Contacts of the strand formed by residues 155 - 160 (chain A) in PDB entry 3TQI
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 GLU 155 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ASN* 2.7 33.7 + - - +
150A LEU* 3.7 12.3 - - - -
153A GLY 5.4 1.1 - - - +
154A PHE* 1.3 77.6 - - - +
156A ALA* 1.3 71.4 + - - +
157A THR* 3.2 4.5 + - - +
168A MET* 3.5 3.8 - - - -
169A ALA* 3.1 32.0 + - + +
170A ASP 5.5 0.4 - - - +
171A PHE* 3.7 19.1 - - + -
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Residues in contact with ALA 156 (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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116A LEU* 4.0 28.4 - - + +
117A ASN* 4.8 1.6 - - - +
150A LEU* 3.6 15.3 - - + +
155A GLU* 1.3 79.3 - - - +
157A THR* 1.3 59.9 + - - +
158A ALA 3.5 2.0 - - - +
164A PRO 4.5 13.9 - - - +
165A LEU* 4.6 9.9 - - + -
167A ALA 3.6 7.4 - - - +
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Residues in contact with THR 157 (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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115A VAL* 3.9 1.7 - - - +
116A LEU 2.6 26.8 + - - +
117A ASN* 3.2 21.3 + - - +
119A ALA* 3.9 8.5 - - - +
121A LEU* 6.3 1.1 - - + -
122A PHE* 3.6 21.4 - - + -
155A GLU* 3.2 5.6 + - - -
156A ALA* 1.3 72.8 - - - +
158A ALA* 1.3 64.6 + - - +
167A ALA* 2.9 40.1 + - + -
168A MET 3.3 15.9 - - - +
169A ALA* 4.2 10.0 - - + +
171A PHE* 5.3 1.8 - - - -
176A PHE* 6.0 0.7 - - + -
177A GLY 4.8 0.2 - - - +
178A LEU* 5.9 0.2 - - + -
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Residues in contact with ALA 158 (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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113A LEU* 3.9 27.6 - - + -
114A ARG 3.4 11.7 - - - +
115A VAL* 4.5 2.0 - - - -
116A LEU* 4.0 7.0 - - - +
122A PHE* 4.3 5.2 - - + -
156A ALA* 3.5 2.6 - - - +
157A THR* 1.3 82.5 + - - +
159A CYS* 1.3 62.0 + - - +
164A PRO 4.1 0.5 - - - +
165A LEU* 3.9 3.5 - - - -
166A ALA* 3.0 21.0 + - - -
167A ALA* 3.2 26.5 + - + +
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Residues in contact with CYS 159 (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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113A LEU* 3.7 2.8 - - - +
114A ARG* 2.9 70.5 + - - +
116A LEU* 4.1 12.3 - - + -
158A ALA* 1.3 73.9 - - - +
160A THR* 1.3 69.3 + - - +
163A SER 3.6 6.3 - - - +
164A PRO* 3.2 26.7 - - + +
166A ALA* 4.0 8.7 - - - -
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Residues in contact with THR 160 (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* 4.1 11.8 - - + +
112A GLN 3.0 25.6 + - - -
113A LEU* 4.7 3.6 - - - -
114A ARG* 5.8 0.4 - - - -
141A MET* 3.6 20.0 - - + -
143A HIS* 6.2 1.8 - - + -
159A CYS* 1.3 81.0 - - - +
161A ASP* 1.3 70.5 + - - +
162A ASN* 3.5 9.0 - - + +
163A SER* 2.9 53.1 + - - +
164A PRO* 4.0 1.4 - - - +
166A ALA* 4.4 0.6 - - - +
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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