Contacts of the helix formed by residues 394 - 409 (chain A) in PDB entry 2VR1
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 ASN 394 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332A GLY 5.1 0.2 - - - -
333A HIS* 3.7 10.1 - - - -
392A GLY 3.8 2.2 - - - +
393A GLU* 1.3 85.2 - - - +
395A ARG* 1.3 64.9 + - - +
396A ASP* 3.1 12.8 + - - +
397A VAL* 2.8 35.8 + - - +
398A ALA* 3.1 19.6 + - - +
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Residues in contact with ARG 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A GLU* 2.7 36.6 + - - +
246A PRO* 3.5 14.0 - - - +
333A HIS* 3.6 38.7 + - + +
335A VAL* 5.4 0.9 - - + +
394A ASN* 1.3 75.0 - - - +
396A ASP* 1.3 63.4 + - - +
398A ALA* 3.0 2.8 + - - +
399A ILE* 2.9 45.5 + - + +
430A PHE* 2.7 48.1 + - - -
431A GLN 3.1 20.0 + - - -
432A HIS 4.1 1.0 + - - -
433A GLY* 3.6 18.5 - - - -
434A GLY 5.0 0.2 - - - +
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Residues in contact with ASP 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A ASN* 3.1 10.3 + - - +
395A ARG* 1.3 83.5 + - - +
397A VAL* 1.3 62.8 + - + +
399A ILE* 3.8 10.6 + - - +
400A ALA* 3.2 23.4 + - - +
431A GLN 4.7 9.7 - - - +
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Residues in contact with VAL 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A GLY* 3.7 19.1 - - - -
393A GLU* 3.8 16.8 - - - +
394A ASN* 2.8 32.5 + - - +
396A ASP* 1.3 75.0 - - + +
398A ALA* 1.3 67.6 + - - +
400A ALA* 3.2 5.4 + - - +
401A ARG* 3.0 39.9 + - - +
23B GLU* 4.4 1.7 - - - +
310B LYS* 3.6 30.1 - - - +
314B ARG* 5.5 3.8 - - - +
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Residues in contact with ALA 398 (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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333A HIS 3.3 28.0 - - - +
335A VAL* 4.0 17.7 - - + +
390A CYS* 3.8 17.8 - - - +
391A TYR 4.4 2.2 - - - -
392A GLY* 4.2 7.2 - - - +
394A ASN 3.1 8.9 + - - +
395A ARG* 3.0 11.3 + - - +
397A VAL* 1.3 78.7 - - - +
399A ILE* 1.3 62.4 + - - +
401A ARG* 3.4 4.4 + - - +
402A MET* 3.0 21.3 + - - +
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Residues in contact with ILE 399 (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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335A VAL* 4.6 7.6 - - + +
395A ARG* 2.9 53.4 + - + +
396A ASP* 3.9 11.7 - - - +
398A ALA* 1.3 76.4 - - - +
400A ALA* 1.3 62.2 + - - +
402A MET* 3.0 19.0 + - - +
403A LYS* 3.0 24.2 + - - +
425A MET* 4.0 25.5 - - - +
430A PHE* 3.8 30.5 - - + -
431A GLN* 4.5 15.3 - - + +
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Residues in contact with ALA 400 (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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396A ASP 3.2 17.1 + - - +
397A VAL* 3.2 6.2 + - - +
399A ILE* 1.3 80.6 - - + +
401A ARG* 1.3 62.2 - - - +
403A LYS* 3.4 13.9 + - + +
404A ASN* 3.4 27.1 + - - -
22B LYS 5.5 0.8 - - - +
23B GLU* 4.1 28.7 - - + +
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Residues in contact with ARG 401 (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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363A PHE* 3.3 47.6 + - - +
364A GLY* 3.9 7.8 - - - -
365A VAL* 4.5 6.8 - - + +
390A CYS* 3.9 13.2 - - + -
391A TYR* 2.9 31.8 + - - -
392A GLY* 3.9 8.9 - - - -
393A GLU* 4.4 6.5 + - - -
397A VAL* 3.0 23.5 + - - +
398A ALA 3.7 4.3 - - - +
400A ALA* 1.3 72.3 - - - +
402A MET* 1.3 61.5 + - - +
404A ASN* 3.3 4.4 + - - +
405A ALA* 2.9 31.7 + - - +
23B GLU* 3.3 37.8 + - + +
307B ASP* 3.1 26.9 + - - +
310B LYS* 3.8 7.3 - - - +
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Residues in contact with MET 402 (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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335A VAL* 3.0 39.7 - - + +
337A CYS* 3.6 24.7 - - - +
388A LEU* 3.2 44.2 - - - +
390A CYS* 3.8 15.8 - - + +
398A ALA 3.0 11.0 + - - +
399A ILE* 3.0 12.4 + - - +
401A ARG* 1.3 75.5 - - - +
403A LYS* 1.3 63.6 + - - +
405A ALA* 3.2 2.4 + - - +
406A LEU* 2.9 31.4 + - + +
425A MET* 3.5 29.6 - - + -
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Residues in contact with LYS 403 (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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399A ILE* 3.0 20.8 + - - +
400A ALA* 3.6 14.1 - - - +
401A ARG 3.3 0.4 - - - -
402A MET* 1.3 76.4 - - - +
404A ASN* 1.3 66.3 + - - +
406A LEU* 3.5 9.5 + - - +
407A GLN* 3.2 33.1 + - + +
422A ILE* 5.0 5.3 - - + +
425A MET* 3.5 34.1 - - + -
426A ASN* 3.3 26.3 + - - +
431A GLN* 3.3 18.5 - - - +
22B LYS* 5.8 0.2 - - - +
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Residues in contact with ASN 404 (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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400A ALA 3.4 14.5 + - - +
401A ARG* 3.3 6.1 + - - +
402A MET 3.2 0.2 - - - -
403A LYS* 1.3 78.1 - - - +
405A ALA* 1.3 67.0 + - - +
406A LEU 3.2 0.2 - - - -
407A GLN* 3.3 4.9 + - - +
408A GLU* 3.2 32.5 + - - +
19B ARG* 3.9 10.1 + - + +
22B LYS* 2.6 68.5 + - + +
23B GLU* 3.3 24.2 - - - +
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Residues in contact with ALA 405 (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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360A PRO* 3.3 30.8 - - + +
361A GLY 5.7 0.7 - - - +
365A VAL* 4.3 10.8 - - + -
388A LEU* 3.9 18.8 - - + -
390A CYS* 4.0 13.5 - - - -
401A ARG 2.9 19.0 + - - +
402A MET 3.6 2.9 - - - +
404A ASN* 1.3 76.7 - - - +
406A LEU* 1.3 56.7 + - - +
408A GLU* 3.3 4.9 + - - -
409A LEU* 3.1 22.5 + - - +
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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
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337A CYS* 4.5 2.0 - - + -
339A ILE* 4.4 14.8 - - + -
388A LEU* 3.6 22.7 - - + -
402A MET* 2.9 36.5 + - + +
403A LYS* 3.7 3.1 - - - +
404A ASN 3.2 0.2 - - - -
405A ALA* 1.3 72.1 - - - +
407A GLN* 1.3 65.4 + - - +
408A GLU 3.0 3.0 + - - -
409A LEU* 3.1 24.8 + - + +
418A VAL* 3.9 22.8 - - + +
421A GLN* 3.8 19.5 - - + -
422A ILE* 3.6 46.9 - - + +
425A MET* 4.1 5.2 - - + -
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Residues in contact with GLN 407 (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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403A LYS* 3.2 17.5 + - + +
404A ASN* 3.3 7.6 + - - +
406A LEU* 1.3 76.4 - - - +
408A GLU* 1.3 59.3 + - + +
409A LEU 4.4 2.8 - - - +
410A ILE* 5.6 1.6 - - - +
422A ILE* 3.7 38.1 - - - +
426A ASN* 5.7 0.6 - - - +
22B LYS* 4.1 21.3 - - + +
44B LEU* 4.7 12.2 - - + +
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Residues in contact with GLU 408 (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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358A HIS* 4.0 19.2 + - + +
359A ALA 4.6 1.4 - - - +
360A PRO* 3.5 23.7 - - + +
361A GLY 3.6 2.1 + - - +
404A ASN* 3.2 19.5 + - - +
405A ALA* 3.5 10.0 - - - +
406A LEU 3.0 0.8 - - - -
407A GLN* 1.3 78.8 - - + +
409A LEU* 1.3 65.2 + - - +
410A ILE* 3.2 15.9 + - - +
15B LEU* 5.4 0.8 - - - +
18B LEU* 5.8 0.3 - - - +
19B ARG* 3.0 51.0 + - - +
40B LYS* 4.9 6.6 + - - +
44B LEU* 3.9 33.3 - - + +
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Residues in contact with LEU 409 (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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339A ILE* 4.1 12.1 - - + -
357A PHE* 4.0 9.6 - - + -
358A HIS 3.3 19.3 - - - +
360A PRO* 3.9 16.6 - - + -
367A TRP* 3.9 25.6 - - + -
388A LEU* 4.8 3.6 - - + -
405A ALA 3.1 13.5 + - - +
406A LEU* 3.1 23.2 + - + +
407A GLN 4.4 2.3 - - - +
408A GLU* 1.3 74.6 - - - +
410A ILE* 1.3 61.0 + - - +
411A ILE* 3.8 29.9 + - + -
418A VAL* 3.9 29.4 - - + +
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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
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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