Contacts of the helix formed by residues 432 - 446 (chain B) in PDB entry 4OIV
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 GLN 432 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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430B ASN* 3.0 14.7 - - - +
431B PRO* 1.3 92.1 + - + +
433B HIS* 1.3 63.3 + - - +
434B PHE 3.4 1.5 + - - -
435B ALA* 3.5 26.2 + - - +
436B GLU* 3.0 39.4 + - + +
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Residues in contact with HIS 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B LEU* 3.3 31.1 - - + +
380B LYS 5.3 0.2 + - - -
385B GLU* 3.0 30.2 + - - -
423B CYS* 3.5 35.4 - - + -
427B GLN* 3.4 40.3 + - + +
430B ASN* 3.2 24.7 + - - +
431B PRO 3.4 0.8 - - - -
432B GLN* 1.3 75.2 - - - +
434B PHE* 1.3 64.2 + - - +
436B GLU* 3.1 11.6 + - - +
437B LEU* 3.0 38.8 + - + +
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Residues in contact with PHE 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B LEU* 3.7 39.7 - - + -
419B LEU* 3.9 27.4 - - + -
420B GLN* 3.6 51.6 - - + -
423B CYS* 3.9 20.0 - - + +
431B PRO 4.5 5.3 + - - +
432B GLN 3.4 0.8 - - - -
433B HIS* 1.3 76.7 - - - +
435B ALA* 1.3 66.9 + - + +
437B LEU* 3.1 13.7 + - - +
438B LEU* 3.1 42.5 + - + +
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Residues in contact with ALA 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B PRO 5.3 0.6 + - - -
432B GLN* 3.5 37.3 + - - +
433B HIS 3.4 0.2 - - - -
434B PHE* 1.3 83.8 - - + +
436B GLU* 1.3 59.3 + - + +
438B LEU* 3.4 8.5 + - - +
439B GLY* 2.8 25.8 + - - -
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Residues in contact with GLU 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B LEU* 4.1 27.4 - - + +
430B ASN* 3.3 20.9 + - - +
432B GLN* 3.0 40.3 + - + +
433B HIS* 3.1 7.6 + - - +
435B ALA* 1.3 77.8 - - + +
437B LEU* 1.3 65.5 + - - +
439B GLY* 3.3 3.9 + - - +
440B ARG* 3.3 23.4 + - - +
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Residues in contact with LEU 437 (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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379B LEU* 3.9 18.2 - - + -
381B MET* 4.1 23.8 - - + -
385B GLU* 4.1 22.9 - - + -
389B LEU* 4.1 24.8 - - + +
419B LEU* 4.1 14.8 - - + -
423B CYS* 3.8 25.6 - - - -
433B HIS* 3.0 40.0 + - + +
434B PHE 3.1 5.6 + - - +
436B GLU* 1.3 75.9 - - - +
438B LEU* 1.3 57.0 + - - +
440B ARG* 3.0 27.0 + - - +
441B LEU 3.5 3.8 + - - -
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Residues in contact with LEU 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B LEU* 4.3 17.7 - - + -
392B ILE* 4.6 2.9 - - + -
416B LEU* 3.9 25.1 - - + -
419B LEU* 4.9 1.1 - - + -
434B PHE* 3.1 46.1 + - + +
435B ALA* 3.9 8.7 - - - +
437B LEU* 1.3 74.6 - - - +
439B GLY* 1.3 56.1 + - - +
441B LEU* 3.2 18.5 + - + +
442B THR* 3.0 29.5 + - - +
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Residues in contact with GLY 439 (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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435B ALA 2.8 17.6 + - - -
436B GLU* 3.6 4.7 - - - -
437B LEU 3.2 0.8 - - - -
438B LEU* 1.3 73.3 - - - +
440B ARG* 1.3 67.6 + - - +
442B THR* 3.3 9.9 + - - -
443B GLU* 3.0 27.9 + - - +
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Residues in contact with ARG 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B LEU* 5.9 0.4 - - + -
372B PHE* 3.7 12.4 - - + +
375B SER* 2.8 34.8 + - - -
376B ILE* 3.4 31.2 - - + -
379B LEU* 3.5 31.1 - - + +
381B MET* 5.9 0.9 - - - -
389B LEU* 5.3 4.5 - - + -
436B GLU 3.3 7.8 + - - +
437B LEU* 3.0 12.0 + - + +
439B GLY* 1.3 84.1 + - - +
441B LEU* 1.3 67.8 + - + +
443B GLU* 3.0 47.3 + - - +
444B LEU* 3.0 25.7 + - - +
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Residues in contact with LEU 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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330B GLU* 4.9 1.4 - - - +
334B LEU* 4.2 22.0 - - + -
389B LEU* 3.7 46.4 - - + +
392B ILE* 4.0 22.7 - - + -
393B VAL* 4.0 30.2 - - + +
437B LEU 3.5 1.0 + - - -
438B LEU* 3.2 16.9 + - + +
440B ARG* 1.3 81.7 - - + +
442B THR* 1.3 63.1 + - - +
444B LEU* 3.2 21.9 + - + +
445B ARG* 3.3 19.3 + - - +
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Residues in contact with THR 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B LEU 3.0 14.8 + - - -
439B GLY* 3.6 12.0 - - - +
440B ARG 3.3 0.2 - - - -
441B LEU* 1.3 74.1 - - - +
443B GLU* 1.3 63.4 - - - +
445B ARG* 3.2 21.9 + - - +
446B THR* 3.6 13.3 + - + +
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Residues in contact with GLU 443 (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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372B PHE* 4.1 9.0 - - + -
439B GLY 3.0 14.6 + - - +
440B ARG* 3.0 46.1 + - - +
442B THR* 1.3 75.1 - - - +
444B LEU* 1.3 65.5 + - - +
446B THR* 2.7 35.7 + - - -
447B PHE* 3.5 29.4 - - + -
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Residues in contact with LEU 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B GLU* 4.0 37.8 - - + +
333B PHE* 3.9 29.4 - - + -
334B LEU* 4.4 12.6 - - + -
372B PHE* 3.6 43.3 - - + -
393B VAL* 5.8 0.7 - - + -
440B ARG 3.0 17.4 + - - +
441B LEU* 3.2 18.3 + - + +
443B GLU* 1.3 74.8 - - - +
445B ARG* 1.3 63.2 + - - +
447B PHE* 3.0 33.5 + - + +
449B HIS* 3.6 8.1 - - - -
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Residues in contact with ARG 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B GLU* 3.6 26.2 + - - +
393B VAL* 6.1 0.6 - - - +
396B SER* 3.7 20.2 + - - -
398B ASP* 2.8 45.8 + - - -
399B ARG* 3.8 18.0 - - - +
441B LEU* 3.3 12.1 + - - +
442B THR* 3.2 12.0 + - - +
443B GLU 3.1 0.8 - - - -
444B LEU* 1.3 77.2 - - - +
446B THR* 1.3 61.7 + - + +
447B PHE 3.5 1.6 + - - +
449B HIS* 3.6 10.7 - - - -
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Residues in contact with THR 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B THR* 3.6 18.4 - - + +
443B GLU* 2.7 26.8 + - - +
445B ARG* 1.3 77.8 - - + +
447B PHE* 1.3 70.9 + - - +
448B ASN 3.8 1.0 + - - -
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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