Contacts of the helix formed by residues 474 - 484 (chain B) in PDB entry 2VZE
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 GLY 474 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B SER* 3.4 9.6 - - - -
223B GLY 3.4 16.6 - - - -
226B GLY 5.3 1.3 - - - -
473B ILE* 1.3 78.1 - - - +
475B PRO* 1.3 74.5 - - - +
476B SER* 3.3 3.1 - - - -
477B GLU* 3.0 36.4 + - - +
478B VAL 3.6 2.4 + - - -
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Residues in contact with PRO 475 (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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223B GLY 3.8 4.7 - - - +
224B THR 3.3 27.4 - - - +
464B ASP* 3.5 28.5 - - + +
465B ILE* 4.4 0.2 - - - -
466B ILE* 4.6 4.2 - - + -
473B ILE 4.0 3.6 - - - +
474B GLY* 1.3 81.5 - - - +
476B SER* 1.3 61.3 + - - +
478B VAL* 3.0 5.4 + - + +
479B GLU* 2.9 32.2 + - - +
493B VAL* 3.4 34.0 - - + +
560B ARG* 3.4 18.4 - - - +
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Residues in contact with SER 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B SER* 3.4 11.0 - - - -
226B GLY* 2.9 42.5 + - - -
227B LEU* 4.9 0.4 - - - -
474B GLY 3.3 0.8 - - - -
475B PRO* 1.3 79.4 - - - +
477B GLU* 1.3 57.3 + - - +
479B GLU* 3.8 14.1 + - - -
480B ASN* 2.8 46.1 + - - -
560B ARG* 4.5 5.2 + - - -
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Residues in contact with GLU 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ARG* 5.6 0.2 + - - -
222B SER* 2.5 37.2 + - - -
223B GLY 4.7 0.7 + - - -
226B GLY 4.5 4.9 + - - +
227B LEU* 4.1 23.3 - - + -
228B PRO* 3.6 22.7 - - + +
473B ILE* 5.0 2.1 - - + -
474B GLY* 3.0 20.2 + - - +
476B SER* 1.3 78.4 - - - +
478B VAL* 1.3 60.3 + - + +
480B ASN* 3.8 3.4 + - - +
481B ALA* 3.5 18.2 + - - +
535B THR* 5.0 5.1 + - - +
538B TYR* 4.7 3.3 + - - -
539B LYS* 3.1 38.9 + - + +
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Residues in contact with VAL 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B ILE* 3.8 25.8 - - + -
474B GLY 4.0 3.8 - - - +
475B PRO 3.0 4.6 + - - +
477B GLU* 1.3 72.4 - - - +
479B GLU* 1.3 63.1 + - - +
481B ALA* 3.2 7.9 + - - +
482B LEU* 3.0 36.3 + - + +
493B VAL* 3.6 32.8 - - + -
505B VAL* 4.4 2.2 - - + -
531B VAL* 4.6 5.8 - - + -
535B THR* 5.8 0.2 - - - -
539B LYS* 3.4 36.1 - - + +
541B PRO* 4.3 14.1 - - + -
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Residues in contact with GLU 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B PRO* 2.9 19.4 + - - +
476B SER* 3.8 11.4 + - - +
478B VAL* 1.3 74.7 - - - +
480B ASN* 1.3 67.4 + - - +
482B LEU* 3.2 1.3 + - - -
483B MET* 3.0 29.8 + - + +
491B THR* 3.7 34.0 - - + +
492B ALA* 3.5 2.4 - - - -
493B VAL* 3.1 33.7 + - + +
558B ILE* 5.6 0.9 - - - +
560B ARG* 2.8 43.4 + - - -
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Residues in contact with ASN 480 (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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227B LEU* 3.7 29.7 - - - +
476B SER* 2.8 30.9 + - - +
477B GLU 4.0 4.3 - - - +
479B GLU* 1.3 76.7 - - - +
481B ALA* 1.3 63.1 + - - +
483B MET* 3.4 13.7 + - - +
484B GLU* 3.4 20.2 + - - +
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Residues in contact with ALA 481 (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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477B GLU 3.5 11.3 + - - +
478B VAL 3.2 9.8 + - - +
479B GLU 3.1 0.4 - - - -
480B ASN* 1.3 80.2 - - - +
482B LEU* 1.3 57.6 + - - +
484B GLU* 3.4 14.0 + - - +
530B HIS* 2.8 31.1 + - - -
531B VAL* 4.3 17.3 - - + -
534B VAL* 3.7 26.5 - - + -
535B THR* 4.3 7.2 - - + -
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Residues in contact with LEU 482 (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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478B VAL* 3.0 25.0 + - + +
479B GLU 3.2 3.8 + - - +
481B ALA* 1.3 76.8 - - - +
483B MET* 1.3 56.9 + - - +
485B HIS* 2.9 22.5 + - - +
488B VAL* 3.3 30.1 - - + +
491B THR* 3.6 26.5 - - + +
493B VAL* 4.1 8.7 - - + -
507B ALA* 3.6 24.9 - - + -
509B VAL* 4.5 6.5 - - + -
527B LEU* 4.2 25.8 - - + +
530B HIS* 4.6 3.1 - - + -
531B VAL* 3.8 21.1 - - + -
541B PRO* 4.5 7.6 - - + -
544B ILE* 4.9 1.1 - - + -
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Residues in contact with MET 483 (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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479B GLU* 3.0 22.7 + - + +
480B ASN* 3.7 8.5 - - - +
481B ALA 3.4 0.2 - - - -
482B LEU* 1.3 73.2 - - - +
484B GLU* 1.3 61.6 + - - +
485B HIS 3.2 6.6 + - - +
488B VAL* 3.6 28.1 - - - +
489B VAL* 3.5 28.9 - - - +
490B GLU* 3.9 8.3 - - + -
491B THR* 3.9 11.2 - - + -
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Residues in contact with GLU 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B THR* 6.0 1.9 - - - +
480B ASN* 3.4 18.6 + - - +
481B ALA* 3.6 12.2 - - - +
482B LEU 3.2 1.0 - - - -
483B MET* 1.3 74.3 - - - +
485B HIS* 1.3 60.0 + - - +
486B PRO* 3.7 6.1 - - - +
530B HIS* 4.0 10.5 - - + +
534B VAL* 3.8 30.5 - - - +
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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