Contacts of the helix formed by residues 448 - 452 (chain B) in PDB entry 4R1Z
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 448 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96B LYS* 5.8 0.2 - - + -
99B LEU* 3.3 36.0 - - + +
100B ILE* 3.9 21.3 - - + -
444B LEU* 4.0 17.0 - - + -
447B GLY* 1.3 77.7 - - - +
449B GLY* 1.3 69.4 + - - +
450B VAL 3.4 0.5 + - - -
451B ARG 3.9 7.6 + - - -
452B VAL* 3.8 14.8 + - - +
600B HEM 4.9 0.4 + - - -
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Residues in contact with GLY 449 (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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356A SER* 3.9 26.7 + - - -
99B LEU 3.5 8.3 - - - -
100B ILE* 3.8 13.5 - - - +
448B ALA* 1.3 73.2 - - - +
450B VAL* 1.3 64.9 + - - +
452B VAL* 3.0 22.7 - - - +
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Residues in contact with VAL 450 (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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354A GLN* 5.4 0.7 - - - +
356A SER* 4.0 20.4 - - - +
99B LEU 3.4 5.2 + - - +
100B ILE 5.2 1.6 - - - +
103B GLY* 3.8 37.5 - - - +
104B LYS* 4.1 16.4 - - + +
107B ALA* 4.5 2.9 - - + -
130B TYR* 4.3 12.1 - - + -
134B TRP* 3.6 35.6 - - + -
138B ARG* 4.2 5.5 + - - -
449B GLY* 1.3 72.9 - - - +
451B ARG* 1.3 66.9 + - - +
452B VAL* 3.1 8.7 + - - +
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Residues in contact with ARG 451 (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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99B LEU 4.9 1.0 + - - -
103B GLY 5.4 0.7 - - - +
107B ALA* 2.7 53.1 + - + +
109B ARG* 3.1 31.9 - - - +
125B ILE 2.9 24.0 + - - -
128B ALA 2.8 22.4 + - - -
130B TYR* 4.2 4.9 - - - +
134B TRP* 3.4 26.2 - - - +
138B ARG* 4.1 2.2 - - - -
384B HIS* 3.7 32.0 - - + -
448B ALA 3.9 4.3 + - - +
449B GLY 3.6 0.4 - - - -
450B VAL* 1.3 75.6 - - + +
452B VAL* 1.3 65.5 + - - +
453B CYS 3.6 0.9 + - - -
600B HEM 2.8 61.1 + - - +
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Residues in contact with VAL 452 (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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138B ARG* 2.7 48.5 + - - +
446B PHE 3.3 13.0 - - - +
447B GLY 4.2 2.0 - - - +
448B ALA* 3.8 24.7 + - - +
449B GLY 3.0 21.3 + - - +
450B VAL 3.1 2.1 + - - +
451B ARG* 1.3 77.0 - - - +
453B CYS* 1.3 71.2 + - + +
456B GLU* 3.9 17.5 - - - +
600B HEM 4.0 1.2 - - - +
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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