Contacts of the helix formed by residues 130 - 135 (chain R) in PDB entry 4DOH
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 TYR 130 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A ASP* 3.7 21.8 - - - +
167A ILE* 4.4 14.4 - - + +
170A GLN* 4.0 19.8 - - - +
174A GLU* 5.4 0.7 + - - -
104R TYR 3.5 25.6 + - - -
105R GLU* 4.7 6.8 + - - -
106R HIS 3.7 10.5 - - - -
107R GLN* 3.7 31.6 - - + -
128R ARG* 5.6 0.9 - - + +
129R PHE* 1.3 76.4 - - - +
131R PRO* 1.3 67.7 - - - +
132R PHE* 3.6 16.4 - - + -
133R LEU* 2.9 39.3 + - + +
134R GLU* 3.0 30.1 + - + +
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Residues in contact with PRO 131 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47R SER* 4.9 0.2 - - - +
50R MET* 3.8 16.8 - - + -
52R ASN* 3.8 11.4 - - - +
101R THR 3.8 17.7 - - - +
103R ASP 4.2 9.9 - - - +
106R HIS 4.0 7.2 - - - +
108R TYR* 4.0 20.2 - - + -
129R PHE* 3.6 38.6 - - + +
130R TYR* 1.3 83.2 - - - +
132R PHE* 1.3 64.3 + - - +
134R GLU 4.4 1.1 - - - +
135R THR* 3.0 32.1 + - - +
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Residues in contact with PHE 132 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A GLN* 3.6 32.3 - - + -
174A GLU* 5.9 0.2 - - - -
50R MET* 5.0 4.0 - - - -
104R TYR* 3.2 54.7 - + + +
130R TYR* 2.9 11.3 + - + -
131R PRO* 1.3 81.4 - - - +
133R LEU* 1.3 70.7 + - + +
175R ILE* 4.0 21.8 - - + -
176R TYR* 2.7 51.2 + + - -
227R ARG* 3.4 8.9 + - - -
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Residues in contact with LEU 133 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ARG* 4.0 4.5 - - - +
166A ASP* 3.8 28.3 - - + +
170A GLN* 3.2 27.4 - - + +
130R TYR* 2.9 44.9 + - + +
132R PHE* 1.3 90.1 - - + +
134R GLU* 1.3 64.1 + - + +
225R PRO* 4.0 31.1 - - + +
226R PRO 5.1 1.0 - - - +
227R ARG* 3.2 32.8 + - - +
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Residues in contact with GLU 134 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ARG* 4.0 34.1 + - - +
54A GLN* 5.4 0.2 + - - -
166A ASP* 5.2 0.3 - - - +
47R SER* 4.5 3.1 - - - +
128R ARG 3.9 11.1 - - - +
129R PHE* 3.5 24.8 - - + -
130R TYR* 3.0 39.2 + - + +
133R LEU* 1.3 82.6 - - + +
135R THR* 1.3 65.2 + - - +
136R GLN* 3.4 6.1 + - - +
227R ARG* 4.6 8.4 - - - +
228R ARG* 5.0 6.2 + - - +
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Residues in contact with THR 135 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47R SER* 2.7 33.9 + - - -
49R ASN 3.3 3.1 + - - -
50R MET* 3.2 30.0 + - - -
131R PRO* 3.0 16.0 + - - +
133R LEU 3.6 0.4 - - - -
134R GLU* 1.3 76.7 - - - +
136R GLN* 1.3 65.2 + - - +
137R ILE* 3.5 0.4 + - + -
172R MET* 4.5 6.3 - - + -
176R TYR* 3.4 33.0 - - + +
227R ARG* 3.1 23.2 + - - +
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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