Contacts of the helix formed by residues 433 - 446 (chain F) in PDB entry 6CP3
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 ARG 433 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135F GLU* 2.9 44.9 + - - +
136F THR 6.0 0.4 - - - -
137F GLY* 4.9 6.3 - - - +
142F ASP* 5.7 0.4 - - - -
431F LEU* 3.7 20.7 + - - +
432F VAL* 1.3 77.8 - - - +
434F LEU* 1.3 58.5 + - - +
435F LYS* 3.5 4.9 - - + +
436F ASP* 4.0 8.4 + - + +
437F THR* 2.6 31.1 + - - -
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Residues in contact with LEU 434 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F ILE* 5.2 13.0 - - + -
135F GLU* 2.6 42.6 + - + +
142F ASP* 4.3 34.3 - - + +
146F PRO* 6.2 2.2 - - + -
367F HIS* 4.0 12.8 - - + +
433F ARG* 1.3 72.2 - - - +
435F LYS* 1.3 76.3 + - + +
437F THR* 3.0 9.6 + - - -
438F VAL* 2.9 45.7 + - + +
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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
----------------------------------------------------------
135F GLU* 5.0 10.3 + - - +
433F ARG* 3.5 3.2 - - + +
434F LEU* 1.3 86.6 - - + +
436F ASP* 1.3 57.8 + - - +
438F VAL* 3.3 9.8 + - - +
439F ALA* 3.0 29.7 + - - +
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Residues in contact with ASP 436 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432F VAL* 3.8 11.4 - - + +
433F ARG* 4.0 13.2 + - + +
434F LEU 3.3 0.4 - - - -
435F LYS* 1.3 78.4 - - - +
437F THR* 1.3 53.5 + - - +
439F ALA* 3.8 5.9 - - - +
440F SER* 2.3 48.2 + - - -
462F GLY* 3.6 20.3 - - - -
463F ILE* 4.3 6.3 + - - +
464F GLU* 4.4 17.8 - - - +
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Residues in contact with THR 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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138F ILE 5.5 0.3 + - - -
139F LYS* 4.3 32.9 - - + +
142F ASP* 5.8 4.3 - - - +
143F LEU* 4.6 8.5 - - + +
413F PHE* 5.9 0.2 - - + -
432F VAL* 3.3 15.7 + - + +
433F ARG 2.6 22.3 + - - -
434F LEU* 3.0 10.4 + - - -
436F ASP* 1.3 78.0 - - - +
438F VAL* 1.3 60.7 + - - +
440F SER* 3.5 5.3 - - - -
441F PHE* 2.9 62.0 + - + -
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Residues in contact with VAL 438 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142F ASP 5.4 0.4 - - - +
143F LEU* 5.0 10.5 - - + -
366F GLU* 4.5 22.9 - - + +
367F HIS* 3.5 48.2 - - + +
370F VAL* 4.3 8.8 - - + +
434F LEU* 2.9 24.1 + - + +
435F LYS* 3.3 8.5 + - - +
437F THR* 1.3 77.7 - - - +
439F ALA* 1.3 58.1 + - - +
441F PHE* 3.5 1.7 + - - +
442F LYS* 2.9 27.7 + - - +
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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
----------------------------------------------------------
366F GLU* 5.5 2.2 - - - +
435F LYS 3.0 16.8 + - - +
436F ASP* 4.0 7.0 - - - +
438F VAL* 1.3 77.6 - - - +
440F SER* 1.3 56.9 + - - +
442F LYS* 3.4 9.3 + - - +
443F ALA* 2.9 30.5 + - - +
463F ILE* 5.5 1.3 - - + -
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Residues in contact with SER 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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413F PHE* 4.0 19.1 - - - -
436F ASP* 2.3 34.8 + - - -
437F THR* 3.5 7.7 - - - -
438F VAL 3.2 0.2 - - - -
439F ALA* 1.3 76.6 - - - +
441F PHE* 1.3 58.2 + - - +
443F ALA* 3.2 4.4 + - - +
444F VAL* 3.0 34.0 + - - +
462F GLY* 4.4 0.6 - - - -
463F ILE* 3.3 38.2 + - - +
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Residues in contact with PHE 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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139F LYS* 4.3 7.6 - - + -
143F LEU* 3.6 30.1 - - + -
370F VAL* 3.7 20.0 - - + -
374F VAL* 3.9 12.8 - - + -
410F ILE* 3.6 28.5 - - + -
413F PHE* 3.5 36.8 - + - -
414F LEU* 3.6 23.6 - - + -
437F THR* 2.9 45.8 + - + +
440F SER* 1.3 75.7 - - - +
442F LYS* 1.3 56.9 + - - +
444F VAL* 3.4 4.8 + - + +
445F LEU* 2.9 35.9 + - - +
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Residues in contact with LYS 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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366F GLU* 3.3 39.2 + - + +
370F VAL* 4.0 18.6 - - + +
373F LYS* 5.2 10.3 - - - +
438F VAL 2.9 18.2 + - - +
439F ALA* 3.6 8.1 - - - +
441F PHE* 1.3 75.6 - - - +
443F ALA* 1.3 57.7 + - - +
445F LEU* 3.5 4.8 + - - +
446F GLU* 3.0 59.8 + - + +
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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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439F ALA 2.9 17.7 + - - +
440F SER* 3.2 7.4 + - - +
442F LYS* 1.3 77.7 - - - +
444F VAL* 1.3 61.9 + - - +
446F GLU* 3.4 7.1 + - - -
447F GLY 3.4 0.2 + - - -
448F LYS* 3.4 44.8 + - + +
449F TYR* 3.6 26.6 - - + +
463F ILE* 5.0 3.4 - - + -
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Residues in contact with VAL 444 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406F ARG* 3.4 21.9 + - + -
409F LYS* 4.9 5.8 - - + -
410F ILE* 4.1 26.2 - - + -
413F PHE* 5.2 9.4 - - + -
440F SER 3.0 18.3 + - - +
441F PHE* 4.1 6.5 - - + +
443F ALA* 1.3 77.0 - - - +
445F LEU* 1.3 62.7 + - - +
447F GLY* 3.4 8.7 + - - -
448F LYS 5.2 0.4 - - - +
449F TYR* 4.3 12.3 - - + +
450F ASP* 4.3 2.7 - - - +
457F PHE* 4.3 26.5 - - + -
463F ILE* 3.9 24.2 - - + -
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Residues in contact with LEU 445 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370F VAL* 3.8 24.7 - - + +
373F LYS* 3.7 55.4 - - + +
374F VAL* 3.8 15.3 - - + -
377F THR* 4.1 11.4 - - - +
406F ARG* 2.4 35.8 + - - +
410F ILE* 4.3 13.7 - - + -
441F PHE 2.9 21.9 + - - +
442F LYS* 3.8 6.3 - - - +
444F VAL* 1.3 77.7 - - - +
446F GLU* 1.3 57.9 + - + +
447F GLY 3.1 0.2 - - - -
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Residues in contact with GLU 446 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373F LYS* 5.6 8.8 + - - +
406F ARG* 4.5 1.3 - - - -
442F LYS* 3.0 52.2 + - + +
443F ALA 3.4 4.5 + - - +
444F VAL 3.4 0.2 - - - -
445F LEU* 1.3 77.0 - - + +
447F GLY* 1.3 60.1 + - - +
448F LYS* 3.5 28.6 + - + +
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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