Contacts of the helix formed by residues 441 - 453 (chain A) in PDB entry 1ZVR
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 441 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437A GLY 4.1 6.1 - - - +
438A TYR* 2.8 26.1 + - + +
440A ARG* 1.3 80.7 - - - +
442A ILE* 1.3 67.2 + - - +
443A ARG* 3.9 4.1 + - - +
444A GLY* 2.7 26.0 + - - -
445A PHE* 2.8 21.3 + - - +
499A GLU* 3.5 16.8 - - - +
500A PHE* 4.5 0.2 - - - -
556A TYR* 3.7 21.1 - - + +
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Residues in contact with ILE 442 (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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440A ARG 3.8 0.2 + - - -
441A THR* 1.3 72.9 - - - +
443A ARG* 1.3 61.4 + - + +
445A PHE* 3.3 4.0 + - - +
446A GLU* 3.1 34.1 + - - +
499A GLU* 2.9 35.5 + - + +
500A PHE* 3.7 25.3 - - + -
504A PHE* 3.9 22.5 - - + -
544A ILE* 4.6 1.1 - - + -
545A ASN* 4.1 0.9 - - - +
548A LEU* 3.7 34.1 - - + +
551A PHE* 3.6 19.5 - - + +
552A THR* 3.6 24.0 - - - +
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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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203A GLU* 3.7 24.4 + - - +
208A LEU* 4.1 16.2 - - + +
438A TYR* 4.9 4.0 - - + +
441A THR* 3.2 5.0 + - - +
442A ILE* 1.3 77.4 - - + +
444A GLY* 1.3 65.9 + - - +
446A GLU* 3.3 19.9 + - - +
447A VAL* 3.2 25.8 + - - +
499A GLU* 4.5 1.4 + - - +
545A ASN* 3.2 38.2 + - - +
548A LEU* 3.2 34.9 - - - +
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Residues in contact with GLY 444 (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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438A TYR* 3.3 31.8 - - - -
439A TYR* 3.7 10.8 - - - -
441A THR* 2.7 25.4 + - - -
443A ARG* 1.3 72.4 - - - +
445A PHE* 1.3 56.8 + - - +
447A VAL* 3.1 5.5 + - - +
448A LEU* 2.9 26.7 + - - +
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Residues in contact with PHE 445 (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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433A LEU* 3.9 28.0 - - + -
439A TYR 3.2 14.8 + - - +
441A THR 2.8 15.3 + - - +
442A ILE 3.5 5.4 - - - +
444A GLY* 1.3 73.9 - - - +
446A GLU* 1.3 64.8 + - - +
448A LEU* 3.1 10.9 + - + +
449A VAL* 3.0 37.5 + - + +
483A PHE* 3.9 24.5 - + - -
484A ILE* 4.0 10.8 - - + -
487A VAL* 3.9 19.5 - - + -
500A PHE* 3.6 21.5 - + + -
504A PHE* 3.3 23.1 - + + -
505A LEU* 4.1 4.9 - - + -
508A ILE* 3.8 21.8 - - + -
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Residues in contact with GLU 446 (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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208A LEU* 2.9 31.0 - - + +
442A ILE* 3.1 20.1 + - - +
443A ARG* 3.5 10.1 - - - +
444A GLY 3.3 0.4 - - - -
445A PHE* 1.3 75.4 - - - +
447A VAL* 1.3 57.1 + - - +
449A VAL* 3.3 3.3 + - - +
450A GLU* 2.9 34.2 + - - +
504A PHE* 4.2 4.9 - - + -
541A TRP* 3.4 47.8 - - + +
544A ILE* 3.5 8.7 - - - +
545A ASN* 2.4 41.0 + - - +
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Residues in contact with VAL 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LEU* 4.2 28.5 - - + +
209A TYR* 3.4 28.9 - - + -
214A GLU* 3.9 23.3 - - + +
438A TYR* 3.6 20.2 - - + +
439A TYR* 4.7 2.7 - - + -
443A ARG 3.2 13.8 + - - +
444A GLY* 3.1 9.7 + - - +
446A GLU* 1.3 74.5 - - - +
448A LEU* 1.3 57.5 + - - +
450A GLU* 3.1 8.0 + - - +
451A LYS* 2.8 39.2 + - + +
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Residues in contact with LEU 448 (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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429A SER* 3.6 36.8 - - - +
432A MET* 3.9 19.3 - - + -
433A LEU* 3.7 26.9 - - + -
439A TYR* 4.1 22.6 - - + -
444A GLY 2.9 11.8 + - - +
445A PHE* 3.1 15.9 + - + +
447A VAL* 1.3 75.3 - - - +
449A VAL* 1.3 57.8 + - + +
451A LYS* 4.4 3.4 - - - -
452A GLU* 2.8 57.9 + - + +
453A TRP* 4.2 1.0 - - + -
483A PHE* 4.4 7.6 - - + -
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Residues in contact with VAL 449 (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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445A PHE* 3.0 38.4 + - + +
446A GLU* 3.5 8.1 - - - +
448A LEU* 1.3 74.4 - - + +
450A GLU* 1.3 66.0 + - - +
453A TRP* 3.1 19.3 + - + +
454A LEU* 2.9 26.9 + - + -
480A PHE* 4.2 22.2 - - + -
483A PHE* 4.8 4.7 - - + -
508A ILE* 5.5 0.7 - - + -
520A PHE* 3.9 28.3 - - + -
541A TRP* 4.2 18.2 - - + -
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Residues in contact with GLU 450 (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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205A GLY 5.6 2.2 - - - +
206A TRP* 5.1 13.2 - - - -
208A LEU* 5.1 2.0 - - + -
209A TYR* 3.8 32.5 - - + +
446A GLU 2.9 23.2 + - - +
447A VAL 3.6 4.5 - - - +
449A VAL* 1.3 75.7 - - - +
451A LYS* 1.3 53.9 + - - +
454A LEU* 3.0 34.0 - - - +
455A SER* 2.7 33.8 + - - -
519A THR* 3.7 6.8 + - - +
539A SER* 4.9 0.5 + - - -
541A TRP* 2.6 35.0 + - + +
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Residues in contact with LYS 451 (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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209A TYR* 3.7 22.7 - - + +
214A GLU* 4.0 20.9 - - + -
215A TYR* 4.6 12.4 + - + +
218A GLN* 4.1 5.6 + - - -
270A LEU 4.5 3.6 + - - -
271A SER* 2.6 30.8 + - - +
432A MET* 3.4 26.7 - - + -
439A TYR* 3.5 11.7 - - + +
447A VAL* 2.8 22.5 + - + +
448A LEU* 3.8 2.2 - - - +
450A GLU* 1.3 71.1 - - - +
452A GLU* 1.3 77.8 + - + +
453A TRP 3.3 0.2 - - - -
455A SER* 2.5 26.5 + - - -
456A PHE* 3.1 25.7 + - + -
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Residues in contact with GLU 452 (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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271A SER* 3.4 13.5 + - - -
283A ARG* 2.9 42.8 + - - +
425A ALA* 3.8 10.0 - - - +
428A THR* 2.8 22.1 + - - +
429A SER* 4.1 9.2 - - - -
432A MET* 3.5 15.7 - - + +
448A LEU* 2.8 37.1 + - + +
451A LYS* 1.3 105.7 + - + +
453A TRP* 1.3 70.7 + - + +
456A PHE* 3.5 9.2 - - - +
458A HIS 5.3 0.7 + - - -
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Residues in contact with TRP 453 (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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425A ALA* 3.7 28.0 + - + -
426A GLN* 3.8 22.0 - - + -
429A SER* 3.1 20.8 + - - -
448A LEU 4.2 1.1 - - - -
449A VAL* 3.1 26.6 + - + +
452A GLU* 1.3 90.4 - - + +
454A LEU* 1.3 64.2 + - - +
456A PHE 4.2 0.2 - - - -
457A GLY 3.5 2.3 + - - -
458A HIS* 2.9 84.7 + + + +
460A PHE* 3.9 13.2 - + + -
479A VAL* 4.0 5.4 - - + -
480A PHE* 3.6 28.9 - + - -
483A PHE* 3.5 38.1 - + + -
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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