Contacts of the helix formed by residues 152 - 161 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118B LEU* 4.0 21.0 - - - +
119B ASP 4.6 2.1 + - - -
151B ASP* 4.6 3.3 + - - -
151C ASP* 1.3 78.5 - - - +
153C GLN* 1.3 65.0 + - - +
154C PHE* 3.2 10.2 + - - +
155C THR* 3.0 28.6 + - - -
156C HIS* 3.0 22.7 + - - -
178C SER* 3.4 7.0 - - - -
180C LEU* 3.8 29.2 - - - +
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Residues in contact with GLN 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C THR* 3.9 34.3 + - + +
92C ALA 5.2 0.2 - - - -
93C VAL* 3.5 12.1 - - + +
98C PHE* 3.4 46.5 - - + +
152C SER* 1.3 77.0 - - - +
154C PHE* 1.3 81.5 + - + +
156C HIS* 3.3 2.6 + - - -
157C LEU 2.9 23.4 + - - -
178C SER* 3.6 19.2 + - - -
180C LEU* 4.3 7.6 - - - +
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Residues in contact with PHE 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A PRO* 4.6 6.1 - - + -
118B LEU* 3.8 23.8 - - + -
119B ASP 4.1 6.5 - - - +
120B PHE* 3.8 23.2 - - - +
121B THR* 3.6 24.5 - - + -
122B PHE* 3.7 30.1 - + - -
98C PHE* 3.6 29.8 - + - -
152C SER* 3.1 5.7 - - - +
153C GLN* 1.3 98.7 - - + +
155C THR* 1.3 65.7 + - - +
157C LEU* 3.3 4.1 + - - +
158C ALA* 3.0 22.2 + - - +
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Residues in contact with THR 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ASP 4.4 2.6 + - - -
120B PHE* 4.1 11.7 - - - +
151B ASP* 3.7 8.5 + - - -
155B THR* 3.3 43.5 - - + +
119C ASP* 3.5 22.9 - - + +
120C PHE* 3.9 7.4 - - + -
151C ASP* 4.0 11.0 - - - +
152C SER* 3.0 21.0 + - - -
154C PHE* 1.3 77.9 - - - +
156C HIS* 1.3 62.1 + - - +
158C ALA* 3.1 2.4 + - - +
159C TRP* 3.0 21.5 + - - +
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Residues in contact with HIS 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C VAL* 3.7 11.0 - - + -
116C TYR* 3.2 9.6 + - - -
119C ASP* 2.6 38.6 + - - -
148C CYS* 5.3 0.2 - - - -
149C SER* 3.2 22.1 + - - -
151C ASP* 3.8 8.1 - - + +
152C SER 3.0 14.9 + - - -
153C GLN* 3.5 9.8 - - - +
155C THR* 1.3 76.0 - - - +
157C LEU* 1.3 62.4 + - - +
159C TRP* 3.3 3.0 + - - +
160C ILE* 3.0 28.4 + - - +
176C LEU* 3.3 33.6 + - + +
177C LEU 2.9 33.3 - - - -
178C SER* 3.7 12.6 - - - -
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Residues in contact with LEU 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A PRO* 3.6 37.2 - - + -
93C VAL* 4.1 16.1 - - + +
96C GLY* 3.7 31.6 - - - +
98C PHE* 4.2 12.3 - - + -
153C GLN 2.9 17.1 + - - +
154C PHE* 3.8 5.2 - - - +
155C THR 3.2 0.2 - - - -
156C HIS* 1.3 74.1 - - - +
158C ALA* 1.3 66.6 + - - +
160C ILE* 3.4 11.4 + - + +
161C ASN* 3.0 41.9 + - - +
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Residues in contact with ALA 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B PHE* 3.5 46.9 - - + -
120C PHE* 3.9 2.9 - - + -
154C PHE 3.0 12.2 + - - +
155C THR 3.1 8.0 + - - +
157C LEU* 1.3 76.6 - - - +
159C TRP* 1.3 52.5 + - - +
161C ASN* 3.1 21.9 + - - +
162C THR* 2.8 24.1 + - - -
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Residues in contact with TRP 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C TYR* 3.5 20.2 - + - -
119C ASP* 3.2 36.3 - - - +
120C PHE* 3.3 52.5 - + + +
124C CYS* 4.1 2.2 - - + -
125C PRO* 3.6 40.6 - - + -
128C ILE* 3.6 25.1 - - + -
155C THR 3.0 15.5 + - - +
156C HIS 3.6 3.4 - - - +
158C ALA* 1.3 75.0 - - - +
160C ILE* 1.3 64.2 + - - +
162C THR* 3.1 13.1 + - - -
167C GLY 2.9 18.6 + - - -
168C GLY* 3.7 9.2 - - - -
169C LEU* 3.1 40.6 + - + -
176C LEU* 4.4 3.1 - - + -
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Residues in contact with ILE 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C VAL* 3.7 31.9 - - + +
96C GLY* 5.7 5.6 - - - +
156C HIS 3.0 21.4 + - - +
157C LEU* 3.7 11.4 - - + +
159C TRP* 1.3 75.3 - - - +
161C ASN* 1.3 65.6 + - - +
162C THR 3.1 4.5 + - - -
169C LEU* 4.1 4.3 - - + -
170C GLY* 3.3 39.5 + - - +
171C PRO* 4.3 10.5 - - + +
172C ILE* 4.1 24.9 - - + +
176C LEU* 3.8 22.7 - - + -
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Residues in contact with ASN 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C LEU* 3.0 39.1 + - - +
158C ALA* 3.1 13.1 + - - +
160C ILE* 1.3 82.3 - - - +
162C THR* 1.3 57.9 + - - +
163C PRO* 3.7 7.2 - - - +
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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