Contacts of the helix formed by residues 433 - 447 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135E GLU* 2.8 32.5 + - - +
142E ASP* 5.8 0.9 - - - -
177E ALA* 3.6 32.5 + - - +
178E HIS* 6.1 1.0 - - - -
431E LEU* 3.7 15.8 + - - +
432E VAL* 1.3 77.5 - - - +
434E LEU* 1.3 58.0 + - - +
435E LYS* 3.5 8.3 - - + +
436E ASP* 3.7 12.6 + - + +
437E THR* 2.3 34.1 + - - -
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Residues in contact with LEU 434 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E ILE* 4.9 16.4 - - + -
135E GLU* 3.5 41.0 + - + +
142E ASP* 3.3 43.0 + - + +
367E HIS* 4.3 9.9 - - + +
433E ARG* 1.3 74.5 - - - +
435E LYS* 1.3 75.2 + - - +
437E THR* 2.9 21.4 + - + -
438E VAL* 2.9 36.2 + - + +
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Residues in contact with LYS 435 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E GLU* 5.2 4.9 + - - +
363E VAL 5.7 2.6 + - - -
366E GLU* 5.8 1.4 + - - -
367E HIS* 6.2 2.0 - - - +
433E ARG* 3.5 4.5 - - + +
434E LEU* 1.3 96.4 - - + +
436E ASP* 1.3 60.1 + - - +
438E VAL* 4.5 14.1 - - - +
439E ALA* 3.7 18.9 + - - +
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Residues in contact with ASP 436 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432E VAL* 3.5 19.8 - - + +
433E ARG* 3.7 18.6 + - + +
434E LEU 3.2 0.4 - - - -
435E LYS* 1.3 78.3 - - - +
437E THR* 1.3 56.7 + - - +
438E VAL 3.5 0.2 - - - -
439E ALA* 3.5 2.7 + - - +
440E SER* 2.5 49.5 + - - -
462E GLY* 3.5 16.0 - - - -
463E ILE* 4.2 12.8 + - - +
464E GLU* 4.8 11.8 - - - +
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Residues in contact with THR 437 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E LYS* 4.1 28.2 - - + +
142E ASP* 5.3 3.2 - - + +
143E LEU* 4.4 9.6 - - + +
432E VAL* 3.2 13.4 + - - +
433E ARG 2.3 27.3 + - - -
434E LEU* 2.9 15.0 + - + +
436E ASP* 1.3 77.2 - - - +
438E VAL* 1.3 66.1 + - - +
440E SER* 3.3 2.8 + - - -
441E PHE* 3.0 56.1 + - + -
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Residues in contact with VAL 438 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E LEU* 5.1 6.3 - - + -
366E GLU* 4.3 23.6 - - + +
367E HIS* 3.5 50.3 - - + +
370E VAL* 4.3 9.9 - - + +
434E LEU* 2.9 26.8 + - + +
435E LYS* 4.9 14.4 - - - +
437E THR* 1.3 75.5 - - - +
439E ALA* 1.3 57.9 + - - +
441E PHE* 3.6 3.6 + - - +
442E LYS* 2.9 30.5 + - - +
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Residues in contact with ALA 439 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366E GLU* 5.3 3.1 - - - +
435E LYS 3.7 18.8 + - - +
436E ASP* 3.5 3.5 + - - +
437E THR 3.3 0.4 - - - -
438E VAL* 1.3 78.6 - - - +
440E SER* 1.3 58.0 + - - +
442E LYS* 3.5 10.2 - - + +
443E ALA* 2.9 31.0 + - - +
463E ILE* 4.9 2.4 - - + +
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Residues in contact with SER 440 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413E PHE* 4.0 20.2 - - - -
436E ASP* 2.5 35.5 + - - -
437E THR* 3.7 5.2 - - - -
439E ALA* 1.3 75.2 - - - +
441E PHE* 1.3 64.3 + - - +
443E ALA* 3.3 3.6 + - - +
444E VAL* 3.0 29.3 + - - +
462E GLY 5.1 0.2 - - - -
463E ILE* 3.4 37.2 + - - +
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Residues in contact with PHE 441 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E LYS* 4.5 12.3 - - + -
143E LEU* 3.6 31.0 - - + -
370E VAL* 3.8 20.2 - - + -
374E VAL* 4.4 10.5 - - + -
410E ILE* 4.3 17.7 - - + +
413E PHE* 3.5 39.7 - + - -
414E LEU* 3.6 30.3 - - + -
437E THR* 3.0 47.7 + - + +
440E SER* 1.3 76.6 - - - +
442E LYS* 1.3 57.1 + - - +
444E VAL* 3.4 5.4 + - + +
445E LEU* 2.9 33.1 + - - +
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Residues in contact with LYS 442 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366E GLU* 2.6 43.7 + - + +
370E VAL* 3.8 19.7 - - + +
438E VAL 2.9 18.8 + - - +
439E ALA* 3.5 9.0 - - + +
441E PHE* 1.3 77.4 - - - +
443E ALA* 1.3 57.0 + - - +
445E LEU* 3.2 5.9 + - + +
446E GLU* 2.9 53.1 + - + +
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Residues in contact with ALA 443 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439E ALA 2.9 17.2 + - - +
442E LYS* 1.3 76.7 - - - +
444E VAL* 1.3 62.4 + - - +
446E GLU* 3.4 13.4 + - - +
447E GLY 3.3 15.9 + - - -
448E LYS* 3.5 18.4 + - + +
449E TYR* 4.2 12.4 - - + -
463E ILE* 3.8 24.7 - - + -
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Residues in contact with VAL 444 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406E ARG* 3.0 24.1 + - - +
409E LYS* 4.5 24.7 - - + +
410E ILE* 4.2 25.3 - - + +
413E PHE* 5.1 17.9 - - + -
440E SER 3.0 18.1 + - - +
441E PHE* 3.9 6.7 - - + +
443E ALA* 1.3 75.3 - - - +
445E LEU* 1.3 58.8 + - - +
446E GLU 3.4 0.3 + - - -
447E GLY* 3.6 4.5 + - - -
448E LYS 5.4 0.2 - - - +
449E TYR* 5.1 20.4 - - + +
450E ASP* 4.6 3.4 - - - +
457E PHE* 5.1 11.4 - - + -
463E ILE* 5.1 6.1 - - + -
466E VAL* 6.4 1.3 - - + -
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Residues in contact with LEU 445 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370E VAL* 3.4 45.8 - - + +
373E LYS* 3.7 20.0 - - + -
374E VAL* 3.7 13.9 - - + -
377E THR* 4.0 16.8 - - + +
406E ARG* 2.7 21.3 + - + +
410E ILE* 3.8 26.5 - - + -
441E PHE* 2.9 16.9 + - + +
442E LYS* 3.2 5.1 + - - +
444E VAL* 1.3 75.7 - - - +
446E GLU* 1.3 59.7 + - - +
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Residues in contact with GLU 446 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406E ARG* 2.6 21.6 + - - -
442E LYS* 2.9 42.8 + - + +
443E ALA* 3.7 10.0 - - - +
444E VAL 3.2 0.4 - - - -
445E LEU* 1.3 79.3 - - + +
447E GLY* 1.3 53.8 + - - +
448E LYS* 3.5 35.0 + - + +
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Residues in contact with GLY 447 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406E ARG* 3.2 10.8 - - - +
443E ALA 3.3 3.6 + - - -
444E VAL 3.6 2.0 + - - -
446E GLU* 1.3 78.5 - - - +
448E LYS* 1.3 60.9 + - - +
449E TYR 3.2 5.6 - - - -
450E ASP* 2.9 40.7 + - - +
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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