Contacts of the helix formed by residues 447 - 452 (chain A) in PDB entry 3RBH
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 MSE 447 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A TRP* 4.9 15.0 - - + -
78A PHE* 4.4 30.7 - - + -
87A TYR* 3.9 32.5 - - + -
132A TRP* 5.4 7.9 - - + -
443A LEU* 3.8 22.9 - - + -
444A PRO* 3.1 29.2 + - + +
445A ALA 3.6 2.4 - - - +
446A SER* 1.3 97.5 + - - +
448A SER* 1.3 64.8 + - - +
449A GLN* 3.3 14.1 - - - +
450A TYR* 3.2 19.6 - - - +
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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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87A TYR* 5.2 2.5 - - - -
89A MSE 6.0 0.2 - - - -
130A GLU* 2.8 27.5 + - - -
147A ARG* 5.8 5.8 - - - -
152A ARG* 3.6 46.6 + - - +
154A ARG* 5.4 1.9 + - - -
446A SER 3.6 3.5 + - - -
447A MSE 1.3 75.0 - - - +
449A GLN* 1.3 68.7 + - - +
450A TYR 3.1 1.9 + - - -
451A VAL* 4.0 9.4 + - - +
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Residues in contact with GLN 449 (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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45A ASP* 3.0 29.6 + - - +
74A ARG* 6.1 2.9 - - - +
76A TRP* 4.4 7.1 - - - +
87A TYR* 4.0 10.9 + - - -
89A MSE 3.3 24.4 - - + +
152A ARG* 4.6 7.2 - - - +
443A LEU* 3.3 30.9 - - + +
447A MSE 3.4 15.3 - - - +
448A SER* 1.3 83.7 + - - +
450A TYR* 1.3 60.2 + - - +
451A VAL* 3.2 2.9 - - - -
452A ASP* 3.1 8.1 + - + +
453A GLU* 2.8 32.5 + - + +
489A ARG* 4.0 5.6 - - - +
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Residues in contact with TYR 450 (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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267A ARG* 4.5 14.6 + - - -
360A ARG* 5.0 3.8 + - - -
443A LEU* 3.2 31.0 - - + -
444A PRO 3.8 4.5 - - - +
445A ALA* 3.6 37.0 - - + +
447A MSE 3.2 19.1 + - + +
448A SER 3.1 1.2 - - - -
449A GLN* 1.3 80.6 - - - +
451A VAL* 1.3 64.6 + - - +
452A ASP 3.3 0.3 + - - -
453A GLU 4.4 0.9 - - - -
454A PRO* 3.4 51.1 - - + +
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Residues in contact with VAL 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ARG* 5.2 1.8 - - - +
154A ARG* 3.8 35.7 - - - +
355A ASN* 5.0 3.3 + - - +
360A ARG 3.6 19.8 - - - +
361A SER* 5.5 0.2 - - - -
362A ARG* 4.1 18.3 + - - +
448A SER 4.0 7.6 + - - +
449A GLN 3.1 1.2 + - - -
450A TYR* 1.3 84.0 - - - +
452A ASP* 1.3 64.5 + - - +
454A PRO* 4.8 2.1 - - - +
459A ARG* 5.6 0.2 + - - -
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Residues in contact with ASP 452 (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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102A ASP* 5.4 5.4 - - - +
103A THR* 4.0 13.7 + - - -
152A ARG* 3.7 14.7 + - - -
362A ARG* 3.0 51.2 + - - +
449A GLN* 3.1 7.1 + - + +
451A VAL* 1.3 77.2 - - - +
453A GLU* 1.3 63.0 + - + +
454A PRO* 3.5 3.9 - - - +
457A LEU* 3.6 7.6 - - - +
459A ARG* 3.2 34.2 + - - +
487A ILE* 4.6 0.9 - - - +
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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