Contacts of the helix formed by residues 434 - 447 (chain F) in PDB entry 5I4V
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 ASP 434 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386F HIS* 3.7 3.9 + - - -
432F ARG 3.3 3.7 + - - +
433F MET* 1.3 77.6 - - - +
435F LYS* 1.3 58.3 + - - +
436F THR* 2.8 8.4 + - - -
437F GLU* 2.7 38.1 + - - +
438F LEU* 3.1 22.3 + - - +
474F TYR* 2.8 28.8 + - - -
478F LYS* 4.4 2.7 - - - +
479F TYR* 2.7 26.1 + - - +
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Residues in contact with LYS 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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305F LEU* 3.8 18.4 - - + -
308F GLU* 4.1 18.0 + - + +
309F LEU* 4.0 23.3 - - + +
312F GLU 4.1 18.4 + - - -
386F HIS* 4.1 23.0 + - + +
434F ASP* 1.3 73.2 + - - +
436F THR* 1.3 65.7 + - - +
438F LEU* 3.3 11.1 + - + +
439F GLY* 3.0 20.1 + - - -
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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
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301F VAL* 3.9 31.4 - - + +
304F ILE* 4.3 1.1 - - + +
305F LEU* 3.5 35.1 - - - +
434F ASP* 2.8 8.0 + - - -
435F LYS* 1.3 77.8 - - - +
437F GLU* 1.3 64.5 + - - +
439F GLY* 3.2 1.8 + - - -
440F CYS* 3.0 30.0 + - - -
474F TYR* 3.8 38.9 + - + -
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Residues in contact with GLU 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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433F MET* 3.4 12.1 - - + -
434F ASP* 2.7 51.0 + - - +
436F THR* 1.3 71.9 - - - +
438F LEU* 1.3 62.4 + - - +
440F CYS* 3.4 2.1 + - - +
441F LEU* 3.1 29.5 + - - +
471F LEU* 4.4 11.2 - - + +
474F TYR* 3.9 13.7 - - + -
475F CYS* 4.2 2.1 - - - -
479F TYR* 3.4 9.3 - - - -
485F ARG* 2.6 51.2 + - - +
489F LEU* 3.9 24.9 - - + +
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Residues in contact with LEU 438 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308F GLU* 3.3 22.7 - - + +
382F ALA* 3.9 13.9 - - + +
383F SER* 4.6 8.5 - - - +
386F HIS* 3.6 35.2 - - + +
428F MET* 3.8 29.2 - - + -
433F MET* 4.1 7.8 - - - -
434F ASP 3.1 13.4 + - - +
435F LYS* 3.4 12.6 - - + +
437F GLU* 1.3 76.5 - - - +
439F GLY* 1.3 57.7 + - - +
441F LEU* 3.2 9.0 + - + +
442F ARG* 2.8 45.9 + - + +
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Residues in contact with GLY 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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304F ILE* 3.4 21.3 - - - +
308F GLU* 3.7 25.8 - - - +
353F TRP* 4.1 3.0 - - - -
435F LYS 3.0 10.7 + - - -
436F THR 3.2 1.3 + - - -
438F LEU* 1.3 77.4 - - - +
440F CYS* 1.3 57.6 + - - +
442F ARG* 3.2 3.3 + - - +
443F ALA* 2.8 28.9 + - - +
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Residues in contact with CYS 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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301F VAL* 4.1 21.3 - - - -
304F ILE* 4.1 21.8 - - - -
436F THR* 3.0 23.8 + - - +
437F GLU 3.8 4.0 - - - +
439F GLY* 1.3 72.9 - - - +
441F LEU* 1.3 61.2 + - - +
443F ALA* 3.1 3.5 + - - -
444F ILE* 2.9 28.0 + - - +
467F VAL* 3.4 21.9 - - + +
470F SER* 5.6 0.4 - - - -
471F LEU* 3.8 35.9 - - + -
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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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382F ALA* 6.5 0.7 - - + -
428F MET* 5.9 1.3 - - + -
433F MET* 4.0 28.9 - - + -
437F GLU 3.1 18.6 + - - +
438F LEU* 3.5 10.1 - - + +
440F CYS* 1.3 76.4 - - - +
442F ARG* 1.3 62.0 + - + +
444F ILE* 3.3 6.8 + - + +
445F ILE* 3.0 29.7 + - + +
471F LEU* 4.2 13.5 - - + -
489F LEU* 3.9 43.5 - - + +
490F LEU* 4.2 12.3 - - + -
492F ARG* 5.1 4.7 - - + -
493F LEU* 4.3 21.6 - - + +
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Residues in contact with ARG 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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308F GLU* 2.5 39.5 + - - -
311F VAL* 5.5 4.0 - - - +
350F LEU* 3.4 29.5 - - - +
353F TRP* 3.3 39.5 - - + +
379F LEU* 3.2 44.8 + - + +
380F LEU* 5.0 2.6 - - - +
382F ALA* 4.2 17.0 - - + -
383F SER* 3.9 18.3 + - - +
438F LEU* 2.8 37.3 + - + +
439F GLY 3.6 4.7 - - - +
441F LEU* 1.3 77.4 - - + +
443F ALA* 1.3 57.9 + - - +
445F ILE* 3.3 4.2 + - + -
446F LEU* 2.8 26.7 + - - +
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Residues in contact with ALA 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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304F ILE* 4.6 6.5 - - + -
353F TRP* 3.9 4.6 - - - -
357F ILE* 4.4 17.0 - - + -
439F GLY 2.8 16.3 + - - +
440F CYS* 3.1 8.0 + - - +
442F ARG* 1.3 75.0 - - - +
444F ILE* 1.3 59.9 + - - +
446F LEU* 3.4 6.9 - - - +
447F PHE* 2.9 46.1 + - + -
467F VAL* 4.0 18.8 - - + -
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Residues in contact with ILE 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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423E MET* 4.3 2.9 - - - -
440F CYS 2.9 17.8 + - - +
441F LEU* 3.5 12.1 - - + +
443F ALA* 1.3 73.9 - - - +
445F ILE* 1.3 61.2 + - - +
447F PHE 3.5 4.0 + - - -
464F ARG* 2.7 55.1 + - - +
467F VAL* 3.5 23.8 - - + -
468F TYR* 3.9 32.5 - - + +
471F LEU* 4.1 13.9 - - + -
490F LEU* 3.9 20.2 - - + -
493F LEU* 3.8 21.5 - - + -
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Residues in contact with ILE 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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375F GLY* 4.4 10.1 - - - +
378F GLU* 3.9 38.6 - - + +
379F LEU* 4.0 15.5 - - + -
382F ALA* 4.9 5.4 - - + -
441F LEU* 3.0 22.5 + - + +
442F ARG* 3.5 12.8 - - + +
444F ILE* 1.3 74.3 - - - +
446F LEU* 1.3 69.1 - - - +
447F PHE 3.4 0.2 + - - -
448F ASN* 3.5 16.8 + - - +
464F ARG* 4.0 5.7 + - - +
493F LEU* 3.9 19.3 - - + -
496F LEU* 3.4 33.0 - - + -
497F ARG* 5.9 2.4 + - - +
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Residues in contact with LEU 446 (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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353F TRP* 3.8 24.0 - - + -
354F ALA* 4.4 4.7 - - + -
357F ILE* 4.1 22.9 - - + -
360F PHE* 4.0 36.1 - - + -
371F LEU* 3.6 30.7 - - + +
372F LEU* 4.4 13.7 - - + -
375F GLY* 5.7 1.1 - - - -
379F LEU* 4.4 20.0 - - + -
442F ARG 2.8 17.7 + - - +
443F ALA* 3.4 4.5 - - - +
445F ILE* 1.3 79.3 - - - +
447F PHE* 1.3 67.3 + - + +
448F ASN* 2.8 10.2 + - - +
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Residues in contact with PHE 447 (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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299F MET* 4.2 15.9 - - + -
357F ILE* 3.7 31.4 - - + -
358F PRO 3.7 13.2 - - - -
360F PHE* 4.2 24.7 - + + -
363F LEU* 4.3 4.0 - - + -
371F LEU* 4.3 13.2 - - + -
443F ALA* 2.9 30.8 + - + +
444F ILE 3.7 3.4 - - - -
445F ILE 3.3 0.4 - - - -
446F LEU* 1.3 73.9 - - + +
448F ASN* 1.3 54.9 + - - +
449F PRO* 3.3 5.9 - - - +
460F VAL* 3.6 22.1 - - + +
463F LEU* 3.8 33.9 - - + -
464F ARG* 2.8 34.0 + - + +
467F VAL* 4.2 13.7 - - + -
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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