Contacts of the helix formed by residues 474 - 484 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A SER* 3.4 11.4 - - - -
223A GLY 3.3 16.8 - - - -
226A GLY 5.2 0.9 - - - -
473A ILE* 1.3 78.3 - - - +
475A PRO* 1.3 73.1 - - - +
476A SER* 3.3 2.9 - - - -
477A GLU* 3.0 36.1 + - - +
478A VAL 3.7 2.3 + - - -
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Residues in contact with PRO 475 (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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223A GLY 3.7 5.6 - - - +
224A THR 3.1 28.0 - - - +
225A SER* 4.8 0.4 - - - -
464A ASP* 3.3 32.1 - - + +
465A ILE* 4.3 0.2 - - - -
466A ILE* 4.6 2.9 - - + -
473A ILE 3.9 3.8 - - - +
474A GLY* 1.3 80.8 - - - +
476A SER* 1.3 63.9 + - - +
477A GLU 3.1 0.9 + - - -
478A VAL* 3.2 4.7 + - - +
479A GLU* 3.0 34.7 + - - +
493A VAL* 3.6 35.1 - - + +
560A ARG* 4.3 7.6 - - - +
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Residues in contact with SER 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A SER* 3.4 10.6 - - - -
226A GLY* 2.8 43.5 + - - -
227A LEU* 4.8 0.2 - - - -
474A GLY 3.3 1.0 - - - -
475A PRO* 1.3 79.8 - - - +
477A GLU* 1.3 56.4 + - - +
479A GLU* 3.8 14.6 + - - -
480A ASN* 2.9 45.5 + - - +
560A ARG* 5.6 1.7 + - - -
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Residues in contact with GLU 477 (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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148A ARG* 5.8 0.2 + - - -
222A SER* 2.4 37.5 + - - -
226A GLY 4.6 5.3 - - - +
227A LEU* 4.0 24.2 - - + -
228A PRO* 3.7 19.9 - - + +
473A ILE* 5.0 1.7 - - - -
474A GLY* 3.0 20.6 + - - +
476A SER* 1.3 79.1 - - - +
478A VAL* 1.3 62.1 + - - +
480A ASN* 3.6 3.0 + - - +
481A ALA* 3.3 18.7 + - - +
535A THR* 5.1 2.8 - - - +
538A TYR* 4.8 2.4 + - - -
539A LYS* 2.5 48.5 + - + +
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Residues in contact with VAL 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A ILE* 3.9 24.5 - - + -
474A GLY 4.1 3.8 - - - +
475A PRO 3.2 1.9 + - - +
477A GLU* 1.3 72.4 - - - +
479A GLU* 1.3 61.6 + - - +
481A ALA* 3.3 7.6 + - - +
482A LEU* 2.9 37.3 + - + +
493A VAL* 3.5 34.1 - - + -
505A VAL* 4.4 2.7 - - + -
531A VAL* 4.7 6.3 - - + -
539A LYS* 3.5 36.3 - - + +
541A PRO* 4.2 15.0 - - + -
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Residues in contact with GLU 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A PRO* 3.0 21.3 + - - +
476A SER* 3.8 16.8 + - - +
478A VAL* 1.3 73.8 - - - +
480A ASN* 1.3 68.4 + - - +
482A LEU* 3.2 2.5 + - - +
483A MET* 2.9 31.4 + - + +
491A THR* 3.8 26.4 - - + +
492A ALA* 3.5 0.7 - - - -
493A VAL* 2.9 33.0 + - + +
560A ARG* 2.8 45.6 + - - -
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Residues in contact with ASN 480 (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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226A GLY* 6.2 0.2 - - - -
227A LEU* 3.9 29.7 - - + +
476A SER* 2.9 29.5 + - - +
477A GLU 3.9 3.4 - - - +
479A GLU* 1.3 75.5 - - - +
481A ALA* 1.3 67.7 + - - +
483A MET* 3.2 16.0 + - - +
484A GLU* 3.4 20.5 + - - +
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Residues in contact with ALA 481 (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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477A GLU 3.3 10.0 + - - +
478A VAL* 3.3 11.5 + - - +
480A ASN* 1.3 80.2 - - - +
482A LEU* 1.3 62.0 + - - +
484A GLU* 3.2 13.5 + - - +
530A HIS* 2.8 25.2 + - - -
531A VAL* 4.0 20.6 - - + -
534A VAL* 3.6 29.4 - - + -
535A THR* 4.5 4.9 - - + -
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Residues in contact with LEU 482 (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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478A VAL* 2.9 20.0 + - + +
479A GLU 3.6 4.0 - - - +
481A ALA* 1.3 75.9 - - - +
483A MET* 1.3 57.2 + - - +
485A HIS* 3.1 18.5 + - - +
488A VAL* 3.3 25.6 - - + +
491A THR* 3.6 22.9 - - + +
493A VAL* 4.0 14.1 - - + -
507A ALA* 3.5 32.1 - - + -
509A VAL* 4.4 4.7 - - + -
527A LEU* 4.3 31.2 - - + +
530A HIS* 4.5 3.4 - - + -
531A VAL* 3.7 22.7 - - + -
541A PRO* 4.5 6.1 - - + -
544A ILE* 5.0 1.1 - - + -
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Residues in contact with MET 483 (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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479A GLU* 2.9 23.0 + - + +
480A ASN* 3.2 9.1 + - - +
482A LEU* 1.3 72.9 - - - +
484A GLU* 1.3 63.8 + - + +
485A HIS 3.2 7.9 - - - +
488A VAL* 3.9 25.2 - - - +
489A VAL* 3.4 26.5 - - - +
490A GLU* 4.0 8.7 - - + -
491A THR* 3.9 11.0 - - + -
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Residues in contact with GLU 484 (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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143A THR* 6.0 2.1 - - - +
480A ASN* 3.4 19.0 - - - +
481A ALA* 3.2 16.6 + - - +
483A MET* 1.3 76.2 - - - +
485A HIS* 1.3 61.5 + - - +
486A PRO* 3.7 5.2 - - - +
530A HIS* 3.9 10.2 - - + +
534A VAL* 3.9 25.3 - - - +
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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