Contacts of the helix formed by residues 117 - 127 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106B ARG* 4.7 0.2 - - - +
116B LEU* 1.3 76.7 - - - +
118B ASP* 1.3 76.5 + - + +
119B GLU* 3.0 19.8 + - + +
120B GLU* 2.8 27.3 + - - +
121B VAL* 3.1 13.7 - - - +
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Residues in contact with ASP 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ALA* 5.0 5.9 - - - +
106B ARG* 3.5 23.8 + - - +
117B THR* 1.3 78.4 - - + +
119B GLU* 1.3 62.8 + - - +
121B VAL* 3.9 8.9 - - - +
122B ASP* 3.3 29.3 + - - +
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Residues in contact with GLU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B THR* 3.0 13.9 - - + +
118B ASP* 1.3 74.3 - - - +
120B GLU* 1.3 76.6 + - + +
121B VAL 2.8 11.6 + - - -
122B ASP* 2.8 18.7 + - - +
123B GLU* 3.1 17.7 + - - +
126B ARG* 3.9 20.3 + - - -
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511A ARG* 4.4 9.7 - - - +
512A GLU* 5.2 2.2 - - + +
116B LEU* 3.5 32.9 - - + +
117B THR* 2.8 45.0 + - - +
119B GLU* 1.3 84.2 + - + +
121B VAL* 1.3 55.4 + - - +
123B GLU* 3.9 9.0 - - - +
124B MET* 3.1 29.9 + - + +
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ALA* 3.7 26.7 - - + +
105B LEU* 4.2 11.2 - - + +
106B ARG* 4.4 26.2 - - + +
109B MET* 6.0 2.0 - - + -
116B LEU* 3.7 27.8 - - + +
117B THR 3.1 19.5 - - - +
118B ASP* 3.9 10.5 - - - +
119B GLU 2.8 0.6 + - - -
120B GLU* 1.3 75.6 - - - +
122B ASP* 1.3 62.5 - - - +
123B GLU 3.1 1.8 - - - -
124B MET* 3.2 13.5 + - - +
125B ILE* 2.9 28.8 + - + +
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Residues in contact with ASP 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ALA* 4.4 10.4 - - - +
118B ASP* 3.3 25.3 + - - +
119B GLU* 2.8 12.4 + - - +
121B VAL* 1.3 78.8 - - - +
123B GLU* 1.3 60.9 + - - +
125B ILE* 3.4 19.2 - - - +
126B ARG* 3.3 34.6 + - - +
134B GLY* 4.9 11.4 - - - +
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Residues in contact with GLU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B GLU* 3.1 26.3 + - - +
120B GLU* 4.1 7.4 - - - +
122B ASP* 1.3 74.0 - - - +
124B MET* 1.3 56.3 + - - +
125B ILE 2.7 15.0 + - - -
126B ARG* 3.0 41.6 + - - +
127B GLU* 3.0 12.7 + - + +
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Residues in contact with MET 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512A GLU* 3.9 16.4 - - + -
513A ILE 3.0 25.4 - - - +
514A PRO* 5.1 0.4 - - + -
515A LEU* 3.4 39.8 - - + +
518A LEU* 5.6 0.4 - - - -
105B LEU* 3.8 25.4 - - + -
109B MET* 4.2 14.6 - - + +
116B LEU* 3.7 28.7 - - + -
120B GLU* 3.1 20.5 + - + +
121B VAL* 3.2 9.8 + - - +
123B GLU* 1.3 76.0 - - - +
125B ILE* 1.3 58.2 + - - +
127B GLU* 3.6 21.8 - - - +
128B ALA* 5.9 0.2 - - - +
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Residues in contact with ILE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ILE 4.9 2.7 - - - +
101B SER 4.8 1.6 - - - +
102B ALA* 3.7 36.6 - - + +
105B LEU* 3.4 19.7 - - + -
121B VAL* 2.9 20.4 - - + +
122B ASP* 3.4 21.3 - - - +
123B GLU 2.7 0.8 + - - -
124B MET* 1.3 79.4 - - - +
126B ARG* 1.3 52.9 + - - +
127B GLU 2.7 14.5 + - - -
128B ALA* 2.8 15.1 + - - +
129B ASP* 3.1 9.3 + - + -
134B GLY* 4.0 21.1 - - - +
135B GLN* 4.0 11.7 - - - +
136B VAL* 3.8 26.1 - - + +
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Residues in contact with ARG 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B GLU* 3.9 19.6 + - - -
122B ASP* 3.3 16.4 + - - +
123B GLU* 3.0 31.8 + - - +
125B ILE* 1.3 76.4 - - + +
127B GLU* 1.3 55.9 + - - +
128B ALA 3.0 8.6 + - - -
129B ASP* 3.8 25.5 + - + +
132B GLY* 6.1 3.6 - - - -
134B GLY* 5.3 7.2 - - - -
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Residues in contact with GLU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514A PRO* 3.5 10.9 - - - +
515A LEU* 2.7 34.1 + - + +
516A LYS* 2.9 41.3 + - + +
123B GLU* 3.0 13.7 + - + +
124B MET* 3.6 18.3 - - - +
125B ILE 2.7 0.6 - - - -
126B ARG* 1.3 77.9 - - - +
128B ALA* 1.3 60.5 + - - +
144B MET* 4.9 2.3 - - - +
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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