Contacts of the helix formed by residues 110 - 117 (chain B) in PDB entry 1TW2
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 GLN 110 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ARG* 4.0 7.5 - - - +
103B ARG* 3.2 16.6 - - - +
104B ALA* 3.8 25.5 - - - +
107B ASP* 3.0 45.3 + - + +
109B THR* 1.3 87.9 - - + +
111B ALA* 1.3 65.5 + - - +
112B VAL 3.3 2.1 + - - -
113B ALA 4.6 0.2 - - - -
114B ARG* 3.2 18.2 + - - +
151B LEU* 4.2 3.6 - - - -
154B SER* 3.4 28.1 - - - +
158B LEU* 4.6 8.1 - - + +
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Residues in contact with ALA 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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110B GLN* 1.3 73.0 - - - +
112B VAL* 1.3 58.2 + - - +
114B ARG* 3.8 2.9 - - - +
115B ALA* 3.0 28.6 + - - +
133B TYR* 5.2 1.7 + - - -
141B PHE* 4.8 4.7 - - + -
145B LEU* 4.4 12.1 - - + -
151B LEU* 3.5 36.7 - - - +
154B SER* 3.0 8.7 + - - +
155B PHE* 3.7 26.5 - - + +
158B LEU* 4.7 1.4 - - - +
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Residues in contact with VAL 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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105B TRP* 3.7 34.8 - - + +
110B GLN 3.4 0.6 - - - -
111B ALA* 1.3 75.4 - - - +
113B ALA* 1.3 62.7 + - - +
115B ALA* 3.1 9.3 + - - +
116B ASP* 3.0 25.6 + - - +
141B PHE* 6.0 0.9 - - + -
155B PHE* 4.2 21.8 - - + -
158B LEU* 3.7 24.8 - - + +
159B LEU* 5.3 0.2 - - + -
302B ARG* 4.1 22.9 - - - +
306B PHE* 3.8 2.9 - - + -
1600B ERT 3.7 23.3 - - + +
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Residues in contact with ALA 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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32B ARG* 3.6 20.5 + - - +
104B ALA 5.5 0.8 + - - -
105B TRP 3.5 19.7 + - - +
106B HIS 3.6 8.5 - - - +
107B ASP 3.2 27.6 + - - +
108B LEU* 4.0 7.1 - - + +
110B GLN 3.8 1.2 + - - -
112B VAL* 1.3 74.1 - - - +
114B ARG* 1.3 67.9 + - - +
116B ASP* 3.0 19.9 + - - +
117B ILE* 3.5 10.7 - - - +
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Residues in contact with ARG 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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107B ASP 4.1 1.2 + - - -
108B LEU* 3.5 19.9 + - - +
109B THR* 5.1 1.6 - - - +
110B GLN 3.2 18.1 + - - +
111B ALA 3.8 3.8 - - - +
113B ALA* 1.3 79.3 - - - +
115B ALA* 1.3 61.0 + - - +
116B ASP 3.2 0.9 + - - -
117B ILE* 3.3 10.8 + - - +
133B TYR* 3.1 12.3 + - - -
137B TYR* 2.7 70.7 + - + +
144B ASP* 3.0 28.1 + - - -
148B ARG* 3.7 26.8 - - - +
151B LEU* 3.4 32.0 - - - +
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Residues in contact with ALA 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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111B ALA 3.0 20.9 + - - +
112B VAL* 3.1 9.4 + - - +
114B ARG* 1.3 77.7 - - - +
116B ASP* 1.3 54.3 + - - +
118B SER* 2.7 31.9 + - - -
133B TYR* 3.9 25.1 - - + -
141B PHE* 4.1 5.6 - - + -
306B PHE* 3.2 31.0 - - + -
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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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25A LEU* 3.4 15.2 - - + +
26A HIS* 5.1 0.7 - - - -
32B ARG* 2.9 30.3 + - - +
105B TRP 5.1 1.0 - - - +
112B VAL* 3.0 13.6 + - - +
113B ALA* 3.0 14.1 + - - +
115B ALA* 1.3 72.3 - - - +
117B ILE* 1.3 66.3 + - - +
118B SER 2.9 2.7 - - - -
119B PHE* 2.9 37.4 + - + +
302B ARG* 2.8 34.3 + - - -
306B PHE* 3.3 18.0 - - - -
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Residues in contact with ILE 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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25A LEU* 4.3 12.8 - - + -
120A THR* 4.3 28.7 - - + +
29B MET* 5.1 3.4 - - + -
32B ARG* 5.9 0.2 - - - +
108B LEU* 3.8 22.0 - - + -
113B ALA 3.5 17.0 - - - +
114B ARG* 3.6 4.9 - - - +
115B ALA 3.2 1.0 - - - -
116B ASP* 1.3 76.4 - - - +
118B SER* 1.3 51.3 + - - +
120B THR* 2.6 49.9 + - + +
136B ILE* 3.9 30.1 - - + -
137B TYR* 3.5 18.6 - - + +
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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