Contacts of the helix formed by residues 430 - 444 (chain A) in PDB entry 2VZ9
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 THR 430 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428A GLY 3.6 0.8 - - - -
429A ARG* 1.3 88.6 - - - +
431A LEU* 1.3 68.7 + - - +
432A GLU* 2.8 35.3 + - + +
433A ALA* 2.9 15.9 + - - +
434A VAL* 3.4 12.0 + - - +
467A PHE* 3.3 18.7 - - + +
836A TRP 4.3 5.2 + - - -
837A ASP* 4.2 25.1 - - + +
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Residues in contact with LEU 431 (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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430A THR* 1.3 74.8 - - - +
432A GLU* 1.3 61.3 + - + +
434A VAL* 3.6 4.8 + - - +
435A GLN* 2.9 61.0 + - + +
467A PHE* 3.0 26.9 - - + -
482A VAL* 4.6 15.0 - - + +
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Residues in contact with GLU 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A THR* 2.8 29.6 + - - +
431A LEU* 1.3 84.2 - - + +
433A ALA* 1.3 65.8 + - - +
434A VAL 2.8 0.9 + - - -
435A GLN* 2.9 7.3 + - - +
436A THR* 2.8 30.7 + - - +
835A LYS* 3.7 25.3 - - - +
836A TRP 3.4 20.1 - - - +
837A ASP* 5.3 0.9 - - - -
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Residues in contact with ALA 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A GLY* 3.6 8.1 - - - -
429A ARG 3.5 25.1 - - - +
430A THR* 2.9 11.4 + - - +
432A GLU* 1.3 77.1 - - - +
434A VAL* 1.3 58.4 + - - +
436A THR* 4.1 2.5 - - - -
437A LEU* 3.2 32.3 + - + +
833A HIS 4.2 2.1 - - - +
834A ILE* 5.9 0.4 - - - -
835A LYS* 2.9 41.3 - - - +
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Residues in contact with VAL 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ALA* 4.9 2.7 - - - +
427A SER* 4.2 3.8 - - - -
428A GLY 3.8 12.1 - - - +
430A THR 3.4 8.7 + - - +
431A LEU 3.9 3.6 - - - +
432A GLU 2.8 1.0 + - - -
433A ALA* 1.3 75.6 - - - +
435A GLN* 1.3 66.7 + - - +
436A THR 2.9 3.0 + - - -
437A LEU* 3.1 6.2 + - - -
438A LEU* 3.1 36.8 + - + +
467A PHE* 3.6 35.0 - - + +
468A ARG* 4.1 2.7 - - - +
469A GLY* 3.7 21.5 - - - +
482A VAL* 3.2 29.8 - - + -
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Residues in contact with GLN 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A LEU* 2.9 47.9 + - + +
432A GLU* 3.5 7.4 - - - +
434A VAL* 1.3 76.7 - - - +
436A THR* 1.3 62.5 + - - +
438A LEU* 4.1 4.5 - - - +
439A GLU* 3.2 26.9 + - - +
480A GLN* 4.3 19.8 + - - +
482A VAL* 3.6 27.7 - - + +
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Residues in contact with THR 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A GLU* 2.8 20.0 + - - +
433A ALA 4.2 4.7 - - - -
434A VAL 2.9 0.2 + - - -
435A GLN* 1.3 75.1 - - - +
437A LEU* 1.3 66.7 + - - +
439A GLU* 3.0 13.1 + - + +
440A GLN* 2.9 23.6 + - + +
833A HIS* 3.8 40.4 - - + +
835A LYS* 4.1 26.4 - - - +
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Residues in contact with LEU 437 (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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424A LEU* 4.9 0.9 - - - -
426A ALA* 3.7 25.6 - - + -
427A SER 3.6 23.8 - - - +
433A ALA* 3.2 19.5 + - + +
434A VAL* 3.1 6.1 + - - +
436A THR* 1.3 75.9 - - - +
438A LEU* 1.3 57.3 + - - +
440A GLN* 3.0 10.1 + - + +
441A GLY* 2.9 24.3 + - - -
454A LEU* 4.3 26.2 - - + +
457A ILE* 5.7 8.5 - - + -
830A ILE* 5.3 3.4 - - + +
833A HIS* 3.3 34.3 - - + +
834A ILE* 5.0 11.7 - - + -
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Residues in contact with LEU 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A LEU* 4.1 21.5 - - + +
425A GLN 4.8 0.2 - - - -
426A ALA* 4.0 22.7 - - + -
434A VAL* 3.1 31.8 + - + +
435A GLN* 4.2 4.3 - - - +
437A LEU* 1.3 74.4 - - - +
439A GLU* 1.3 65.4 + - - +
441A GLY* 3.1 0.9 + - - -
442A LEU* 3.0 32.1 + - - +
469A GLY* 4.0 15.3 - - - +
470A TYR 3.6 24.9 - - - +
471A ALA* 4.6 5.8 - - + -
480A GLN* 3.9 24.0 - - - +
481A GLU 4.3 4.0 - - - +
482A VAL* 4.8 5.6 - - + -
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Residues in contact with GLU 439 (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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435A GLN* 3.2 17.7 + - - +
436A THR* 3.0 15.1 + - - +
438A LEU* 1.3 75.9 - - - +
440A GLN* 1.3 68.1 + - - +
441A GLY 3.2 0.9 + - - -
442A LEU* 3.4 9.4 + - + +
443A ARG* 3.2 43.0 + - + +
480A GLN* 5.1 1.9 - - - +
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Residues in contact with GLN 440 (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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436A THR* 2.9 17.7 + - + +
437A LEU* 3.0 11.2 + - + +
439A GLU* 1.3 81.6 + - - +
441A GLY* 1.3 64.0 + - - +
443A ARG* 3.1 34.1 + - - +
444A HIS* 3.2 36.4 + - - -
450A PHE* 3.3 23.6 - - + -
454A LEU* 5.4 0.7 - - + -
828A PRO* 5.7 1.6 - - - +
833A HIS* 3.1 53.7 + - + +
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Residues in contact with GLY 441 (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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424A LEU* 3.4 29.4 - - - -
437A LEU 2.9 9.2 + - - -
438A LEU 3.1 1.0 + - - -
439A GLU 3.1 0.6 - - - -
440A GLN* 1.3 79.4 - - - +
442A LEU* 1.3 59.2 + - - +
444A HIS 2.9 31.0 + - - +
445A SER* 3.3 3.1 + - - -
450A PHE* 4.5 2.7 - - - -
451A VAL* 5.1 1.1 - - - +
454A LEU* 4.4 7.2 - - - -
473A LEU* 4.0 6.7 - - - +
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Residues in contact with LEU 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A LEU* 3.0 17.0 + - + +
439A GLU* 3.4 7.6 + - + +
441A GLY* 1.3 75.1 - - - +
443A ARG* 1.3 61.8 - - + +
445A SER* 2.7 24.6 + - - +
471A ALA* 4.2 11.9 - - + -
472A VAL 5.5 1.8 - - - +
473A LEU* 3.4 30.7 - - + -
480A GLN* 3.9 26.9 - - + +
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Residues in contact with ARG 443 (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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20A GLU* 5.9 0.6 + - - -
439A GLU* 3.2 27.5 + - + +
440A GLN* 3.1 34.3 + - - +
441A GLY 3.2 1.4 - - - -
442A LEU* 1.3 78.4 - - + +
444A HIS* 1.3 83.8 + - + +
445A SER 3.7 0.6 + - - -
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Residues in contact with HIS 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A GLN* 3.2 31.5 + - - +
441A GLY 2.9 11.1 + - - +
443A ARG* 1.3 98.0 + - + +
445A SER* 1.3 55.8 + - - +
446A ARG 2.9 12.0 + - - -
447A ASP* 3.0 30.1 + - + +
450A PHE* 4.4 10.3 - + + -
451A VAL* 4.2 6.1 - - - +
828A PRO* 3.6 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