Contacts of the helix formed by residues 435 - 447 (chain A) in PDB entry 5J3V
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 TYR 435 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395A LEU* 5.4 0.7 - - + -
399A LEU* 3.4 36.6 - - + +
403A LYS* 3.6 28.9 - - - +
431A GLY 3.4 24.7 - - - -
432A MET* 3.0 26.8 + - + +
434A PRO* 1.3 85.9 - - + +
436A LEU* 1.3 63.2 + - - +
437A PRO* 3.6 0.7 - - - -
438A GLU* 3.5 13.3 + - - +
439A LEU* 3.2 31.4 + - + +
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Residues in contact with LEU 436 (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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421A LEU* 5.9 0.7 - - + -
429A MET* 5.0 1.8 - - - -
432A MET* 3.1 20.3 + - + +
433A ILE* 3.3 25.4 - - + +
435A TYR* 1.3 75.4 - - - +
437A PRO* 1.4 62.6 - - + +
438A GLU 3.0 5.6 - - - -
439A LEU* 4.3 8.5 - - + +
440A ILE* 2.9 52.8 + - + +
465A TYR* 3.8 37.9 - - + -
468A TRP* 3.5 47.6 - - + -
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Residues in contact with PRO 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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433A ILE 3.3 13.9 - - - +
434A PRO* 3.4 12.8 - - + +
436A LEU* 1.4 89.7 - - + +
438A GLU* 1.3 54.8 + - - +
441A PRO* 3.3 20.4 - - - +
468A TRP* 4.1 15.0 - - + -
477A TYR* 3.7 23.0 + - + +
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Residues in contact with GLU 438 (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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403A LYS* 4.6 17.1 + - - +
407A PHE* 3.8 25.8 - - + -
434A PRO 6.0 0.2 - - - +
435A TYR* 3.5 12.8 + - - +
436A LEU 3.0 0.8 - - - -
437A PRO* 1.3 81.5 - - - +
439A LEU* 1.3 71.7 + - + +
440A ILE 3.5 0.2 - - - -
441A PRO* 3.4 8.7 - - - +
442A HIS* 3.6 13.3 + - - +
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Residues in contact with LEU 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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402A LEU* 5.4 1.8 - - + -
403A LYS* 5.8 6.7 - - + +
406A LEU* 3.7 26.0 - - + -
407A PHE* 4.1 23.3 - - + -
421A LEU* 3.8 26.2 - - + -
432A MET* 3.7 29.8 - - + -
435A TYR* 3.2 20.4 + - + +
436A LEU* 3.2 10.6 + - + +
438A GLU* 1.3 83.3 - - + +
440A ILE* 1.3 61.1 + - - +
442A HIS* 3.0 8.1 + - + +
443A LEU* 2.9 34.6 + - + +
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Residues in contact with ILE 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A LEU* 2.9 40.7 + - + +
439A LEU* 1.3 77.5 - - + +
441A PRO* 1.4 65.0 - - + +
443A LEU* 3.4 10.4 + - + +
444A ILE* 3.2 35.4 + - + +
462A LEU* 4.2 17.8 - - + +
465A TYR* 4.1 21.5 - - + -
468A TRP* 3.7 15.5 - - + -
469A VAL* 4.3 17.0 - - + -
477A TYR* 3.5 30.1 - - + -
481A LEU* 6.0 0.7 - - + -
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Residues in contact with PRO 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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437A PRO 3.3 27.6 - - - +
438A GLU* 3.4 10.1 - - - +
440A ILE* 1.4 94.3 - - + +
442A HIS* 1.3 58.6 + - - +
444A ILE* 3.6 13.1 + - + +
445A GLN* 3.4 26.2 + - - +
476A THR 5.6 2.0 - - - +
477A TYR* 4.0 15.9 - - + -
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Residues in contact with HIS 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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406A LEU* 3.5 26.9 + - + +
407A PHE* 3.4 35.4 - + + -
414A LYS* 4.2 8.0 + - - -
418A ILE* 6.5 0.4 - - + -
438A GLU 3.6 12.0 + - - +
439A LEU* 3.0 14.0 + - + +
441A PRO* 1.3 79.9 - - - +
443A LEU* 1.3 71.5 + - + +
445A GLN* 3.1 14.5 + - + +
446A CYS* 3.1 41.8 + - - -
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Residues in contact with LEU 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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406A LEU* 5.2 3.8 - - + -
418A ILE* 4.2 27.4 - - + -
421A LEU* 3.7 32.1 - - + -
439A LEU* 2.9 23.7 + - + +
440A ILE* 3.8 8.3 - - + +
442A HIS* 1.3 82.8 - - - +
444A ILE* 1.3 61.0 + - - +
446A CYS* 2.9 20.8 + - - -
447A LEU* 3.1 2.3 + - - +
458A THR* 3.1 24.0 - - + +
461A THR* 4.1 12.1 - - + -
462A LEU* 3.6 37.7 - - + +
465A TYR* 5.2 2.2 - - + -
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Residues in contact with ILE 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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440A ILE* 3.2 26.4 + - + +
441A PRO* 3.7 13.0 - - + +
442A HIS 3.3 0.2 - - - -
443A LEU* 1.3 76.0 - - - +
445A GLN* 1.3 67.7 + - - +
447A LEU* 3.4 24.2 - - + +
448A SER* 4.3 3.6 + - - -
462A LEU* 4.2 10.8 - - + -
476A THR 5.3 1.1 - - - +
477A TYR* 3.9 9.2 - - + +
480A PRO* 4.1 19.3 - - + +
481A LEU* 3.8 33.4 - - + +
484A GLU* 3.6 33.3 - - + +
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Residues in contact with GLN 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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441A PRO 3.4 15.6 + - - +
442A HIS* 3.1 15.0 + - + +
443A LEU 3.1 0.4 - - - -
444A ILE* 1.3 83.9 + - - +
446A CYS* 1.3 56.6 + - - +
447A LEU 3.1 4.9 - - - -
448A SER* 3.0 30.1 + - - -
449A ASP* 3.9 2.4 + - - -
484A GLU* 6.3 0.8 - - - +
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Residues in contact with CYS 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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414A LYS* 3.9 21.1 - - - +
418A ILE* 4.3 13.0 - - + -
442A HIS* 3.1 43.7 + - - -
443A LEU* 2.9 15.5 + - - +
445A GLN* 1.3 73.5 - - - +
447A LEU* 1.3 59.7 + - - +
448A SER 3.0 5.9 + - - -
449A ASP* 3.3 22.5 + - - +
454A VAL* 4.3 3.2 - - + +
455A ARG* 3.8 5.7 - - - +
458A THR* 3.7 25.8 + - + +
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Residues in contact with LEU 447 (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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443A LEU 3.1 12.7 + - - +
444A ILE* 3.4 14.4 - - - +
445A GLN 3.1 0.6 - - - -
446A CYS* 1.3 78.4 - - - +
448A SER* 1.3 56.6 + - - +
449A ASP 3.4 1.3 - - - -
455A ARG* 3.2 11.9 - - - +
458A THR* 3.7 18.8 - - + -
459A CYS* 3.6 37.5 - - - +
462A LEU* 3.7 18.6 - - + -
481A LEU* 4.3 5.8 - - + -
484A GLU* 3.8 36.3 - - + +
485A LEU* 4.3 10.5 - - + +
488A ARG* 3.1 35.0 + - + +
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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