Contacts of the helix formed by residues 438 - 451 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421B CYS* 3.4 10.5 - - + +
424B CYS* 3.6 6.1 - - - -
426B ASP* 4.2 9.4 - - + +
427B GLU 3.5 24.0 - - - +
428B ALA* 4.1 0.9 - - - +
429B SER* 4.0 4.7 - - - +
432B HIS* 3.9 0.9 - - - -
437B THR* 1.3 81.4 + - - +
439B GLY* 1.3 65.3 + - - +
440B SER* 3.6 12.3 - - - -
441B CYS* 3.3 18.2 - - - -
442B LYS* 3.3 18.5 + - - +
470B ARG* 3.8 3.8 - - - -
602B ZN 2.3 34.5 - - - -
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Residues in contact with GLY 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B GLU 5.1 0.4 + - - -
429B SER* 3.9 13.7 + - - -
432B HIS* 5.2 0.2 - - - -
438B CYS* 1.3 73.7 - - - +
440B SER* 1.3 64.0 + - - +
442B LYS* 3.3 10.0 + - - +
443B VAL* 3.3 25.5 + - - +
16C T 4.8 13.7 - - - -
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Residues in contact with SER 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B CYS* 3.6 2.3 - - - -
439B GLY* 1.3 74.7 - - - +
441B CYS* 1.3 57.3 + - - +
443B VAL* 3.4 4.8 + - - +
444B PHE* 2.9 31.2 + - - +
470B ARG* 3.0 34.3 + - - -
477B ARG* 3.0 7.7 + - - -
15C C 3.3 45.6 + - - -
16C T 4.9 6.6 - - - +
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Residues in contact with CYS 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B CYS* 3.7 10.1 - - - -
423B VAL* 3.8 21.3 - - + -
424B CYS* 3.8 5.2 - - - -
437B THR* 4.3 7.0 - - + -
438B CYS* 3.3 6.0 - - - +
439B GLY 3.3 0.8 - - - -
440B SER* 1.3 81.4 + - - +
442B LYS* 1.3 57.3 + - - +
444B PHE* 3.8 4.3 - - - +
445B PHE* 2.9 30.7 + - - +
477B ARG* 3.4 28.7 - - - +
481B CYS* 4.6 4.1 - - - -
486B MET* 4.3 3.9 - - - +
602B ZN 2.3 34.8 - - - -
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Residues in contact with LYS 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B HIS* 3.4 45.3 + - + +
433B TYR* 3.4 47.4 - - + +
437B THR* 4.3 4.2 + - - +
438B CYS 3.3 14.1 + - - +
439B GLY* 3.5 11.7 - - - +
440B SER 3.2 0.6 - - - -
441B CYS* 1.3 73.6 - - - +
443B VAL* 1.3 71.8 + - + +
445B PHE* 3.3 1.6 + - - +
446B LYS* 3.1 18.9 + - - +
486B MET* 4.6 2.0 - - - -
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Residues in contact with VAL 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B GLY 3.3 14.8 + - - +
440B SER* 4.1 4.5 - - - +
442B LYS* 1.3 81.3 - - + +
444B PHE* 1.3 66.6 + - - +
446B LYS* 3.4 7.2 + - + +
447B ARG* 2.9 30.2 + - + +
15C C 5.0 18.8 - - + +
16C T 4.5 16.4 - - + +
1D A 6.1 2.0 - - - +
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Residues in contact with PHE 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B SER 2.9 18.6 + - - +
441B CYS 3.8 2.9 - - - +
443B VAL* 1.3 78.0 - - - +
445B PHE* 1.3 62.2 + - - +
447B ARG* 3.3 10.3 + - - +
448B ALA* 2.9 29.2 + - + +
455B TYR* 4.4 15.0 + + - -
474B PRO* 3.4 44.4 - - + -
477B ARG* 3.5 48.0 - - + +
478B TYR* 3.6 30.3 - + + -
481B CYS* 4.2 9.4 - - - -
14C A 5.6 8.3 - - - -
15C C 5.4 0.9 - - - +
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Residues in contact with PHE 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433B TYR* 3.7 19.7 - + + -
441B CYS 2.9 19.3 + - - +
442B LYS 3.7 2.2 - - - +
444B PHE* 1.3 81.2 - - - +
446B LYS* 1.3 62.6 + - - +
448B ALA* 3.2 3.8 + - - +
449B VAL* 3.0 52.8 + - + +
478B TYR* 3.8 15.9 - + - -
481B CYS* 3.4 33.2 - - + -
482B LEU* 4.0 11.4 - - + -
486B MET* 3.5 44.0 - - + -
487B ASN* 3.9 12.8 - - - -
488B LEU* 4.0 15.5 - - + -
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Residues in contact with LYS 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B TYR* 3.3 28.3 + - + +
442B LYS 3.1 10.8 + - - +
443B VAL* 3.5 11.7 - - + +
445B PHE* 1.3 84.3 - - - +
447B ARG* 1.3 65.6 + - - +
449B VAL* 3.3 1.7 + - - +
450B GLU* 3.0 54.5 + - + +
488B LEU* 4.2 15.9 - - + +
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Residues in contact with ARG 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443B VAL* 2.9 22.4 + - + +
444B PHE* 3.7 9.8 - - - +
446B LYS* 1.3 78.8 - - - +
448B ALA* 1.3 57.6 + - - +
450B GLU* 4.0 3.4 - - - +
451B GLY* 3.1 22.7 + - - -
453B HIS* 3.5 32.8 + - + -
455B TYR* 5.0 7.5 + - - +
13C C 4.3 28.3 + - - +
14C A 3.9 18.4 + - - -
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Residues in contact with ALA 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444B PHE* 2.9 21.7 + - + +
445B PHE* 3.2 6.0 + - - +
447B ARG* 1.3 77.5 - - - +
449B VAL* 1.3 62.0 + - - +
451B GLY 3.3 15.8 + - - +
453B HIS* 3.8 12.4 + - - +
455B TYR* 3.7 30.3 + - + +
478B TYR* 3.9 30.9 + - + -
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Residues in contact with VAL 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B PHE* 3.0 51.9 + - + +
446B LYS 4.0 2.2 - - - +
448B ALA* 1.3 76.3 - - - +
450B GLU* 1.3 61.3 + - - +
451B GLY 3.4 6.2 + - - +
478B TYR* 3.8 18.8 - - + +
482B LEU* 5.8 0.7 - - + -
488B LEU* 3.9 26.7 - - + -
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Residues in contact with GLU 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B LYS* 3.0 49.0 + - + +
447B ARG* 4.3 3.6 - - - +
449B VAL* 1.3 77.6 - - - +
451B GLY* 1.3 60.2 + - - +
488B LEU* 4.3 15.7 - - - +
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Residues in contact with GLY 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B ARG 3.1 17.7 + - - -
448B ALA 3.3 7.6 + - - +
449B VAL 3.2 6.8 - - - +
450B GLU* 1.3 82.3 - - - +
452B GLN* 1.3 58.5 + - - -
453B HIS* 2.9 26.7 + - - -
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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