Contacts of the helix formed by residues 122 - 127 (chain R) in PDB entry 3H1I
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 HIS 122 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109R GLU 4.7 0.2 - - - -
110R ALA* 3.2 50.0 + - + -
114R VAL* 3.6 27.2 - - + +
121R GLN* 1.3 73.0 - - - +
123R ASP* 1.3 69.1 + - - +
124R LEU* 2.6 45.0 + - + +
125R ASP* 2.7 37.2 + - - +
126R ARG* 3.4 5.5 + - - +
170R ARG* 4.1 2.0 - - - +
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Residues in contact with ASP 123 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101R ARG* 2.9 27.0 + - - -
106R ILE* 4.3 10.4 - - - +
109R GLU* 2.8 49.2 - - - +
110R ALA* 4.5 2.5 - - + -
122R HIS* 1.3 79.8 + - + +
124R LEU* 1.3 60.4 + - + +
126R ARG* 3.5 2.7 + - - +
127R VAL* 3.1 32.7 + - - +
130R PRO* 6.3 0.7 - - - -
168R SER* 3.6 19.7 + - - -
170R ARG* 3.3 8.6 - - - +
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Residues in contact with LEU 124 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106R ILE* 6.1 2.7 - - + -
110R ALA* 5.4 5.4 - - + -
122R HIS* 2.6 36.5 + - + +
123R ASP* 1.3 77.1 - - + +
125R ASP* 1.3 55.2 + - - +
126R ARG 3.3 4.3 - - - -
127R VAL* 3.1 17.8 - - + +
128R LYS* 5.3 0.2 - - - -
130R PRO* 4.3 24.9 - - + -
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Residues in contact with ASP 125 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121R GLN* 3.5 21.6 - - - +
122R HIS* 2.7 43.2 + - - +
124R LEU* 1.3 74.2 - - + +
126R ARG* 1.3 59.9 + - - +
127R VAL 4.9 0.4 - - - -
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Residues in contact with ARG 126 (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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121R GLN* 2.7 55.5 + - + +
122R HIS 4.0 9.4 - - - +
123R ASP 3.6 9.0 - - - +
124R LEU 3.3 0.2 - - - -
125R ASP* 1.3 80.1 - - - +
127R VAL* 1.3 65.4 + - + +
134R ILE 5.5 0.2 + - - -
135R LEU* 3.8 9.1 - - - +
168R SER* 2.6 47.4 + - - +
169R GLY* 3.3 22.0 + - - -
170R ARG* 3.7 16.5 - - - +
179R ASN* 3.8 13.5 - - - +
180R LEU 3.6 17.8 + - - -
182R VAL* 3.2 49.8 - - + +
185R TYR* 3.3 5.4 + - - -
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Residues in contact with VAL 127 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101R ARG* 3.0 28.0 - - - +
123R ASP* 3.1 20.0 - - - +
124R LEU* 3.1 22.6 - - + +
125R ASP 5.2 0.4 - - - -
126R ARG* 1.3 88.6 - - + +
128R LYS* 1.3 65.5 + - - +
130R PRO* 4.5 8.7 - - + +
132R TRP 3.4 11.2 - - - +
133R VAL* 3.6 33.7 - - + -
134R ILE 4.0 4.5 - - - +
168R SER* 5.6 0.4 - - - +
182R VAL* 5.3 0.2 - - + -
185R TYR* 3.2 17.9 - - - +
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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