Contacts of the helix formed by residues 438 - 451 (chain A) in PDB entry 5E6C
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 CYS 438 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421A CYS* 3.5 7.5 - - + +
424A CYS* 3.7 4.3 - - - -
426A ASP* 4.1 8.1 - - + +
427A GLU 3.4 24.9 - - - +
429A SER* 4.0 4.9 - - - +
437A THR* 1.3 77.9 - - - +
439A GLY* 1.3 67.0 + - - +
440A SER* 2.9 28.0 + - - +
441A CYS 3.3 4.7 + - - -
442A LYS* 3.0 23.8 + - - +
470A ARG* 4.1 3.6 - - - -
601A ZN 2.3 36.8 - - - -
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Residues in contact with GLY 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A SER* 3.6 15.5 + - - -
438A CYS* 1.3 74.2 - - - +
440A SER* 1.3 60.3 + - - +
442A LYS* 3.4 12.7 - - - +
443A VAL* 3.2 18.9 + - - +
9D T 3.4 25.2 + - - +
10D T 5.7 5.2 - - - -
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Residues in contact with SER 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ASP* 4.8 0.2 + - - -
438A CYS* 2.9 19.3 - - - +
439A GLY* 1.3 76.0 - - - +
441A CYS* 1.3 56.9 + - - +
443A VAL* 3.5 8.5 - - - +
444A PHE* 2.8 29.8 + - - +
447A ARG* 4.6 0.7 + - - -
470A ARG* 3.1 33.0 + - - -
477A ARG* 3.3 4.7 + - - -
8D A 3.7 30.8 + - - -
9D T 4.0 11.2 + - - +
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Residues in contact with CYS 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A CYS* 3.5 9.9 - - - -
423A VAL* 4.0 16.8 - - + -
424A CYS* 3.6 10.1 - - - -
437A THR* 4.3 6.7 - - + -
438A CYS* 3.3 5.3 + - - +
440A SER* 1.3 78.5 + - - +
442A LYS* 1.3 58.5 + - - +
444A PHE* 3.6 5.2 - - - +
445A PHE* 2.8 32.7 + - - +
477A ARG* 3.2 32.1 - - - +
481A CYS* 4.8 3.9 - - - -
486A MET* 4.2 3.8 - - - +
601A ZN 2.2 35.7 - - - -
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Residues in contact with LYS 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A HIS* 3.5 42.8 - - + +
433A TYR* 3.4 35.8 + - + -
437A THR* 4.2 5.5 + - - -
438A CYS 3.0 13.2 + - - +
439A GLY* 3.4 15.9 - - - +
441A CYS* 1.3 76.7 - - - +
443A VAL* 1.3 62.7 + - + +
445A PHE* 3.2 1.2 + - - +
446A LYS* 3.0 22.2 + - - +
486A MET* 4.5 4.9 - - - -
5C G 3.6 23.5 + - - -
6C A 3.0 41.6 + - - +
7C A 5.3 2.6 - - - +
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Residues in contact with VAL 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A GLY 3.2 14.8 + - - +
440A SER 3.5 5.6 - - - +
442A LYS* 1.3 81.8 - - + +
444A PHE* 1.3 70.1 + - - +
446A LYS* 4.1 11.4 - - + -
447A ARG* 2.8 53.5 + - + +
7C A 5.3 5.8 - - - +
8C A 4.6 9.9 - - - +
8D A 3.8 15.9 - - + +
9D T 3.9 22.2 - - + +
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Residues in contact with PHE 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A SER 2.8 19.5 + - - +
441A CYS 3.6 3.6 - - - +
443A VAL* 1.3 79.7 - - - +
445A PHE* 1.3 61.7 + - - +
447A ARG* 3.6 13.6 - - + +
448A ALA* 2.8 27.7 + - + +
455A TYR* 4.2 19.7 - + - -
474A PRO* 3.5 30.3 - - + -
477A ARG* 3.6 46.9 - - + +
478A TYR* 3.6 35.4 - + + -
481A CYS* 4.2 9.2 - - - -
7D A 3.9 29.6 - - - -
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Residues in contact with PHE 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433A TYR* 3.7 19.5 - + - -
441A CYS 2.8 17.8 + - - +
442A LYS 3.6 2.0 - - - +
444A PHE* 1.3 78.5 - - - +
446A LYS* 1.3 66.4 + - - +
448A ALA* 3.1 3.1 + - - -
449A VAL* 2.9 52.6 + - + +
478A TYR* 3.7 17.5 - + - -
481A CYS* 3.6 26.2 - - + -
482A LEU* 3.9 15.0 - - + -
486A MET* 3.5 43.3 - - + -
487A ASN* 3.9 16.4 - - - -
488A LEU* 4.2 12.6 - - + -
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Residues in contact with LYS 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A TYR* 3.6 16.8 - - - +
442A LYS* 3.0 13.6 + - - +
443A VAL* 3.8 13.9 - - + +
445A PHE* 1.3 76.5 - - - +
447A ARG* 1.3 65.3 + - + +
449A VAL* 3.4 6.4 - - - +
450A GLU* 3.2 43.1 + - + +
488A LEU* 3.6 24.1 - - + +
6C A 3.0 52.0 + - + +
7C A 4.9 11.9 - - - -
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Residues in contact with ARG 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440A SER 4.6 1.0 + - - -
443A VAL* 2.8 46.0 + - + +
444A PHE* 3.6 27.1 - - + +
446A LYS* 1.3 74.1 - - + +
448A ALA* 1.3 63.5 + - - +
450A GLU* 4.1 1.6 - - - +
451A GLY* 3.2 20.8 + - - -
455A TYR* 5.3 1.1 - - - +
6D G 4.9 5.4 - - - -
7D A 3.5 64.8 + - - +
8D A 3.1 30.2 + - - +
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Residues in contact with ALA 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444A PHE* 2.8 22.4 + - + +
445A PHE* 3.1 2.9 + - - +
447A ARG* 1.3 79.0 - - - +
449A VAL* 1.3 59.9 + - - +
451A GLY* 3.6 11.3 - - - +
453A HIS* 3.5 22.8 + - + +
455A TYR* 3.7 27.8 + - + +
478A TYR* 3.6 30.3 - - + -
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Residues in contact with VAL 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A PHE* 2.9 47.9 + - + +
446A LYS* 3.4 7.0 - - - +
448A ALA* 1.3 76.0 - - - +
450A GLU* 1.3 68.1 + - + +
451A GLY 3.4 4.0 - - - +
453A HIS* 5.9 0.4 - - - -
478A TYR* 3.5 24.5 - - + +
482A LEU* 5.4 0.4 - - + -
488A LEU* 3.9 37.7 - - + -
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Residues in contact with GLU 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A LYS* 3.2 43.5 + - + +
447A ARG* 4.6 1.8 - - - +
449A VAL* 1.3 82.0 - - - +
451A GLY* 1.3 60.0 + - - +
488A LEU* 3.8 18.3 - - + +
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Residues in contact with GLY 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447A ARG 3.2 15.5 + - - -
448A ALA 3.6 9.7 - - - +
449A VAL 4.0 4.3 - - - +
450A GLU* 1.3 81.8 - - - +
452A GLN* 1.3 68.1 + - - -
453A HIS* 4.5 2.3 + - - -
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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