Contacts of the helix formed by residues 413 - 429 (chain B) in PDB entry 2VLH
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 413 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B GLU* 3.9 17.7 - - + +
10B ILE* 5.4 13.0 - - + -
321B GLN* 3.7 7.9 - - - +
411B VAL 5.5 0.7 - - - +
412B TYR* 1.3 78.7 - - - +
414B TYR* 1.3 59.2 + - - +
415B ALA* 3.1 21.2 + - - +
416B HIS* 3.0 32.3 + - + +
417B MET* 3.1 27.5 + - - +
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Residues in contact with TYR 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B TYR* 3.4 18.7 - - + +
4B PRO* 2.6 47.0 + - - +
5B ALA* 4.6 4.5 - - - -
6B GLU* 4.0 12.6 + - - -
317B HIS* 3.7 19.2 - + - -
320B LYS 4.4 0.2 - - - -
321B GLN* 3.8 23.4 + - + +
324B TYR* 3.5 49.5 - + + -
413B THR* 1.3 71.5 - - - +
415B ALA* 1.3 60.9 + - - +
417B MET* 3.3 7.4 + - - +
418B ASP* 2.8 33.5 + - - +
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Residues in contact with ALA 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B THR* 3.1 11.4 + - - +
414B TYR* 1.3 77.9 - - - +
416B HIS* 1.3 58.5 + - + +
418B ASP* 3.2 13.1 + - - +
419B VAL* 3.0 31.0 + - - +
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Residues in contact with HIS 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TYR* 3.4 33.6 + + - -
45B ILE* 3.8 22.8 - - + +
411B VAL 4.6 4.0 - - - -
412B TYR* 3.4 33.1 - + + -
413B THR* 3.0 43.9 + - + +
415B ALA* 1.3 74.2 - - + +
417B MET* 1.3 69.4 + - + +
419B VAL* 3.1 6.2 + - + +
420B VAL* 3.0 27.1 + - - +
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Residues in contact with MET 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE* 5.4 0.4 - - + -
47B LEU* 4.8 4.9 - - + -
321B GLN* 3.8 33.7 - - + +
324B TYR* 3.8 19.1 - - + -
325B LEU* 3.8 23.9 - - + +
407B ILE* 4.0 35.4 - - + -
412B TYR* 3.8 31.0 - - + -
413B THR 3.1 14.1 + - - +
414B TYR* 3.3 11.7 - - - +
416B HIS* 1.3 79.2 - - + +
418B ASP* 1.3 57.4 + - - +
420B VAL* 3.4 11.1 + - + +
421B ALA* 2.8 30.5 + - - +
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Residues in contact with ASP 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B TYR* 2.6 32.5 + - - -
328B LYS* 2.7 26.5 + - - +
414B TYR* 2.8 17.6 + - - +
415B ALA* 3.4 14.4 - - - +
416B HIS 3.2 0.2 - - - -
417B MET* 1.3 73.1 - - - +
419B VAL* 1.3 57.7 + - - +
421B ALA* 4.3 0.9 - - - +
422B ASP* 2.6 46.3 + - - +
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Residues in contact with VAL 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TYR* 4.2 21.8 - - + +
45B ILE* 3.9 15.7 - - + -
374B THR* 3.7 38.1 - - + +
376B VAL* 4.3 0.4 - - + -
415B ALA 3.0 19.2 + - - +
416B HIS* 3.1 11.2 + - - +
418B ASP* 1.3 76.2 - - - +
420B VAL* 1.3 64.0 + - - +
422B ASP* 4.3 3.4 - - - +
423B GLY 3.2 15.1 + - - -
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Residues in contact with VAL 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE* 4.3 5.6 - - + -
47B LEU* 3.7 28.3 - - + -
325B LEU* 3.8 18.4 - - + -
370B ILE* 5.7 1.3 - - + +
374B THR* 4.8 2.4 - - - +
376B VAL* 3.5 30.5 - - + -
405B LEU* 4.4 6.3 - - + -
416B HIS 3.0 17.2 + - - +
417B MET* 3.5 10.3 - - + +
419B VAL* 1.3 75.8 - - - +
421B ALA* 1.3 63.7 + - - +
423B GLY* 3.4 0.7 + - - -
424B ILE* 3.0 48.3 + - + +
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Residues in contact with ALA 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B LEU* 3.9 14.1 - - + -
328B LYS* 3.8 37.2 - - + -
329B LEU* 4.0 14.6 - - + -
417B MET 2.8 21.8 + - - +
418B ASP 3.9 1.8 - - - +
420B VAL* 1.3 75.2 - - - +
422B ASP* 1.3 57.7 + - - +
424B ILE* 3.2 2.1 + - - +
425B ILE* 2.8 36.3 + - + +
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Residues in contact with ASP 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LYS* 3.0 30.4 + - - -
418B ASP* 2.6 32.9 + - - +
419B VAL* 4.3 3.0 - - - +
421B ALA* 1.3 71.4 - - - +
423B GLY* 1.3 57.9 + - - +
425B ILE* 3.8 7.1 - - - +
426B LYS* 2.9 30.8 + - - +
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Residues in contact with GLY 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B ILE* 6.1 0.2 - - - -
373B GLU* 5.0 4.5 - - - +
374B THR* 3.6 28.0 - - - -
419B VAL 3.2 7.4 + - - -
421B ALA 3.2 0.8 - - - -
422B ASP* 1.3 78.0 - - - +
424B ILE* 1.3 58.8 + - - +
426B LYS* 3.4 7.4 + - - +
427B LEU* 2.9 35.3 + - - +
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Residues in contact with ILE 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B LEU* 3.8 21.1 - - + -
334B VAL* 4.1 7.4 - - + -
347B LEU* 4.1 13.7 - - + -
352B PHE* 3.6 24.6 - - + -
370B ILE* 4.0 25.1 - - + -
405B LEU* 3.7 26.2 - - + -
420B VAL* 3.0 38.5 + - + +
421B ALA 3.8 2.9 - - - +
423B GLY* 1.3 73.4 - - - +
425B ILE* 1.3 60.1 + - - +
427B LEU* 3.3 8.6 + - - +
428B TYR* 2.8 27.4 + - - +
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Residues in contact with ILE 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LYS* 3.8 33.7 - - + +
329B LEU* 4.1 11.0 - - + -
332B ALA* 3.6 35.2 - - + -
334B VAL* 4.1 3.1 - - + -
421B ALA* 2.8 27.5 + - + +
422B ASP* 3.8 7.0 - - - +
424B ILE* 1.3 76.8 - - - +
426B LYS* 1.3 62.7 + - - +
428B TYR* 3.2 8.9 + - + +
429B GLN* 3.1 44.8 + - + +
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Residues in contact with LYS 426 (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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373B GLU* 6.1 6.3 - - + +
422B ASP 2.9 18.6 + - - +
423B GLY* 3.7 7.0 - - - +
424B ILE 3.3 0.2 - - - -
425B ILE* 1.3 77.2 - - - +
427B LEU* 1.3 60.3 + - - +
429B GLN* 3.4 22.0 + - - +
430B HIS* 2.9 33.7 + - + +
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Residues in contact with LEU 427 (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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352B PHE* 4.1 10.0 - - + -
366B LEU* 4.5 5.4 - - + -
369B SER* 3.8 45.8 - - - +
370B ILE* 3.9 19.3 - - + +
373B GLU* 3.9 24.9 - - + +
423B GLY 2.9 19.7 + - - +
424B ILE* 3.5 9.0 - - - +
426B LYS* 1.3 75.2 - - - +
428B TYR* 1.3 57.7 + - - +
430B HIS* 3.1 24.2 + - + +
431B LYS* 3.0 26.3 + - - -
434B ILE* 4.4 13.8 - - + +
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Residues in contact with TYR 428 (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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332B ALA* 4.0 15.3 - - + -
333B GLY* 3.3 26.1 + - - -
334B VAL* 3.9 14.1 - - + -
335B PRO* 3.6 23.6 - - + +
351B ARG* 5.3 2.9 - - + +
352B PHE* 3.6 28.5 - + + -
424B ILE 2.8 20.7 + - - +
425B ILE* 3.2 7.1 + - + +
427B LEU* 1.3 73.1 - - - +
429B GLN* 1.3 68.1 + - + +
430B HIS 3.1 0.2 - - - -
431B LYS* 3.2 55.4 + - + +
432B GLU* 4.7 0.9 - - - +
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Residues in contact with GLN 429 (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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332B ALA* 6.0 0.4 - - - +
425B ILE* 3.1 33.2 + - + +
426B LYS* 3.7 18.9 - - - +
427B LEU 3.3 0.4 - - - -
428B TYR* 1.3 81.4 - - + +
430B HIS* 1.3 62.1 + - + +
431B LYS 3.8 0.2 - - - -
432B GLU* 4.2 4.7 - - - +
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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