Contacts of the strand formed by residues 443 - 448 (chain A) in PDB entry 6J95
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 VAL 443 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A PHE* 5.2 3.4 - - + -
129A PHE* 4.5 18.2 - - + -
132A LEU* 5.2 4.7 - - + -
441A PRO* 3.3 21.9 - - - +
442A PRO* 1.3 84.3 - - + +
444A LEU* 1.3 62.3 + - - +
445A ILE* 4.4 4.1 - - + +
466A PHE* 3.6 31.4 - - + -
467A ILE 3.2 12.8 - - - +
468A SER* 4.3 10.1 - - - -
469A VAL* 4.3 1.6 - - - +
602A RET 3.5 44.8 - - + +
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Residues in contact with LEU 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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165A LEU* 4.0 33.2 - - + -
441A PRO* 4.0 10.3 - - + -
443A VAL* 1.3 78.6 - - - +
445A ILE* 1.3 62.0 + - - +
446A ARG* 4.5 7.6 - - - +
465A ILE 3.7 0.5 - - - +
466A PHE* 3.4 5.2 - - - -
467A ILE* 2.8 47.1 + - + +
469A VAL* 3.8 21.8 - - + -
507A LEU* 4.5 4.0 - - + +
510A GLY* 4.4 16.2 - - - -
601A HEM 3.8 46.7 - - + +
602A RET 5.2 1.1 - - + -
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Residues in contact with ILE 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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174A LYS* 3.7 23.7 - - - +
176A ILE* 4.0 25.8 - - + +
177A LEU* 3.7 32.6 - - + +
180A ILE* 4.4 2.2 - - + -
443A VAL* 4.4 4.9 - - + +
444A LEU* 1.3 79.0 - - - +
446A ARG* 1.3 90.6 + - - +
464A ASP* 6.3 1.1 - - + -
465A ILE 3.5 6.7 - - - +
466A PHE* 3.6 37.0 - - + -
601A HEM 5.0 1.4 + - - -
602A RET 4.1 27.6 - - + -
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Residues in contact with ARG 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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164A ILE* 3.9 23.1 + - + +
165A LEU* 3.4 29.3 + - + +
172A TYR* 4.2 23.7 - - + +
173A SER 3.2 17.7 - - - +
174A LYS* 3.3 25.8 - - - +
175A GLY* 4.9 0.2 - - - -
444A LEU* 4.3 3.2 + - - +
445A ILE* 1.3 101.5 + - - +
447A ARG* 1.3 63.7 + - - +
464A ASP* 3.7 2.4 - - - +
465A ILE* 2.8 39.7 + - + +
467A ILE* 4.9 5.8 - - + -
511A GLY 5.1 1.6 + - - -
514A ARG* 3.7 15.6 - - - +
601A HEM 2.8 41.6 + - - -
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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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172A TYR* 3.2 6.2 - - - -
173A SER* 2.8 40.8 + - - +
175A GLY* 3.7 31.6 + - - -
176A ILE* 3.2 34.8 - - - +
179A GLU* 5.1 3.6 + - - -
446A ARG* 1.3 75.6 - - - +
448A SER* 1.3 77.0 + - - +
449A ILE* 5.6 2.7 - - - -
462A GLY* 4.0 16.3 + - - -
463A GLU 3.1 12.8 - - - +
464A ASP* 2.8 16.7 + - - +
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Residues in contact with SER 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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171A ALA 3.5 6.5 - - - -
172A TYR* 3.6 21.4 - - - -
447A ARG* 1.3 76.4 - - - +
449A ILE* 1.3 59.3 + - - +
450A ASP 3.5 11.7 - - - -
459A ILE* 4.0 9.9 - - - -
460A LYS 2.7 27.3 + - - -
462A GLY* 2.7 27.4 + - - -
463A GLU* 2.9 30.4 + - - +
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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