Contacts of the helix formed by residues 443 - 448 (chain A) in PDB entry 2J3Q
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A GLU* 3.2 10.2 - - - +
225A GLN* 2.9 30.6 + - - +
226A SER* 4.2 3.2 + - - -
324A ASN* 2.8 34.1 + - - +
421A TYR* 4.2 14.6 - - + +
423A PHE* 3.4 43.0 - - + -
441A GLY* 3.3 14.2 + - - -
442A TYR* 1.3 77.9 - - - +
444A ILE* 1.3 79.5 + - - +
445A GLU 3.4 1.1 - - - -
446A PHE* 3.4 8.7 + - - +
447A VAL* 3.4 22.3 + - + +
469A ILE* 5.5 0.7 - - - +
473A TRP* 6.2 0.2 - - + -
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Residues in contact with ILE 444 (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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84A TRP* 4.4 6.7 - - + -
114A TRP* 3.7 8.7 - - + -
129A VAL* 4.0 8.7 - - + +
130A TYR* 3.6 33.4 - - + +
199A GLU* 3.5 32.8 - - + +
225A GLN* 4.0 4.7 - - - +
441A GLY 3.3 15.9 - - - +
442A TYR 3.3 0.6 - - - -
443A GLU* 1.3 94.4 - - - +
445A GLU* 1.3 67.0 + - - +
446A PHE 3.0 2.2 - - - -
447A VAL* 2.9 16.5 + - - +
448A PHE* 3.0 35.4 + - + -
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Residues in contact with GLU 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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83A MET* 4.9 8.1 - - - +
129A VAL* 3.5 23.2 - - + +
427A ALA* 4.1 10.0 - - - +
429A ASN* 4.4 1.9 - - - +
430A LEU* 4.8 1.7 - - - +
441A GLY 5.0 0.2 + - - -
442A TYR* 3.6 38.5 - - - +
444A ILE* 1.3 78.6 - - - +
446A PHE* 1.3 79.9 + - + +
448A PHE 3.7 0.7 + - - +
449A GLY 3.4 2.3 + - - -
450A LEU* 2.9 43.0 + - + +
451A PRO* 3.2 2.4 - - - +
458A TYR* 2.7 33.5 + - + +
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Residues in contact with PHE 446 (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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423A PHE* 4.0 22.9 - + + -
425A HIS* 3.5 31.6 - + - -
427A ALA* 4.4 9.6 - - + -
442A TYR 4.1 6.7 - - - -
443A GLU 3.7 7.2 - - - +
444A ILE 3.0 0.8 - - - -
445A GLU* 1.3 101.0 - - + +
447A VAL* 1.3 65.3 + - - +
448A PHE 3.1 1.8 - - - -
449A GLY 3.1 2.9 + - - -
451A PRO* 3.8 19.5 - - + -
458A TYR* 4.5 4.7 - + - -
462A GLU* 3.8 27.1 - - + -
465A LEU* 4.1 12.6 - - + -
466A SER* 2.9 45.8 + - - +
469A ILE* 4.0 17.4 - - + +
470A MET* 3.8 0.5 - - - +
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Residues in contact with VAL 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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135A LEU* 3.6 12.6 - - + +
197A PHE* 3.9 20.6 - - + -
225A GLN* 3.9 15.7 - - - +
443A GLU* 3.4 15.0 + - + +
444A ILE* 2.9 10.1 + - - +
446A PHE* 1.3 77.7 - - - +
448A PHE* 1.3 63.9 + - + +
449A GLY 3.3 0.2 - - - -
469A ILE* 3.9 16.8 - - + -
470A MET* 3.5 16.3 - - - +
473A TRP* 3.5 51.1 - - + +
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Residues in contact with PHE 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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114A TRP* 3.3 55.6 - + - -
129A VAL 3.5 15.3 - - - +
130A TYR* 3.8 21.8 - + - -
131A ASN 3.8 19.8 - - - +
132A GLY* 4.4 2.7 - - - -
134A TYR* 3.3 24.1 - - - +
135A LEU* 4.0 10.9 + - + -
143A LEU* 4.4 16.4 - - + -
197A PHE* 3.7 19.3 - + - -
444A ILE* 3.0 31.5 + - + +
445A GLU 3.7 2.4 + - - +
447A VAL* 1.3 83.8 - - + +
449A GLY* 1.3 61.2 + - - +
450A LEU* 3.3 6.9 + - + -
470A MET* 4.0 4.5 - - - -
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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