Contacts of the helix formed by residues 49 - 54 (chain V) in PDB entry 5A0Q
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 49 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20V THR* 5.1 4.7 - - + -
45V ARG* 3.9 11.0 - - - +
48V SER* 1.3 72.7 + - - +
50V ALA* 1.4 57.8 + - - +
52V THR 3.2 1.6 + - - -
53V GLN* 2.9 41.4 + - - +
300V KNM 3.7 46.9 + - + +
118W SER* 3.9 14.8 - - - +
120W ASP* 6.1 0.4 - - - +
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Residues in contact with ALA 50 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48V SER* 3.3 11.5 + - - +
49V ALA* 1.4 76.7 - - - +
51V ASP* 1.3 66.7 + - - +
53V GLN* 3.5 7.3 + - - +
54V ALA 3.8 2.3 + - - -
300V KNM 4.9 3.8 - - + +
88W PHE* 3.3 20.8 - - + -
116W HIS* 3.6 38.8 - - + +
117W GLY 3.4 17.2 - - - +
118W SER* 3.8 6.1 + - - +
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Residues in contact with ASP 51 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48V SER* 3.8 17.7 + - - +
49V ALA 3.5 0.2 - - - -
50V ALA* 1.3 78.2 - - - +
52V THR* 1.3 58.8 + - - +
54V ALA* 3.5 3.8 + - - +
55V VAL* 3.2 30.1 + - - +
93V ASP 3.8 13.4 - - - +
94V LEU* 3.3 26.3 - - + +
95V MET* 3.4 30.0 + - - +
88W PHE* 3.6 20.7 - - + -
91W GLN* 4.9 2.6 - - - +
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Residues in contact with THR 52 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43V CYS* 4.9 1.3 - - - -
45V ARG* 3.5 37.2 - - + +
46V SER 4.0 12.8 + - - -
48V SER 2.8 18.0 + - - -
49V ALA 3.2 3.7 + - - -
51V ASP* 1.3 76.7 - - - +
53V GLN* 1.4 56.9 + - - +
55V VAL* 2.6 30.4 - - + +
56V ALA* 3.4 13.8 - - + +
57V ASP* 5.0 0.2 - - - +
95V MET 4.3 0.3 + - - -
96V ALA* 4.2 10.5 - - + +
98V ILE* 3.6 21.3 - - + -
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Residues in contact with GLN 53 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45V ARG* 4.0 24.6 + - - +
49V ALA* 2.9 37.2 + - - +
50V ALA 3.9 5.2 - - - +
51V ASP 3.3 0.4 - - - -
52V THR* 1.4 82.9 - - - +
54V ALA* 1.4 54.0 + - - +
55V VAL 2.8 12.1 - - - +
57V ASP* 3.1 25.9 + - - +
84W LYS* 3.2 43.6 - - + +
88W PHE* 5.9 0.7 - - + -
117W GLY 3.5 20.4 - - - +
118W SER* 4.3 6.3 - - - +
119W THR 4.4 12.9 + - - +
120W ASP* 5.6 1.2 + - - -
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Residues in contact with ALA 54 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103O TYR* 4.1 9.6 + - - -
50V ALA 3.8 1.6 + - - -
51V ASP 3.5 4.2 + - - +
52V THR 3.4 0.2 - - - -
53V GLN* 1.4 76.1 - - - +
55V VAL* 1.3 65.5 + - + +
57V ASP* 4.9 0.2 - - - +
58V ALA* 3.5 21.3 + - - +
86V MET* 4.5 3.4 - - + +
84W LYS* 5.8 0.2 - - - +
88W PHE* 3.4 51.7 - - + -
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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