Contacts of the helix formed by residues 416 - 429 (chain B) in PDB entry 2VF7
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 ASP 416 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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367B GLY* 5.9 8.0 - - - +
412B LEU* 3.3 27.6 - - + +
413B HIS* 2.7 14.8 + - - +
415B ALA* 1.3 90.5 - - - +
417B THR* 1.3 60.9 + - - +
418B GLU 3.3 2.7 - - - -
419B ALA* 3.4 20.4 + - + +
420B LEU 3.4 5.0 + - - -
531B VAL* 3.0 31.4 - - - +
532B SER* 4.3 9.0 + - - -
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Residues in contact with THR 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B SER* 5.0 2.5 - - - -
412B LEU* 3.7 23.3 - - + +
413B HIS 4.1 8.5 - - - +
414B PRO* 3.4 21.2 + - + +
415B ALA 3.6 0.4 - - - -
416B ASP* 1.3 75.5 - - - +
418B GLU* 1.3 60.9 + - - +
420B LEU* 3.2 4.7 + - + +
421B LEU* 2.9 36.2 + - - +
440B ASP* 4.0 25.6 - - - +
442B ASP* 4.4 17.8 + - + +
443B VAL* 4.9 10.1 - - + -
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Residues in contact with GLU 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B ALA 4.9 5.8 + - - +
416B ASP 3.3 0.4 - - - -
417B THR* 1.3 81.8 + - - +
419B ALA* 1.3 55.2 + - - +
421B LEU* 3.8 10.1 - - - +
422B SER* 3.0 38.2 + - - +
446B ARG* 2.7 46.1 + - - -
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Residues in contact with ALA 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B HIS 3.3 27.2 - - - +
366B LEU* 4.5 11.3 - - - +
367B GLY* 5.3 0.4 - - - +
416B ASP* 3.4 17.8 + - + +
417B THR 3.3 0.4 - - - -
418B GLU* 1.3 79.1 - - - +
420B LEU* 1.3 61.7 + - - +
422B SER* 3.6 6.9 + - - -
423B ALA* 3.3 20.4 + - - +
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Residues in contact with LEU 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B LEU* 5.2 6.2 - - + +
387B ARG* 4.2 13.2 - - + -
390B LEU* 3.8 26.9 - - + -
408B PRO* 4.0 25.1 - - + +
409B SER* 3.9 35.9 - - - +
412B LEU* 3.8 17.9 - - + +
416B ASP 3.4 2.8 + - - -
417B THR* 3.2 9.6 + - - +
419B ALA* 1.3 79.0 - - - +
421B LEU* 1.3 62.1 + - + +
423B ALA* 3.1 7.4 + - + +
424B LEU* 3.1 31.4 + - + +
443B VAL* 4.5 14.6 - - + -
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Residues in contact with LEU 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 4.3 23.3 - - + -
417B THR* 2.9 28.6 + - - +
418B GLU* 3.4 20.4 + - - +
420B LEU* 1.3 70.4 - - + +
422B SER* 1.3 64.8 + - - +
424B LEU* 3.4 12.1 + - + +
425B GLU* 3.0 23.8 + - - +
442B ASP* 4.3 10.3 - - + +
443B VAL* 4.5 23.8 - - + -
446B ARG* 4.1 47.8 - - + +
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Residues in contact with SER 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B GLU* 3.0 25.8 + - - +
419B ALA* 3.7 8.8 - - - -
420B LEU 3.4 0.2 - - - -
421B LEU* 1.3 73.7 - - - +
423B ALA* 1.3 57.0 + - - +
425B GLU* 3.4 7.8 + - - +
426B ASN* 3.0 39.8 + - - +
446B ARG* 5.7 0.2 - - - +
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Residues in contact with ALA 423 (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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366B LEU* 3.8 28.0 - - + -
390B LEU* 3.9 18.7 - - + +
394B LEU* 3.6 16.0 - - + +
419B ALA 3.3 10.2 + - - +
420B LEU* 3.1 12.1 + - - +
422B SER* 1.3 76.4 - - - +
424B LEU* 1.3 64.7 + - - +
426B ASN* 3.3 7.8 + - - +
427B LEU* 3.1 19.6 + - - +
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Residues in contact with LEU 424 (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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38B LEU* 4.0 25.8 - - + -
390B LEU* 3.8 26.7 - - + -
405B LEU* 4.2 19.7 - - + -
408B PRO* 4.8 5.8 - - + -
420B LEU* 3.1 31.8 + - + +
421B LEU* 3.7 22.7 - - + +
423B ALA* 1.3 75.8 - - - +
425B GLU* 1.3 61.3 + - - +
427B LEU* 3.4 5.0 + - + +
428B LYS* 3.2 18.7 + - - +
434B LEU* 3.3 32.2 - - + +
436B VAL* 4.8 5.4 - - + -
443B VAL* 5.0 6.7 - - + -
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Residues in contact with GLU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B LEU 3.0 13.9 + - - +
422B SER* 3.5 11.7 - - - +
423B ALA 3.2 0.2 - - - -
424B LEU* 1.3 74.1 - - - +
426B ASN* 1.3 63.8 + - - +
428B LYS* 3.3 34.9 + - - +
429B ARG* 3.1 53.1 + - - +
448B ASP* 5.5 0.2 - - - +
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Residues in contact with ASN 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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394B LEU* 3.8 18.7 - - + +
422B SER* 3.0 30.0 + - - +
423B ALA* 3.6 8.5 - - - +
425B GLU* 1.3 77.3 - - - +
427B LEU* 1.3 61.5 + - - +
429B ARG* 2.7 36.9 + - - +
430B GLY* 3.5 13.7 + - - -
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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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97B LEU* 5.0 4.5 - - + -
390B LEU* 4.5 18.2 - - + -
393B GLN* 4.1 21.5 - - + +
394B LEU* 3.3 23.5 - - + +
403B TYR* 3.5 41.5 - - + +
405B LEU* 5.5 0.7 - - + -
423B ALA 3.1 9.5 + - - +
424B LEU* 3.5 12.1 - - + +
426B ASN* 1.3 75.6 - - - +
428B LYS* 1.3 63.7 + - - +
430B GLY* 3.1 10.3 + - - -
432B ASN* 3.2 26.1 + - - +
434B LEU* 3.7 25.6 - - + -
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Residues in contact with LYS 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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36B ASP* 3.9 16.0 + - - +
37B ALA* 3.7 31.6 - - - +
38B LEU* 3.8 7.0 - - + +
424B LEU 3.2 10.5 + - - +
425B GLU* 3.4 40.8 + - - +
427B LEU* 1.3 73.9 - - - +
429B ARG* 1.3 64.7 + - - +
430B GLY 2.9 10.6 + - - -
431B GLY* 3.0 13.0 + - - -
432B ASN 3.1 30.1 + - - +
434B LEU* 4.3 9.4 - - + +
448B ASP* 3.8 17.1 + - - +
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Residues in contact with ARG 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B GLU* 3.1 39.8 + - - +
426B ASN* 2.7 46.8 + - - +
427B LEU 3.4 0.4 - - - -
428B LYS* 1.3 80.7 - - - +
430B GLY* 1.3 56.2 + - - +
431B GLY 3.1 6.5 + - - -
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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
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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