Contacts of the helix formed by residues 117 - 127 (chain H) in PDB entry 3HR4
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 THR 117 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116H LEU* 1.3 73.6 - - - +
118H ASP* 1.3 59.4 + - + +
119H GLU* 3.5 20.0 - - + +
120H GLU* 2.5 41.5 + - - +
121H VAL* 2.7 36.6 + - - +
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Residues in contact with ASP 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106H ARG* 2.7 42.1 + - - +
116H LEU 4.7 0.7 - - - +
117H THR* 1.3 73.1 - - + +
119H GLU* 1.3 56.3 + - - +
120H GLU 2.9 11.8 + - - -
121H VAL* 4.2 0.9 - - - -
122H ASP* 2.5 37.2 + - - +
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Residues in contact with GLU 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117H THR* 3.2 16.1 - - + +
118H ASP* 1.3 77.4 - - - +
120H GLU* 1.3 57.7 + - - +
122H ASP* 4.6 5.5 - - - +
123H GLU* 4.3 8.2 + - - +
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Residues in contact with GLU 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115H LYS 4.4 1.9 - - - +
116H LEU* 3.4 24.3 - - + +
117H THR* 2.5 58.6 + - - +
118H ASP 2.9 0.4 - - - -
119H GLU* 1.3 80.9 - - - +
121H VAL* 1.3 60.1 + - - +
122H ASP 2.9 2.2 - - - -
123H GLU* 2.7 38.4 + - + +
124H MET* 3.2 8.8 + - - +
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Residues in contact with VAL 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102H ALA* 3.1 35.7 - - + +
105H LEU* 3.6 16.9 - - + +
106H ARG* 3.4 43.3 - - + +
116H LEU* 3.5 25.8 - - + -
117H THR 2.7 30.1 + - - +
118H ASP 3.3 3.1 + - - +
120H GLU* 1.3 74.3 - - - +
122H ASP* 1.3 62.4 + - - +
124H MET* 3.5 6.4 + - + +
125H ILE* 3.1 15.0 + - + +
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Residues in contact with ASP 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102H ALA* 4.1 11.2 - - - +
118H ASP* 2.5 29.9 + - - +
119H GLU* 4.6 4.8 - - - +
120H GLU 2.9 0.2 - - - -
121H VAL* 1.3 76.8 - - - +
123H GLU* 1.3 65.0 + - - +
125H ILE* 2.7 31.0 + - - +
126H ARG* 3.0 13.2 + - - +
134H GLY* 5.6 1.4 - - - +
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Residues in contact with GLU 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119H GLU 4.3 5.5 + - - +
120H GLU* 2.7 35.4 + - + +
122H ASP* 1.3 74.7 - - - +
124H MET* 1.3 65.4 - - + +
126H ARG* 3.4 14.4 + - - +
127H GLU* 3.4 23.6 + - - +
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Residues in contact with MET 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513G ILE* 3.8 17.7 - - - +
514G PRO* 4.8 3.8 - - + +
515G LEU* 3.8 20.2 - - + +
518G LEU* 5.4 0.9 - - - -
105H LEU* 3.2 47.8 - - + -
109H MET* 3.4 24.9 - - + +
116H LEU* 3.2 28.5 - - + -
120H GLU 3.2 7.3 + - - +
121H VAL* 3.8 7.6 - - + +
122H ASP 3.1 0.6 - - - -
123H GLU* 1.3 76.8 - - + +
125H ILE* 1.3 66.3 + - - +
127H GLU* 3.1 42.6 - - - +
128H ALA 4.0 0.5 + - - -
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Residues in contact with ILE 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515G LEU* 4.8 4.0 - - + -
100H ILE* 5.4 2.5 - - + +
101H SER 5.1 0.4 - - - -
102H ALA* 3.5 39.9 - - + -
105H LEU* 3.7 13.5 - - + -
121H VAL* 3.1 21.3 - - + +
122H ASP* 2.7 22.9 + - - +
124H MET* 1.3 72.7 - - - +
126H ARG* 1.3 58.1 + - - +
128H ALA* 3.5 3.3 + - - -
129H ASP* 3.0 35.2 + - - +
134H GLY* 3.4 25.1 - - - +
136H VAL* 3.5 26.9 - - + +
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Residues in contact with ARG 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122H ASP 3.0 9.2 + - - +
123H GLU* 3.6 15.0 - - - +
124H MET 3.2 0.2 - - - -
125H ILE* 1.3 71.5 - - - +
127H GLU* 1.3 55.5 + - - +
128H ALA 2.6 17.2 + - - -
129H ASP* 2.9 21.3 + - - +
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Residues in contact with GLU 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514G PRO* 3.7 17.0 - - - +
515G LEU* 2.9 34.7 + - + +
516G LYS* 3.3 26.0 + - - +
123H GLU* 3.4 21.9 - - - +
124H MET* 3.1 27.3 + - - +
126H ARG* 1.3 76.8 - - - +
128H ALA* 1.3 59.3 + - + +
144H MET* 5.0 2.5 - - + +
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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