Contacts of the helix formed by residues 443 - 448 (chain B) in PDB entry 6G4O
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 GLU 443 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199B GLU* 3.0 31.2 - - - +
225B GLN* 3.3 28.6 - - + +
226B SER* 3.7 11.9 + - - -
324B ASN* 2.2 50.8 + - - +
421B TYR* 4.9 4.9 - - + +
423B PHE* 3.8 22.0 - - + -
441B GLY 3.1 11.8 + - - -
442B TYR* 1.3 78.1 - - - +
444B ILE* 1.3 68.5 + - + +
445B GLU 3.3 0.9 - - - -
446B PHE* 2.9 20.4 + - - +
447B VAL* 3.4 12.7 + - + +
473B TRP* 6.4 0.2 - - + -
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Residues in contact with ILE 444 (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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84B TRP* 4.0 11.4 - - + -
114B TRP* 4.4 6.1 - - + -
129B VAL* 3.9 11.0 - - + +
130B TYR* 3.7 30.5 - - + +
199B GLU* 3.5 49.1 - - + +
225B GLN* 4.7 0.7 - - - +
441B GLY* 3.0 22.8 + - - +
442B TYR 3.3 0.2 - - - -
443B GLU* 1.3 85.2 - - + +
445B GLU* 1.3 62.0 + - - +
447B VAL* 3.1 7.8 + - - +
448B PHE* 3.0 45.2 + - + -
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Residues in contact with GLU 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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83B MET* 4.7 4.2 - - - +
84B TRP* 5.5 0.3 - - - -
129B VAL* 3.7 17.6 - - + +
427B ALA* 4.5 8.8 - - - +
429B ASN* 5.1 1.2 - - - +
430B LEU* 5.7 0.3 - - - +
441B GLY 4.2 1.7 - - - +
442B TYR* 3.7 44.9 - - - +
444B ILE* 1.3 78.9 - - - +
446B PHE* 1.3 74.6 + - + +
448B PHE* 3.9 1.3 - - - +
449B GLY 3.1 5.0 + - - -
450B LEU* 3.0 52.9 + - + +
451B PRO* 3.0 3.9 - - - +
458B TYR* 3.5 28.4 + - + +
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Residues in contact with PHE 446 (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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423B PHE* 3.8 17.3 - + + -
425B HIS* 3.7 21.3 - + - -
427B ALA* 4.1 20.2 - - + -
442B TYR 3.8 17.0 - - - -
443B GLU 2.9 14.2 + - - +
445B GLU* 1.3 82.8 - - + +
447B VAL* 1.3 66.0 + - - +
449B GLY 3.0 2.6 + - - -
451B PRO* 3.6 17.5 - - + -
458B TYR* 4.5 2.2 - + - -
462B GLU* 3.5 38.8 - - + -
465B LEU* 3.7 19.3 - - + -
466B SER* 2.6 37.3 + - - +
469B ILE* 4.1 20.6 - - + +
470B MET* 3.7 0.2 - - - +
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Residues in contact with VAL 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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112B MET* 5.9 0.2 - - + -
114B TRP* 6.2 0.2 - - + -
135B LEU* 3.7 12.7 - - + +
197B PHE* 4.2 17.0 - - + -
225B GLN* 4.0 13.0 - - - +
443B GLU* 3.4 12.7 + - + +
444B ILE* 3.1 9.5 + - - +
446B PHE* 1.3 76.8 - - + +
448B PHE* 1.3 69.9 + - + +
469B ILE* 3.9 20.0 - - + -
470B MET* 3.2 22.3 - - - +
473B TRP* 3.7 48.5 - - + -
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Residues in contact with PHE 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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114B TRP* 3.6 50.7 - + + -
129B VAL 3.3 21.8 - - - +
130B TYR* 3.8 22.9 - + - -
131B ASN 3.6 21.5 - - - +
132B GLY* 4.2 3.1 - - - -
134B TYR* 3.5 23.2 - - - +
135B LEU* 4.2 11.4 + - + -
143B LEU* 4.4 20.9 - - + -
145B SER* 6.2 0.2 - - - -
197B PHE* 4.6 4.0 - + - -
444B ILE* 3.0 35.0 + - + +
445B GLU 3.7 0.7 - - - +
447B VAL* 1.3 82.7 - - + +
449B GLY* 1.3 62.6 + - - +
450B LEU* 3.3 8.4 + - + -
470B MET* 3.4 7.0 - - - +
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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