Contacts of the helix formed by residues 433 - 445 (chain F) in PDB entry 3VBB
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 433 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204F GLU* 3.2 33.7 + - - +
207F LEU* 4.6 5.6 - - + -
208F ILE* 3.9 24.5 - - + -
322F GLU* 3.1 41.3 + - + +
323F LYS* 5.1 0.4 - - - -
324F ILE* 5.2 3.4 - - + -
431F CYS* 4.4 18.2 - - - +
432F ALA* 1.3 70.8 - - - +
434F THR* 1.3 68.5 + - - +
436F THR* 3.4 1.1 + - - -
437F ILE* 2.9 29.8 + - - +
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Residues in contact with THR 434 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194F TYR* 3.5 27.6 - - + +
196F LEU* 5.3 2.9 - - + -
204F GLU* 4.7 7.0 - - - +
315F ILE* 3.2 36.9 + - + +
316F PHE 4.2 6.4 + - - -
318F VAL* 4.3 3.4 - - + +
321F PHE* 3.9 23.7 - - + +
322F GLU* 4.9 0.4 + - - +
432F ALA* 4.5 1.9 + - - +
433F THR* 1.3 91.2 + - - +
435F ARG* 1.3 71.4 + - - +
437F ILE* 3.2 5.4 + - - +
438F CYS* 3.0 27.1 + - - -
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Residues in contact with ARG 435 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302F ARG* 4.3 19.4 - - - +
315F ILE 4.8 0.2 + - - -
316F PHE* 2.8 73.5 + - + +
317F ARG* 3.7 22.0 - - - +
383F PHE* 4.0 4.3 - - - -
391F GLU* 3.4 29.9 + - - +
392F LEU* 3.9 14.1 - - + +
432F ALA* 2.9 28.0 + - + +
434F THR* 1.3 80.7 + - - +
436F THR* 1.3 62.9 + - - +
438F CYS* 3.1 7.4 + - - +
439F ALA* 3.1 19.9 + - - +
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Residues in contact with THR 436 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207F LEU* 3.4 33.9 - - + -
352F TYR* 3.1 35.8 + - + -
355F LEU* 4.8 2.2 - - + -
357F ILE* 5.8 0.7 - - + -
392F LEU* 4.2 7.2 - - + +
431F CYS* 3.3 15.6 - - - -
432F ALA 3.0 14.5 + - - -
433F THR 3.7 3.4 - - - -
435F ARG* 1.3 72.6 - - - +
437F ILE* 1.3 55.9 + - - +
439F ALA* 2.8 9.7 + - + +
440F ILE* 2.7 42.0 + - + +
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Residues in contact with ILE 437 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196F LEU* 5.0 4.9 - - + -
200F LEU* 4.0 17.7 - - + +
203F LEU* 4.0 22.4 - - + -
204F GLU* 3.3 46.7 - - + +
207F LEU* 3.5 16.4 - - + -
315F ILE* 4.4 14.4 - - + -
433F THR 2.9 20.1 + - - +
434F THR* 3.6 7.2 - - - +
436F THR* 1.3 76.3 - - - +
438F CYS* 1.3 58.1 + - - +
440F ILE* 3.4 7.7 + - - +
441F LEU* 2.9 39.4 + - + +
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Residues in contact with CYS 438 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F HIS* 3.5 34.9 - - + +
174F VAL* 5.0 3.1 - - - -
315F ILE* 3.5 34.1 - - - -
316F PHE* 4.3 12.3 - - + -
383F PHE* 3.6 13.2 - - + -
434F THR 3.0 12.6 + - - -
435F ARG 3.3 9.2 - - - +
437F ILE* 1.3 77.3 - - - +
439F ALA* 1.3 62.1 + - - +
441F LEU* 3.2 5.9 + - - +
442F GLU* 3.0 27.9 + - - +
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Residues in contact with ALA 439 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357F ILE* 4.5 9.2 - - + -
381F ALA* 4.3 6.7 - - + -
383F PHE* 3.3 32.6 - - + -
392F LEU* 4.2 19.3 - - + -
435F ARG 3.1 7.8 + - - +
436F THR* 2.8 11.1 + - + +
438F CYS* 1.3 71.8 - - - +
440F ILE* 1.3 64.8 + - - +
442F GLU* 3.4 0.7 + - - -
443F ASN* 3.0 36.1 + - - +
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Residues in contact with ILE 440 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203F LEU* 4.7 15.7 - - + -
207F LEU* 4.1 11.4 - - + -
355F LEU* 4.7 5.4 - - + -
357F ILE* 4.2 18.8 - - + +
436F THR* 2.7 37.5 + - + +
437F ILE* 3.6 9.9 - - - +
439F ALA* 1.3 72.5 - - - +
441F LEU* 1.3 58.7 + - + +
443F ASN* 4.7 0.7 - - - -
444F TYR* 2.9 37.9 + - + +
450F ILE* 5.2 3.1 - - + -
453F PRO* 3.8 29.2 - - + -
456F LEU* 3.6 28.5 - - + -
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Residues in contact with LEU 441 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F HIS* 4.8 2.5 - - + +
173F LEU* 4.0 24.1 - - + +
174F VAL* 3.9 30.7 - - + +
177F VAL* 5.4 1.3 - - + -
200F LEU* 4.1 28.9 - - + -
203F LEU* 4.2 12.8 - - + -
437F ILE* 2.9 31.9 + - + +
438F CYS* 3.2 6.9 + - - +
440F ILE* 1.3 71.8 - - + +
442F GLU* 1.3 67.0 + - - +
445F GLN* 3.3 25.8 + - - +
450F ILE* 3.5 38.4 - - + +
468F ILE* 5.4 2.2 - - + -
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Residues in contact with GLU 442 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166F LYS* 4.1 2.1 - - - +
168F TYR 4.1 3.1 - - - +
169F SER* 3.7 0.4 - - - -
170F HIS* 3.0 38.2 + - + +
173F LEU* 4.2 1.1 - - + -
383F PHE* 3.2 21.0 - - + +
384F PRO* 3.8 20.6 - - + +
385F GLY* 2.8 13.4 + - - +
386F SER* 2.5 49.5 + - - -
438F CYS 3.0 18.3 + - - +
439F ALA 4.1 1.8 - - - +
441F LEU* 1.3 76.8 - - - +
443F ASN* 1.3 61.3 + - - +
445F GLN* 3.4 25.3 + - - +
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Residues in contact with ASN 443 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F VAL* 5.6 1.0 - - - +
166F LYS* 3.3 23.6 + - - -
356F GLY 5.0 1.8 - - - +
357F ILE* 4.4 8.1 - - + +
358F PRO* 3.6 29.9 - - + +
382F TRP 3.1 21.6 + - - -
384F PRO* 2.8 27.7 - - - +
439F ALA* 3.0 30.9 + - - +
440F ILE* 4.7 0.4 - - - -
442F GLU* 1.3 79.8 - - - +
444F TYR* 1.3 77.7 + - + +
445F GLN 3.4 0.9 + - - +
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Residues in contact with TYR 444 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354F SER 5.2 0.5 + - - -
355F LEU 2.7 33.9 + - - -
356F GLY* 3.8 16.1 - - - -
357F ILE* 5.1 3.6 - - + -
440F ILE* 2.9 22.8 + - + +
441F LEU 4.1 1.1 - - - -
443F ASN* 1.3 87.1 - - + +
445F GLN* 1.3 65.5 + - - +
446F THR* 3.8 0.4 - - - +
450F ILE* 4.2 6.5 - - + -
451F THR* 2.9 69.3 + - + +
452F VAL 4.5 1.1 - - - -
453F PRO* 3.6 35.3 - - + +
454F GLU 4.9 2.6 + - - -
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Residues in contact with GLN 445 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166F LYS* 3.8 34.9 - - + +
167F LYS* 3.6 6.2 + - - +
168F TYR* 2.8 65.4 + - - +
173F LEU* 3.6 20.7 - - + +
385F GLY* 4.6 0.2 - - - -
441F LEU 3.3 12.1 + - - +
442F GLU* 3.4 22.9 + - - +
443F ASN 3.4 0.6 - - - +
444F TYR* 1.3 79.5 - - - +
446F THR* 1.3 68.2 + - - +
449F GLY 3.6 7.0 - - - +
450F ILE* 4.0 2.0 - - - -
470F PHE* 4.8 0.2 - - + -
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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