Contacts of the helix formed by residues 394 - 409 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332B GLY* 5.1 0.4 - - - -
333B HIS* 3.6 9.0 - - - -
392B GLY 3.7 5.1 - - - +
393B GLU* 1.3 87.8 + - - +
395B ARG* 1.3 67.0 + - - +
396B ASP* 3.3 11.8 + - - +
397B VAL* 2.9 44.4 + - - +
398B ALA* 3.2 18.5 + - - +
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Residues in contact with ARG 395 (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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242B GLU* 2.8 34.8 + - - +
246B PRO* 3.5 13.7 - - - +
333B HIS* 3.5 40.7 + - + +
335B VAL* 5.4 0.2 - - + -
394B ASN* 1.3 74.7 - - - +
396B ASP* 1.3 67.1 + - - +
398B ALA* 3.2 2.8 + - - +
399B ILE* 3.0 44.7 + - + +
430B PHE* 2.8 36.7 + - - -
431B GLN 3.0 27.3 + - - -
432B HIS 4.2 2.0 + - - -
433B GLY* 3.5 18.0 - - - -
434B GLY 4.8 0.4 - - - +
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Residues in contact with ASP 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B ASN* 3.3 10.8 + - - +
395B ARG* 1.3 82.1 + - - +
397B VAL* 1.3 59.0 + - + +
399B ILE* 3.3 10.7 + - - +
400B ALA* 2.9 28.6 + - - +
431B GLN 4.7 10.0 - - - +
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Residues in contact with VAL 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU* 4.2 1.1 - - - +
310A LYS* 3.7 29.2 - - - +
314A ARG* 6.4 0.2 - - - +
392B GLY* 3.8 11.2 - - - -
393B GLU* 3.7 26.2 - - - +
394B ASN* 2.9 32.7 + - - +
396B ASP* 1.3 73.4 - - + +
398B ALA* 1.3 60.4 + - - +
400B ALA* 3.7 6.2 - - - +
401B ARG* 2.9 43.8 + - - +
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Residues in contact with ALA 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B HIS 3.6 28.7 - - - +
335B VAL* 4.2 13.7 - - + -
390B CYS* 3.6 22.8 - - - +
391B TYR 4.3 4.5 - - - -
392B GLY* 3.8 7.8 - - - +
394B ASN 3.2 9.5 + - - +
395B ARG* 3.2 10.1 + - - +
397B VAL* 1.3 78.7 - - - +
399B ILE* 1.3 63.1 + - - +
401B ARG* 3.3 1.2 + - - -
402B MET* 3.0 18.8 + - - +
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Residues in contact with ILE 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B VAL* 4.5 10.8 - - + -
395B ARG* 3.0 53.9 + - + +
396B ASP* 3.6 9.6 - - - +
398B ALA* 1.3 78.4 - - - +
400B ALA* 1.3 62.3 + - - +
402B MET* 3.0 9.0 + - - +
403B LYS* 3.0 46.2 + - + +
425B MET* 4.2 14.3 - - - +
430B PHE* 3.6 32.3 - - + -
431B GLN* 4.6 11.7 - - + +
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Residues in contact with ALA 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU* 4.0 28.3 - - + +
396B ASP 2.9 17.8 + - - +
397B VAL* 3.3 8.5 + - - +
399B ILE* 1.3 77.4 - - - +
401B ARG* 1.3 62.6 + - - +
403B LYS* 3.6 11.8 + - - +
404B ASN* 3.3 27.9 + - - +
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Residues in contact with ARG 401 (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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23A GLU* 3.2 37.5 + - - +
307A ASP* 3.3 29.7 + - - +
310A LYS* 4.4 2.0 - - - +
363B PHE* 3.4 46.4 + - - +
364B GLY* 4.0 7.5 - - - -
365B VAL* 4.8 7.1 - - + +
390B CYS* 3.8 14.8 - - + -
391B TYR* 3.0 32.8 + - - -
392B GLY* 3.9 8.7 - - - -
393B GLU* 4.3 11.1 + - - -
397B VAL* 2.9 26.2 + - - +
398B ALA 3.7 4.0 - - - +
400B ALA* 1.3 75.6 - - - +
402B MET* 1.3 58.2 + - - +
404B ASN* 3.4 4.7 + - - +
405B ALA* 2.9 28.2 + - - +
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Residues in contact with MET 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B VAL* 3.1 37.9 - - + +
337B CYS* 3.6 27.8 - - - +
388B LEU* 3.3 45.3 - - - +
390B CYS* 3.5 15.2 - - + +
398B ALA 3.0 13.0 + - - +
399B ILE* 3.0 9.6 + - - +
401B ARG* 1.3 74.4 - - - +
403B LYS* 1.3 56.1 + - - +
405B ALA* 3.6 0.6 - - - +
406B LEU* 2.8 45.5 + - + +
425B MET* 3.6 25.1 - - - -
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Residues in contact with LYS 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B ILE* 3.0 25.7 + - - +
400B ALA* 3.7 13.6 - - - +
402B MET* 1.3 75.6 - - - +
404B ASN* 1.3 64.7 + - - +
406B LEU* 3.6 11.2 + - - +
407B GLN* 3.2 35.5 + - - +
422B ILE* 5.3 5.6 - - + +
425B MET* 3.5 36.8 - - + +
426B ASN* 3.6 18.3 + - - +
431B GLN* 3.0 22.0 - - - +
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Residues in contact with ASN 404 (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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19A ARG* 4.4 7.7 - - + +
22A LYS* 3.4 46.9 + - + +
23A GLU* 3.4 19.3 + - + +
400B ALA 3.3 14.0 + - - +
401B ARG* 3.4 8.3 + - - +
402B MET 3.2 0.4 - - - -
403B LYS* 1.3 79.3 - - - +
405B ALA* 1.3 64.1 + - - +
407B GLN* 3.4 19.9 + - - +
408B GLU* 3.2 30.2 + - - +
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Residues in contact with ALA 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B PRO* 3.5 26.1 - - + +
361B GLY 5.7 0.9 - - - -
365B VAL* 4.4 9.0 - - + -
388B LEU* 3.8 20.6 - - + -
390B CYS* 4.0 13.9 - - - -
401B ARG 2.9 18.3 + - - +
402B MET 3.1 4.0 + - - +
404B ASN* 1.3 77.2 - - - +
406B LEU* 1.3 60.7 + - - +
408B GLU* 3.2 4.9 + - - -
409B LEU* 3.1 21.1 + - - +
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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
----------------------------------------------------------
337B CYS* 4.4 4.9 - - + -
339B ILE* 4.6 13.2 - - + -
388B LEU* 4.1 16.6 - - + -
402B MET* 2.8 32.8 + - + +
403B LYS* 3.7 6.3 - - - +
405B ALA* 1.3 74.2 - - - +
407B GLN* 1.3 60.6 + - - +
408B GLU 3.6 0.2 + - - -
409B LEU* 3.6 13.7 + - + +
418B VAL* 3.7 31.7 - - + +
421B GLN* 3.8 34.3 - - + +
422B ILE* 3.9 18.3 - - + +
425B MET* 3.6 29.6 - - + -
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Residues in contact with GLN 407 (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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22A LYS* 3.5 28.4 + - + +
44A LEU* 4.9 10.6 - - + +
403B LYS* 3.2 23.6 + - - +
404B ASN* 3.6 23.3 + - - +
405B ALA 3.2 0.4 - - - -
406B LEU* 1.3 75.8 - - - +
408B GLU* 1.3 61.6 + - + +
409B LEU 3.6 4.0 + - - +
410B ILE* 5.2 3.1 - - - +
422B ILE* 5.2 14.9 - - + +
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Residues in contact with GLU 408 (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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15A LEU* 5.1 2.1 - - - +
18A LEU* 5.6 0.5 - - - +
19A ARG* 2.9 50.1 + - - +
40A LYS* 3.8 18.2 + - - +
44A LEU* 4.0 30.8 - - + +
358B HIS* 4.0 15.3 + - + +
359B ALA 4.4 1.7 - - - +
360B PRO* 3.5 23.7 - - + +
361B GLY 4.4 3.0 - - - +
404B ASN* 3.2 17.4 + - - +
405B ALA* 3.2 10.0 + - - +
407B GLN* 1.3 75.0 - - + +
409B LEU* 1.3 65.1 + - - +
410B ILE* 3.3 12.7 + - - +
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Residues in contact with LEU 409 (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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339B ILE* 4.2 18.2 - - + -
357B PHE* 4.0 4.0 - - + -
358B HIS 3.5 18.4 - - - +
360B PRO* 3.9 15.0 - - + -
367B TRP* 3.9 29.4 - - + -
388B LEU* 4.8 7.6 - - + -
405B ALA 3.1 14.3 + - - +
406B LEU* 3.8 15.4 - - + +
407B GLN 3.4 3.7 - - - +
408B GLU* 1.3 77.2 - - - +
410B ILE* 1.3 64.8 + - - +
411B ILE* 4.0 21.9 + - + -
418B VAL* 3.7 33.0 - - + +
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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