Contacts of the helix formed by residues 443 - 457 (chain D) in PDB entry 5COX
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 ALA 443 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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404D PHE* 3.3 38.1 - - + -
405D LYS* 5.2 9.6 - - - +
441D PRO* 2.7 4.1 + - + +
442D ILE* 1.3 78.2 - - - +
444D VAL* 1.3 54.3 + - - +
445D GLN* 2.7 15.3 + - - +
446D ALA* 3.7 11.3 + - - +
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Residues in contact with VAL 444 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388D HIS* 3.4 40.6 - - + +
391D LEU* 3.5 16.6 - - + -
404D PHE* 3.4 29.4 - - + -
440D VAL* 3.8 7.8 - - - +
441D PRO* 2.9 13.1 + - + +
443D ALA* 1.3 70.9 - - - +
445D GLN* 1.3 61.2 + - - +
446D ALA 3.4 0.9 - - - -
447D VAL* 3.3 32.2 - - + +
448D ALA* 3.5 4.7 + - - +
682D HEM 4.4 15.0 - - + -
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Residues in contact with GLN 445 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D LYS* 3.8 15.1 + - - +
178D LEU* 3.7 24.4 - - + +
179D GLU* 5.3 2.1 - - - +
183D LEU* 3.6 31.4 - - + +
440D VAL* 4.5 4.5 - - - -
441D PRO 3.1 2.6 + - - -
442D ILE* 3.0 34.7 + - - +
443D ALA 2.7 4.0 + - - +
444D VAL* 1.3 74.7 - - - +
446D ALA* 1.3 75.4 + - + +
447D VAL 3.0 2.4 + - - -
448D ALA* 3.4 2.1 + - - -
449D LYS* 3.2 22.1 + - - +
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Residues in contact with ALA 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D LYS* 6.2 1.1 - - - +
443D ALA 3.7 7.8 + - - +
445D GLN* 1.3 85.1 - - + +
447D VAL* 1.3 67.5 + - + +
449D LYS* 3.3 7.5 - - - +
450D ALA* 3.2 20.5 + - - +
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Residues in contact with VAL 447 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386D HIS* 4.9 0.4 - - + -
388D HIS* 3.1 33.0 - - + +
444D VAL* 3.3 29.2 - - + +
445D GLN 3.0 0.2 - - - -
446D ALA* 1.3 76.0 - - + +
448D ALA* 1.3 57.3 + - - +
449D LYS 3.0 3.4 - - - -
450D ALA* 2.7 29.6 + - - +
451D SER* 2.8 17.7 + - - +
682D HEM 3.8 48.2 - - + -
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Residues in contact with ALA 448 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D LEU* 4.1 14.6 - - + -
182D LEU* 4.8 2.5 - - + -
388D HIS* 5.7 1.1 - - - +
440D VAL* 4.0 29.4 - - + -
444D VAL 3.5 1.8 + - - +
445D GLN 3.4 2.8 + - - +
447D VAL* 1.3 79.2 - - - +
449D LYS* 1.3 59.4 + - - +
451D SER* 3.7 3.4 - - - -
452D ILE* 3.1 27.9 + - - +
504D TYR* 3.1 34.0 - - + +
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Residues in contact with LYS 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D SER* 2.9 27.2 + - - +
175D LYS* 3.5 42.8 - - - +
178D LEU* 4.2 20.1 - - + +
445D GLN 3.2 12.2 + - - +
446D ALA* 3.3 14.1 - - - +
447D VAL 2.8 1.8 + - - -
448D ALA* 1.3 69.5 - - - +
450D ALA* 1.3 71.4 + - - +
452D ILE* 2.8 19.2 + - - +
453D ASP* 2.8 39.4 + - - +
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Residues in contact with ALA 450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446D ALA 3.2 9.1 + - - +
447D VAL* 2.7 16.2 + - - +
449D LYS* 1.3 73.8 - - - +
451D SER* 1.3 56.0 + - - +
453D ASP* 2.5 36.6 + - - -
454D GLN* 2.8 21.4 + - + -
682D HEM 4.4 22.0 - - - +
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Residues in contact with SER 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383D THR* 5.4 1.1 + - - -
386D HIS* 3.7 32.1 + - - -
447D VAL* 2.8 18.9 + - - +
448D ALA* 3.6 3.3 - - - -
450D ALA* 1.3 72.0 - - - +
452D ILE* 1.3 62.7 + - - +
454D GLN* 4.6 10.2 - - - +
455D SER* 3.4 25.5 + - - -
504D TYR* 3.5 39.3 + - - +
682D HEM 5.1 3.0 + - - -
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Residues in contact with ILE 452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D SER* 3.7 37.0 - - - +
177D VAL* 4.4 4.7 - - + -
178D LEU* 4.3 6.5 - - + +
182D LEU* 3.5 30.1 - - + -
448D ALA 3.1 12.9 + - - +
449D LYS* 2.8 12.0 + - - +
450D ALA 2.7 3.8 + - - -
451D SER* 1.3 74.1 - - - +
453D ASP* 1.3 59.6 + - - +
455D SER* 3.6 4.0 + - - -
456D ARG* 2.9 46.7 + - - +
495D TYR* 5.6 0.4 - - - +
502D GLU* 3.9 9.6 - - - +
504D TYR* 3.5 17.0 - - + -
505D PRO* 4.0 15.7 - - + -
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Residues in contact with ASP 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D SER* 3.3 24.8 + - - -
449D LYS* 2.8 39.5 + - - +
450D ALA* 2.5 18.4 + - - +
452D ILE* 1.3 69.3 - - - +
454D GLN* 1.3 62.8 + - + +
456D ARG* 2.9 27.9 + - - +
457D GLU* 3.0 15.9 + - - +
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Residues in contact with GLN 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D HIS* 4.7 10.9 + - - -
218D PRO* 4.2 26.6 - - + +
386D HIS* 5.8 3.6 + - - -
450D ALA* 2.8 24.6 + - + +
451D SER* 4.4 8.7 + - - +
453D ASP* 1.3 68.7 - - + +
455D SER* 1.3 56.4 + - - +
456D ARG 2.6 5.3 + - - -
457D GLU* 2.6 47.4 + - + +
458D MET* 2.7 17.4 + - + +
682D HEM 3.2 31.7 + - - +
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Residues in contact with SER 455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383D THR* 3.4 27.2 + - - +
451D SER 3.4 16.6 + - - -
452D ILE* 4.0 3.8 - - - -
454D GLN* 1.3 77.0 - - - +
456D ARG* 1.3 59.4 + - - +
458D MET* 3.9 3.1 - - - +
459D LYS 3.6 1.4 + - - -
460D TYR* 3.1 61.2 + - - +
502D GLU* 5.8 2.5 - - - -
503D LEU* 6.5 0.2 - - - -
504D TYR* 4.8 8.7 + - - +
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Residues in contact with ARG 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D LEU* 3.7 25.6 + - - +
172D PRO* 2.7 30.6 + - - +
173D ASP* 4.9 0.4 - - - +
174D SER* 4.1 16.2 + - - +
177D VAL* 4.6 0.6 - - - +
452D ILE* 2.9 33.3 - - - +
453D ASP* 2.9 22.9 + - - +
454D GLN 2.6 0.4 + - - -
455D SER* 1.3 77.9 - - - +
457D GLU* 1.3 54.5 + - - +
459D LYS* 3.0 23.0 + - - +
460D TYR 4.4 0.2 + - - -
495D TYR* 4.1 6.3 + - - -
502D GLU* 2.6 40.6 + - - +
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Residues in contact with GLU 457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D VAL* 5.8 0.5 - - - +
218D PRO* 4.2 19.5 - - + +
453D ASP* 3.3 10.9 - - - +
454D GLN* 2.6 49.6 + - + +
456D ARG* 1.3 71.5 - - - +
458D MET* 1.3 55.1 + - - +
459D LYS* 2.8 23.2 + - - +
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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