Contacts of the helix formed by residues 110 - 120 (chain B) in PDB entry 5DO7
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 GLY 110 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87B GLY* 4.5 6.2 - - - -
88B ILE* 4.7 9.2 - - - +
108B GLY 3.0 8.1 + - - -
109B CYS* 1.3 77.7 - - - +
111B ARG* 1.3 54.6 + - - +
113B SER* 3.6 22.4 - - - -
114B LEU* 2.8 34.8 + - - +
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Residues in contact with ARG 111 (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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103B ILE* 4.1 18.1 - - + +
105B GLY* 3.3 36.8 - - - +
106B SER 3.6 9.8 + - - +
107B SER* 4.2 0.4 - - - +
108B GLY* 3.6 14.3 - - - +
109B CYS* 3.2 25.8 - - - +
110B GLY* 1.3 73.3 - - - +
112B ALA* 1.3 92.0 + - - +
113B SER* 3.1 1.1 + - - -
114B LEU* 3.2 19.5 + - - +
115B LEU* 3.9 10.2 + - - +
238B GLU* 3.4 29.3 + - - +
268B SER* 4.0 16.3 + - - -
270B HIS* 3.4 35.9 - - - +
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Residues in contact with ALA 112 (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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108B GLY* 5.4 3.4 - - - -
111B ARG* 1.3 99.9 - - - +
113B SER* 1.3 59.1 + - - +
115B LEU 4.4 0.2 + - - -
116B ASP* 3.2 22.5 + - - +
152B ARG* 5.1 0.9 + - - -
153B GLN* 5.9 4.7 - - - +
237B ASP* 3.4 24.3 - - - +
238B GLU* 5.8 0.4 - - + -
268B SER* 4.9 0.2 - - - -
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Residues in contact with SER 113 (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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43B GLN* 6.4 0.9 - - - -
110B GLY* 3.6 22.5 - - - -
112B ALA* 1.3 77.9 - - - +
114B LEU* 1.3 66.0 + - - +
115B LEU 3.2 0.7 - - - -
116B ASP* 2.8 12.4 + - - +
117B VAL* 2.8 29.3 + - - +
123B HIS* 5.3 13.5 - - - +
124B GLY* 5.8 3.7 + - - -
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Residues in contact with LEU 114 (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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38B PHE* 6.1 0.4 - - + -
88B ILE* 4.4 17.0 - - + -
91B LEU* 4.1 24.0 - - + -
93B PHE* 5.2 1.6 - - + -
103B ILE* 3.9 35.4 - - + -
109B CYS* 5.9 0.9 - - - -
110B GLY 2.8 22.9 + - - +
111B ARG* 3.2 12.7 + - + +
113B SER* 1.3 71.6 - - - +
115B LEU* 1.3 58.4 + - + +
117B VAL* 3.1 10.5 + - + +
118B ILE* 2.8 55.4 + - + +
284B LEU* 5.0 3.4 - - + -
286B MET* 4.2 19.7 - - + -
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Residues in contact with LEU 115 (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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103B ILE* 3.6 30.7 - - + -
111B ARG 3.9 7.6 + - - +
113B SER 3.2 0.8 - - - -
114B LEU* 1.3 76.0 - - + +
116B ASP* 1.3 56.9 + - - +
118B ILE* 3.1 14.7 + - + +
119B THR* 2.8 32.8 + - - -
150B HIS* 4.1 4.9 - - + -
235B ILE* 3.8 30.2 - - + +
236B LEU 3.6 18.8 - - - +
237B ASP* 3.6 23.3 - - + +
266B LEU* 4.8 7.9 - - + -
267B ILE 4.7 2.7 - - - +
268B SER* 3.4 28.7 - - - +
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Residues in contact with ASP 116 (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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112B ALA 3.2 16.5 - - - +
113B SER* 2.8 11.3 + - - +
115B LEU* 1.3 74.4 - - - +
117B VAL* 1.3 58.8 + - - +
119B THR* 3.4 7.7 + - - -
120B GLY 3.0 6.2 + - - -
121B ARG* 2.8 60.1 + - + +
122B GLY* 5.4 0.4 - - - -
123B HIS* 5.8 2.3 + - - +
150B HIS* 4.0 7.4 + - - -
152B ARG* 2.8 35.5 + - - -
237B ASP* 3.3 7.4 - - - +
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Residues in contact with VAL 117 (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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43B GLN* 3.0 33.0 - - - +
88B ILE* 4.2 15.0 - - + -
113B SER* 2.8 33.2 + - - +
114B LEU* 3.3 18.2 - - + +
116B ASP* 1.3 69.0 - - - +
118B ILE* 1.3 64.0 + - + +
120B GLY* 2.8 22.4 + - - -
121B ARG 4.0 5.1 + - - -
122B GLY* 4.8 4.9 - - - -
126B LYS* 5.1 4.9 + - - +
127B ILE* 3.6 21.1 - - + -
132B ILE* 4.6 5.1 - - - +
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Residues in contact with ILE 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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36B LEU* 4.9 13.5 - - + -
38B PHE* 3.7 35.0 - - + -
93B PHE* 4.5 15.0 - - + -
103B ILE* 5.1 1.8 - - + -
114B LEU* 2.8 47.0 + - + +
115B LEU* 3.4 18.4 - - + +
117B VAL* 1.3 78.4 - - + +
119B THR* 1.3 60.0 + - - +
120B GLY* 3.4 0.5 + - - -
132B ILE* 4.1 19.2 - - + +
139B SER* 4.7 5.0 + - - -
144B VAL* 4.6 8.5 - - - +
235B ILE* 4.7 16.6 - - + -
266B LEU* 5.2 5.6 - - + -
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Residues in contact with THR 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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115B LEU 2.8 16.1 + - - -
116B ASP* 3.6 10.5 - - - -
117B VAL 3.2 0.2 - - - -
118B ILE* 1.3 76.1 - - - +
120B GLY* 1.3 57.2 + - - +
121B ARG* 3.8 31.5 - - + +
139B SER* 5.4 1.4 + - - -
141B PRO* 4.6 10.9 - - - +
144B VAL* 4.0 37.3 - - + +
148B VAL* 5.4 1.4 - - - +
150B HIS* 3.8 22.7 + - + +
235B ILE* 4.7 8.0 - - - +
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Residues in contact with GLY 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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116B ASP 3.0 1.5 + - - -
117B VAL 2.8 17.3 + - - -
118B ILE 4.5 0.4 - - - -
119B THR* 1.3 78.1 - - - +
121B ARG* 1.3 59.9 + - - +
122B GLY 3.1 8.5 + - - -
126B LYS* 3.4 24.3 + - - -
139B SER* 6.0 1.1 - - - -
141B PRO* 4.8 15.7 - - - +
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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