Contacts of the helix formed by residues 435 - 446 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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399B LEU* 3.5 41.9 - - + +
403B LYS* 5.8 8.7 - - - -
431B GLY 3.4 25.1 - - - -
432B MET* 2.9 13.9 + - + +
434B PRO* 1.3 86.1 - - + +
436B LEU* 1.3 60.1 + - - +
437B PRO 3.4 0.9 - - - -
438B GLU* 3.2 14.7 + - - +
439B LEU* 3.0 45.3 + - + +
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Residues in contact with LEU 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421B LEU* 6.1 0.7 - - + -
429B MET* 4.9 3.4 - - - -
432B MET* 3.0 24.2 + - + +
433B ILE* 3.6 17.3 - - + +
435B TYR* 1.3 73.7 - - - +
437B PRO* 1.4 65.0 - - + +
438B GLU 2.9 6.5 + - - -
439B LEU* 4.2 6.7 - - + +
440B ILE* 2.9 53.1 + - + +
465B TYR* 3.7 37.7 - - + -
468B TRP* 3.4 51.4 - - + -
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Residues in contact with PRO 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B ILE 3.1 15.7 - - - +
434B PRO* 3.4 14.8 - - + +
435B TYR 3.6 0.4 - - - -
436B LEU* 1.4 89.4 - - + +
438B GLU* 1.3 55.6 + - - -
441B PRO* 3.3 18.4 - - - +
468B TRP* 3.9 15.7 - - + -
477B TYR* 3.3 24.4 + - + +
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Residues in contact with GLU 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B PRO 5.3 1.1 + - - +
435B TYR* 3.2 14.9 + - - +
436B LEU 3.0 0.4 - - - -
437B PRO* 1.3 78.4 - - - +
439B LEU* 1.3 70.9 + - + +
441B PRO* 3.5 9.8 - - - +
442B HIS* 3.6 14.6 + - - +
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Residues in contact with LEU 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B LEU* 6.4 0.2 - - + -
402B LEU* 4.7 7.2 - - + -
406B LEU* 3.9 25.4 - - + -
407B PHE* 6.0 2.9 - - + -
421B LEU* 3.8 24.7 - - + -
432B MET* 3.6 30.7 - - + -
435B TYR* 3.0 27.8 + - + +
436B LEU* 4.3 7.2 - - + +
438B GLU* 1.3 84.1 - - + +
440B ILE* 1.3 67.3 + - + +
442B HIS* 3.0 13.6 + - + +
443B LEU* 3.0 26.9 + - + +
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Residues in contact with ILE 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B LEU* 2.9 42.0 + - + +
439B LEU* 1.3 76.3 - - + +
441B PRO* 1.4 63.8 - - + +
442B HIS 3.2 0.5 + - - -
443B LEU* 3.3 15.5 + - + +
444B ILE* 3.2 24.0 + - + +
462B LEU* 4.4 22.0 - - + -
465B TYR* 4.1 24.2 - - + -
468B TRP* 3.7 18.8 - - + -
469B VAL* 4.4 17.5 - - + -
477B TYR* 3.8 20.0 - - + +
481B LEU* 5.7 1.3 - - + -
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Residues in contact with PRO 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436B LEU 3.5 2.5 - - - +
437B PRO 3.3 27.6 - - - +
438B GLU* 3.5 9.6 - - - +
440B ILE* 1.4 95.0 - - + +
442B HIS* 1.3 59.6 + - - +
444B ILE* 3.8 13.6 + - + +
445B GLN* 3.3 27.1 + - - +
477B TYR* 3.6 17.9 - - + -
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Residues in contact with HIS 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406B LEU* 4.3 33.0 + - + +
407B PHE* 3.6 38.7 - + - -
414B LYS* 5.6 2.6 - - + +
418B ILE* 6.3 0.9 - - + -
438B GLU 3.6 13.0 + - - +
439B LEU* 3.0 17.0 + - + +
441B PRO* 1.3 78.5 - - - +
443B LEU* 1.3 69.4 + - + +
445B GLN* 3.4 15.7 + - + +
446B CYS* 3.3 34.6 + - - -
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Residues in contact with LEU 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B LEU* 5.7 1.8 - - + -
418B ILE* 3.8 36.1 - - + -
421B LEU* 3.7 28.9 - - + -
439B LEU 3.0 17.0 + - - +
440B ILE* 3.3 12.1 + - + +
442B HIS* 1.3 79.8 - - + +
444B ILE* 1.3 60.7 + - - +
445B GLN 3.1 2.0 - - - -
446B CYS* 2.9 21.5 + - - -
447B LEU* 3.4 2.1 + - - +
458B THR* 3.1 27.3 - - + +
461B THR* 3.9 16.6 - - + -
462B LEU* 3.6 31.0 - - + +
465B TYR* 5.3 1.3 - - + -
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Residues in contact with ILE 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440B ILE* 3.2 23.3 + - + +
441B PRO* 4.0 13.5 - - + +
442B HIS 3.4 0.4 - - - -
443B LEU* 1.3 76.2 - - - +
445B GLN* 1.3 70.0 + - - +
447B LEU* 3.3 26.1 - - + +
448B SER 4.5 0.3 + - - -
462B LEU* 4.4 2.9 - - + -
476B THR 5.4 1.1 - - - +
477B TYR* 4.2 12.8 - - + +
480B PRO* 4.1 20.6 - - + +
481B LEU* 4.0 36.3 - - + +
484B GLU* 3.8 34.6 - - + +
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Residues in contact with GLN 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441B PRO* 3.3 22.1 + - - +
442B HIS* 3.7 11.7 - - + +
443B LEU 3.1 0.8 - - - -
444B ILE* 1.3 84.1 - - - +
446B CYS* 1.3 60.6 + - - +
447B LEU 3.1 6.1 + - - -
448B SER* 3.4 18.8 + - - -
449B ASP* 4.2 2.6 + - - -
484B GLU* 5.0 5.6 - - - +
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Residues in contact with CYS 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B LYS* 5.1 13.5 - - - +
418B ILE* 4.4 17.3 - - + -
442B HIS* 3.3 38.6 - - - -
443B LEU* 2.9 15.5 + - - +
445B GLN* 1.3 74.5 - - - +
447B LEU* 1.3 56.9 + - - +
448B SER 3.1 6.0 + - - -
449B ASP* 3.4 21.2 + - - +
454B VAL* 4.2 4.5 - - + +
455B ARG* 4.1 6.4 - - - -
458B THR* 3.8 24.4 + - + +
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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