Contacts of the helix formed by residues 152 - 161 (chain A) in PDB entry 3TJK
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 SER 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A VAL 3.8 0.8 + - - -
151A ASP* 1.3 76.6 - - - +
153A GLN* 1.3 62.2 + - - +
154A PHE* 3.1 18.6 + - - +
155A THR* 3.0 27.0 + - - -
156A HIS* 3.0 25.8 + - - -
178A SER* 3.4 7.0 - - - -
180A LEU* 3.8 28.8 - - - +
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Residues in contact with GLN 153 (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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91A THR* 4.0 34.2 + - + +
93A VAL* 3.5 5.3 - - + +
98A PHE* 3.3 43.1 - - + -
152A SER* 1.3 77.4 - - - +
154A PHE* 1.3 81.7 + - + +
156A HIS* 3.4 10.9 + - + +
157A LEU 3.0 22.9 + - - -
178A SER* 3.6 20.1 + - - -
180A LEU* 4.6 7.3 - - - +
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Residues in contact with PHE 154 (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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98A PHE* 3.5 31.4 - + - -
152A SER* 3.1 13.4 + - - +
153A GLN* 1.3 98.6 - - + +
155A THR* 1.3 57.4 + - - +
157A LEU* 3.4 4.7 + - + +
158A ALA* 3.0 26.9 + - - +
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Residues in contact with THR 155 (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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119A ASP* 3.5 27.4 - - + +
120A PHE* 3.9 16.1 - - + -
151A ASP* 3.9 16.2 - - - +
152A SER* 3.0 21.7 + - - -
154A PHE* 1.3 73.6 - - - +
156A HIS* 1.3 65.0 + - - +
158A ALA* 3.2 7.2 + - - +
159A TRP* 2.9 22.3 + - - +
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Residues in contact with HIS 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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93A VAL* 3.6 11.4 - - + -
116A TYR* 3.1 22.4 + - - -
119A ASP* 2.5 30.5 + - - -
149A SER* 3.1 19.1 - - - -
151A ASP* 3.7 10.1 - - + -
152A SER 3.0 13.5 + - - -
153A GLN* 3.5 11.2 - - - +
155A THR* 1.3 75.0 - - - +
157A LEU* 1.3 57.4 + - - +
159A TRP* 3.4 2.9 + - - +
160A ILE* 3.0 34.8 + - - +
176A LEU* 3.2 38.9 - - + +
177A LEU 2.9 25.7 + - - -
178A SER* 3.7 11.5 - - - -
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Residues in contact with LEU 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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93A VAL* 4.0 11.6 - - + +
96A GLY* 3.8 35.4 - - - +
98A PHE* 4.2 24.2 - - + -
153A GLN 3.0 16.9 + - - +
154A PHE* 3.8 5.8 - - + +
155A THR 3.2 0.2 - - - -
156A HIS* 1.3 72.9 - - - +
158A ALA* 1.3 60.2 - - - +
160A ILE* 3.3 6.8 + - + +
161A ASN* 2.9 49.2 + - - +
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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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120A PHE* 3.8 13.7 - - + -
154A PHE 3.0 14.7 + - - +
155A THR* 3.2 9.8 + - - +
157A LEU* 1.3 75.8 - - - +
159A TRP* 1.3 56.1 + - - +
161A ASN* 3.2 9.5 + - - +
162A THR* 2.7 32.4 + - - -
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Residues in contact with TRP 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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116A TYR* 3.6 13.2 - + - -
119A ASP* 3.3 33.2 - - + +
120A PHE* 3.3 52.8 - + + +
121A THR 4.7 0.4 - - - -
124A CYS* 4.1 2.7 - - + -
125A PRO* 3.6 39.9 - - + -
128A ILE* 3.5 33.9 - - + -
155A THR 2.9 16.9 + - - +
156A HIS 3.5 3.1 - - - +
158A ALA* 1.3 76.9 - - - +
160A ILE* 1.3 62.1 + - - +
162A THR* 3.2 10.5 + - - -
167A GLY 2.9 19.3 + - - -
168A GLY* 3.6 8.0 - - - -
169A LEU* 2.9 44.5 + - + -
176A LEU* 4.2 3.4 - - + -
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Residues in contact with ILE 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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93A VAL* 3.5 32.8 - - + +
96A GLY* 5.4 8.1 - - - +
156A HIS 3.0 20.8 + - - +
157A LEU* 3.7 11.0 - - + +
158A ALA 3.3 0.2 - - - -
159A TRP* 1.3 75.1 - - - +
161A ASN* 1.3 65.6 + - - +
162A THR 3.1 3.0 + - - -
169A LEU* 4.1 6.1 - - + -
170A GLY* 3.2 44.6 - - - +
171A PRO* 4.4 8.5 - - + +
172A ILE* 4.0 23.3 - - + +
176A LEU* 3.8 25.4 - - + -
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Residues in contact with ASN 161 (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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157A LEU* 2.9 43.5 + - - +
158A ALA* 3.2 9.1 + - - +
160A ILE* 1.3 81.2 - - - +
162A THR* 1.3 56.5 + - - +
163A PRO* 4.0 5.5 - - - +
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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