - - + -
347F MET* 3.8 54.5 - - + +
350F LEU* 3.6 29.4 - - + -
398F GLN 2.8 24.5 + - - +
399F ARG* 3.7 4.9 - - - +
401F VAL* 1.3 72.8 - - - +
403F ALA* 1.3 58.8 + - - +
405F HIS* 3.3 2.1 + - - +
406F LEU* 2.8 29.0 + - + +
315H ALA* 3.5 25.8 - - + +
318H ALA* 4.7 3.6 - - + -
319H LEU* 4.9 3.4 - - + -
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Residues in contact with ALA 403 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399F ARG 3.0 18.5 + - - +
400F LEU 3.7 4.5 - - - +
402F ILE* 1.3 78.0 - - - +
404F GLY* 1.3 61.1 + - - +
406F LEU* 3.4 7.4 + - - +
407F LEU* 3.0 33.7 + - + +
311H GLN* 3.4 45.1 - - + +
314H LEU* 5.5 2.2 - - + -
315H ALA* 4.2 5.8 - - + +
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Residues in contact with GLY 404 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400F LEU 3.0 16.0 + - - -
401F VAL* 3.3 3.8 + - - -
403F ALA* 1.3 75.1 - - - +
405F HIS* 1.3 59.5 + - - +
407F LEU* 3.9 5.7 - - - +
408F ARG* 3.0 27.9 + - - +
411F ARG* 5.5 1.2 + - - -
311H GLN* 5.5 0.8 + - - -
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Residues in contact with HIS 405 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342F ILE* 3.3 49.8 - - + +
343F LYS* 3.8 29.5 - - + +
401F VAL* 3.1 32.3 + - + +
402F ILE 4.0 0.4 - - - +
404F GLY* 1.3 75.3 - - - +
406F LEU* 1.3 65.8 + - - +
408F ARG* 4.1 7.2 - - + +
409F SER* 3.1 24.8 + - - -
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Residues in contact with LEU 406 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343F LYS* 4.4 12.6 - - + +
402F ILE 2.8 17.9 + - - +
403F ALA* 3.6 5.8 - - - +
405F HIS* 1.3 75.7 - - - +
407F LEU* 1.3 64.9 + - + +
409F SER* 3.2 16.5 + - - +
410F TYR* 3.2 41.0 + - + -
287H LEU* 4.5 10.8 - - + -
291H VAL* 4.4 15.0 - - + -
314H LEU* 3.7 41.1 - - + +
315H ALA* 4.7 0.9 - - - +
318H ALA* 3.8 23.3 - - + -
322H GLU* 4.9 6.7 - - - +
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Residues in contact with LEU 407 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403F ALA* 3.0 23.9 + - + +
404F GLY* 3.9 5.2 - - - +
406F LEU* 1.3 78.2 - - + +
408F ARG* 1.3 64.9 + - - +
410F TYR* 3.2 6.1 + - - +
411F ARG* 3.0 46.0 + - - +
291H VAL* 3.8 23.6 - - + -
295H GLU* 3.8 23.4 - - - +
305H THR* 3.6 40.4 - - + +
311H GLN* 5.0 8.5 - - + -
314H LEU* 4.3 12.1 - - + -
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Residues in contact with ARG 408 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404F GLY 3.0 17.3 + - - +
405F HIS* 4.1 9.2 - - + +
407F LEU* 1.3 75.3 - - - +
409F SER* 1.3 57.3 + - - +
411F ARG* 3.3 15.6 + - - +
412F SER* 2.9 32.4 + - - -
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Residues in contact with SER 409 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343F LYS* 6.0 3.1 - - - -
405F HIS 3.1 20.2 + - - -
406F LEU* 3.3 9.6 + - - +
407F LEU 3.1 0.2 - - - -
408F ARG* 1.3 77.8 - - - +
410F TYR* 1.3 66.4 + - - +
412F SER* 3.9 5.4 - - - -
413F ALA* 3.4 22.2 + - - +
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Residues in contact with TYR 410 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406F LEU* 3.2 49.2 + - + -
407F LEU 3.2 7.7 + - - +
409F SER* 1.3 80.7 - - - +
411F ARG* 1.3 64.3 + - - +
413F ALA* 3.3 21.9 + - - +
284H GLN* 3.5 12.6 + - - -
287H LEU* 3.8 13.0 - - - +
288H ASP* 2.7 41.7 + - + -
291H VAL* 3.7 37.9 - - + -
292H ASN* 5.5 1.8 - - + -
295H GLU* 5.2 3.1 - - + +
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Residues in contact with ARG 411 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404F GLY 5.5 1.0 + - - -
407F LEU* 3.0 41.0 + - - +
408F ARG* 3.3 13.2 + - - +
410F TYR* 1.3 75.3 - - - +
412F SER* 1.3 63.3 + - - +
413F ALA 3.4 6.8 - - - +
295H GLU* 2.9 39.3 + - - +
305H THR* 4.3 3.6 + - - -
306H LYS* 6.1 3.2 - - - +
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Residues in contact with SER 412 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408F ARG 2.9 17.0 + - - -
409F SER* 3.9 7.0 - - - -
411F ARG* 1.3 79.1 - - - +
413F ALA* 1.3 60.6 + - - +
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Residues in contact with ALA 413 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409F SER 3.4 13.1 + - - +
410F TYR* 3.3 17.9 + - - +
411F ARG 3.4 6.2 - - - +
412F SER* 1.3 84.4 - - - +
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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