Contacts of the helix formed by residues 110 - 117 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ARG* 5.5 4.4 - - - +
103A ARG* 4.5 11.5 - - - +
104A ALA* 4.0 23.7 - - - +
107A ASP* 3.1 29.3 + - + +
109A THR* 1.3 87.5 - - + +
111A ALA* 1.3 66.4 + - - +
112A VAL 3.3 1.9 + - - -
113A ALA 4.5 0.2 - - - -
114A ARG* 3.3 19.0 + - - +
151A LEU* 4.9 0.2 - - - -
154A SER* 3.4 27.8 + - - +
157A SER* 5.8 1.4 - - - -
158A LEU* 3.9 23.6 - - + +
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLN* 1.3 72.8 - - - +
112A VAL* 1.3 58.2 + - - +
114A ARG* 3.5 7.1 + - - +
115A ALA* 3.1 27.0 + - - +
133A TYR* 5.4 1.6 + - - -
141A PHE* 5.0 5.1 - - + -
145A LEU* 4.6 6.1 - - + -
151A LEU* 3.7 32.3 - - + +
154A SER* 2.7 18.3 + - - +
155A PHE* 3.7 23.3 - - + +
158A LEU* 4.5 0.6 - - - +
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Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A TRP* 3.7 33.9 - - + +
110A GLN 3.3 0.6 + - - -
111A ALA* 1.3 73.8 - - - +
113A ALA* 1.3 66.7 + - - +
114A ARG 3.1 1.8 - - - -
115A ALA* 3.2 7.9 + - - +
116A ASP* 3.0 22.1 + - - +
141A PHE* 6.2 1.1 - - + -
155A PHE* 4.5 19.7 - - + -
158A LEU* 3.4 28.7 - - + +
159A LEU* 5.1 0.2 - - + -
302A ARG* 3.7 33.0 - - - +
306A PHE* 4.2 3.3 - - + -
600A ERT 4.0 12.1 - - + +
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Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ARG* 3.3 26.8 + - - +
104A ALA 5.6 0.4 + - - -
105A TRP 3.8 5.2 + - - +
106A HIS 3.8 11.0 - - - +
107A ASP 3.1 32.3 + - - +
108A LEU* 3.9 10.5 - - + +
110A GLN 3.7 1.6 + - - -
111A ALA 3.6 0.2 - - - -
112A VAL* 1.3 76.2 - - - +
114A ARG* 1.3 64.9 + - - +
116A ASP* 3.2 15.8 + - - +
117A ILE* 3.5 12.3 - - - +
158A LEU* 5.5 0.2 - - - +
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Residues in contact with ARG 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LEU 3.8 17.3 + - - +
109A THR* 4.7 2.5 - - - +
110A GLN 3.3 15.8 + - - +
111A ALA* 3.5 7.8 + - - +
113A ALA* 1.3 79.6 - - - +
115A ALA* 1.3 62.2 + - - +
117A ILE* 3.3 15.7 + - + +
133A TYR* 3.0 13.7 + - - -
137A TYR* 2.7 70.1 + - - +
144A ASP* 2.8 30.9 + - - -
148A ARG* 4.1 20.7 - - - +
151A LEU* 3.6 33.9 - - - +
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Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ALA 3.1 15.1 + - - +
112A VAL* 3.2 6.7 + - - +
114A ARG* 1.3 75.9 - - - +
116A ASP* 1.3 55.4 + - - +
117A ILE 3.0 5.6 - - - -
118A SER* 2.8 33.1 + - - -
133A TYR* 3.7 29.3 - - + -
137A TYR* 4.5 0.2 - - - -
141A PHE* 4.3 7.0 - - + -
306A PHE* 3.1 30.4 - - + -
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Residues in contact with ASP 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ARG* 3.2 28.7 + - - +
105A TRP 5.0 0.2 - - - +
112A VAL* 3.0 18.9 + - - +
113A ALA* 3.2 11.5 + - - +
115A ALA* 1.3 72.6 - - - +
117A ILE* 1.3 66.3 + - - +
118A SER 3.0 0.4 - - - -
119A PHE* 2.9 39.1 + - + +
302A ARG* 2.6 44.4 + - - -
306A PHE* 3.5 6.0 - - - -
25B LEU* 3.6 15.7 + - + +
26B HIS 5.6 0.2 + - - -
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Residues in contact with ILE 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A MET* 6.3 1.8 - - + -
108A LEU* 4.5 17.3 - - + +
113A ALA 3.5 15.0 - - - +
114A ARG* 3.3 26.2 + - + +
115A ALA 3.0 0.6 - - - -
116A ASP* 1.3 78.2 - - - +
118A SER* 1.3 51.2 + - - +
120A THR* 2.7 55.6 + - + +
136A ILE* 4.0 19.7 - - + +
137A TYR* 3.6 16.6 - - - +
25B LEU* 4.7 4.0 - - + -
120B THR* 4.5 26.0 - - + +
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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