Contacts of the helix formed by residues 468 - 483 (chain A) in PDB entry 2VL7
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 468 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A ARG* 3.3 12.0 - - + +
244A CYS* 2.9 33.7 + - - +
465A ASN* 3.0 27.3 + - - +
466A VAL 3.7 1.5 - - - +
467A SER* 1.3 79.5 + - - +
469A ASP* 1.3 57.9 + - - +
470A MET* 2.9 34.1 + - - +
471A VAL* 3.1 21.1 + - + +
472A ARG* 2.9 27.5 + - - +
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Residues in contact with ASP 469 (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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244A CYS 3.0 14.9 + - - +
245A HIS* 3.3 8.2 + - - +
246A GLU* 2.7 52.3 + - + +
295A TYR* 3.7 11.2 - - + -
467A SER 3.7 10.3 - - - +
468A ASP* 1.3 72.9 + - - +
470A MET* 1.3 56.6 + - - +
472A ARG* 3.7 16.5 + - - +
473A LYS* 2.8 27.9 + - - +
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Residues in contact with MET 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ASP* 3.8 22.0 - - - +
192A LYS* 4.4 19.3 - - + +
195A THR* 3.7 15.9 - - + +
244A CYS* 4.0 24.6 - - + +
295A TYR* 3.6 23.5 - - + +
297A CYS* 4.6 0.2 - - - -
302A VAL* 4.6 9.0 - - - -
304A VAL* 3.4 31.6 - - + -
468A ASP* 2.9 9.9 + - - +
469A ASP* 1.3 76.2 - - - +
471A VAL* 1.3 65.6 + - + +
473A LYS* 3.3 3.2 + - + +
474A ARG* 3.1 27.6 + - - +
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Residues in contact with VAL 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A PRO* 3.9 18.8 - - + -
465A ASN* 3.5 28.7 - - + +
468A ASP* 3.1 23.9 + - + +
470A MET* 1.3 73.6 - - + +
472A ARG* 1.3 66.8 + - - +
474A ARG* 3.1 29.6 + - + +
475A ILE* 3.1 37.5 + - + +
493A LEU* 5.7 2.2 - - + -
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Residues in contact with ARG 472 (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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466A VAL* 3.2 36.4 + - + +
467A SER* 4.8 4.4 - - - +
468A ASP 2.9 17.2 + - - +
469A ASP* 3.7 16.7 + - - +
471A VAL* 1.3 76.1 - - - +
473A LYS* 1.3 64.1 + - - +
475A ILE* 3.1 15.7 + - + +
476A GLU* 3.0 44.8 + - + +
486A GLU* 5.2 8.1 + - - +
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Residues in contact with LYS 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLU* 5.8 4.0 - - - +
293A ASP* 4.0 25.6 + - - +
295A TYR* 3.4 27.6 - - - +
306A SER* 6.0 1.8 - - - -
469A ASP 2.8 15.7 + - - +
470A MET 3.7 3.4 - - - +
471A VAL 3.3 0.2 - - - -
472A ARG* 1.3 73.3 - - - +
474A ARG* 1.3 56.6 + - - +
476A GLU* 3.2 23.4 + - - +
477A ARG* 2.8 32.8 + - + +
480A LYS* 5.2 13.7 - - - +
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Residues in contact with ARG 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LEU 3.4 23.1 - - - +
189A GLU* 3.8 26.1 + - - +
191A ASP* 3.0 34.9 + - - +
192A LYS* 3.5 35.7 - - - +
470A MET* 3.1 21.6 + - - +
471A VAL* 3.1 35.2 + - - +
473A LYS* 1.3 75.3 - - - +
475A ILE* 1.3 59.2 + - - +
477A ARG* 3.3 15.9 + - - +
478A LEU* 3.0 38.9 + - + +
493A LEU* 5.0 13.5 - - + -
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Residues in contact with ILE 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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464A PRO* 4.5 6.1 - - + -
466A VAL* 3.9 20.2 - - + -
471A VAL* 3.1 28.4 + - + +
472A ARG* 3.5 11.7 - - + +
474A ARG* 1.3 74.1 - - - +
476A GLU* 1.3 59.1 + - - +
478A LEU* 3.5 1.6 + - - +
479A SER* 3.0 27.5 + - - -
486A GLU* 3.8 41.5 - - + +
489A ILE* 4.0 13.5 - - + +
490A ILE* 3.8 23.1 - - + -
493A LEU* 3.8 20.9 - - + -
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Residues in contact with GLU 476 (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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472A ARG* 3.0 41.9 + - + +
473A LYS* 3.6 28.1 + - - +
475A ILE* 1.3 72.1 - - - +
477A ARG* 1.3 67.6 + - - +
479A SER* 3.2 2.9 + - - -
480A LYS* 2.9 40.4 + - + +
486A GLU* 3.1 32.4 - - - +
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Residues in contact with ARG 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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187A LEU 4.7 4.8 + - - -
188A LEU 2.9 28.7 + - - -
190A ALA 4.6 0.6 - - - +
191A ASP* 3.0 26.4 + - - +
306A SER 5.1 9.6 - - - -
308A VAL* 3.3 29.2 - - - +
309A ASN* 2.9 45.7 + - - +
312A ILE* 5.4 2.0 - - - +
473A LYS* 2.8 22.3 + - + +
474A ARG* 3.5 13.9 + - - +
476A GLU* 1.3 77.9 - - - +
478A LEU* 1.3 75.8 + - - +
480A LYS* 3.3 13.5 + - - +
481A LEU* 3.0 26.5 + - - +
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Residues in contact with LEU 478 (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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188A LEU* 4.0 38.6 - - + +
332A SER* 4.1 13.9 - - - +
474A ARG* 3.0 35.9 + - + +
475A ILE 4.0 0.2 - - - +
476A GLU 3.2 0.2 - - - -
477A ARG* 1.3 95.5 - - - +
479A SER* 1.3 60.4 + - - +
481A LEU* 4.4 12.1 - - + -
482A THR* 2.7 38.1 + - - +
489A ILE* 3.9 33.0 - - + -
493A LEU* 4.5 9.2 - - + -
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Residues in contact with SER 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A ILE 3.0 18.8 + - - -
476A GLU* 3.2 5.6 + - - -
478A LEU* 1.3 76.5 - - - +
480A LYS* 1.3 57.8 + - - +
482A THR* 3.9 0.7 - - - -
483A GLY* 2.8 31.0 + - - -
484A LYS 2.5 25.7 + - - +
485A ASP* 3.9 1.7 - - - -
486A GLU* 3.6 27.1 + - - +
489A ILE* 3.7 8.0 - - - +
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Residues in contact with LYS 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A LYS* 5.2 13.7 - - - +
476A GLU* 2.9 32.9 + - + +
477A ARG* 3.7 9.2 - - - +
479A SER* 1.3 79.0 - - - +
481A LEU* 1.3 63.1 + - - +
482A THR 3.5 0.2 + - - -
483A GLY* 3.6 6.6 + - - -
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Residues in contact with LEU 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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309A ASN* 3.6 40.6 - - + +
332A SER 5.1 0.9 - - - +
334A THR* 4.0 40.4 - - + +
477A ARG* 3.0 17.2 + - - +
478A LEU* 3.8 16.8 - - + +
480A LYS* 1.3 79.5 - - - +
482A THR* 1.3 60.9 + - + +
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Residues in contact with THR 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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331A GLU 4.9 1.1 - - - +
332A SER* 3.6 26.7 - - - +
334A THR* 3.0 30.3 - - - +
478A LEU 2.7 22.4 + - - +
479A SER 3.5 0.3 + - - -
481A LEU* 1.3 81.1 - - + +
483A GLY* 1.3 60.1 - - - +
484A LYS* 3.2 37.5 + - - +
489A ILE* 3.5 4.9 - - - +
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Residues in contact with GLY 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 SER 2.8 10.9 + - - -
480A LYS 3.6 5.2 + - - -
481A LEU 3.5 2.8 + - - -
482A THR* 1.3 77.6 - - - +
484A LYS* 1.3 59.6 + - - +
485A ASP 4.3 0.3 + - - -
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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