Contacts of the strand formed by residues 182 - 189 (chain C) in PDB entry 3TQS
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 182 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C MSE 3.8 20.1 - - - +
133C LEU 3.3 13.1 + - - -
134C GLN* 4.2 6.3 + - - +
135C LYS* 3.7 4.0 - - - +
168C THR* 3.4 7.8 - - - +
169C VAL* 2.8 34.7 + - - -
174C PHE* 3.7 19.8 - - - -
178C PRO* 4.3 6.9 - - - +
180C VAL 3.7 5.7 + - - -
181C GLU* 1.3 75.0 + - - +
183C ALA* 1.3 65.7 + - - +
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Residues in contact with ALA 183 (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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131C PHE 3.5 1.4 - - - +
132C MSE 3.5 9.0 - - - -
133C LEU 2.9 30.9 + - - +
135C LYS* 4.2 12.1 - - + -
138C VAL* 3.9 21.9 - - + +
165C TYR* 3.9 20.9 - - + -
167C PHE 3.2 13.7 - - - +
168C THR* 4.2 0.9 - - - +
169C VAL 4.4 0.9 - - - +
182C SER* 1.3 79.4 - - - +
184C ILE* 1.3 61.0 + - - +
185C ILE 3.9 0.2 + - - -
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Residues in contact with ILE 184 (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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24C ILE* 3.7 27.1 - - + -
27C ALA* 5.1 3.6 - - + -
130C HIS* 5.0 8.7 - - + -
131C PHE 3.3 15.7 - - - +
132C MSE 3.8 30.7 - - + +
138C VAL* 4.8 0.2 - - - -
165C TYR* 3.8 4.5 - - - -
166C LEU* 2.9 50.4 + - + +
167C PHE* 2.9 48.5 + - + +
169C VAL* 4.6 0.4 - - + +
183C ALA* 1.3 73.5 - - - +
185C ILE* 1.3 68.3 + - - +
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Residues in contact with ILE 185 (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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129C MSE 3.7 0.7 - - - +
130C HIS* 3.3 5.9 - - - +
131C PHE* 3.0 36.7 + - + +
133C LEU* 3.6 27.4 - - + -
138C VAL* 3.9 17.5 - - + -
141C ILE* 3.5 43.1 - - + -
142C THR* 4.0 13.5 - - + -
163C ASN* 4.3 3.1 - - + -
164C THR 3.4 15.5 - - - +
166C LEU* 4.6 0.4 - - - +
184C ILE* 1.3 78.3 - - - +
186C ARG* 1.3 70.6 + - - +
187C LEU* 3.9 15.2 - - + +
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Residues in contact with ARG 186 (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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27C ALA* 3.0 33.3 + - - +
129C MSE 3.3 5.4 - - - +
130C HIS* 2.9 26.9 + - + +
162C ASP 3.8 0.2 - - - +
163C ASN* 3.2 4.5 - - - -
164C THR* 2.8 48.3 + - - +
166C LEU* 3.7 33.6 - - + +
185C ILE* 1.3 76.5 - - - +
187C LEU* 1.3 63.7 + - - +
188C ILE* 3.5 32.8 - - + -
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Residues in contact with LEU 187 (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 LEU* 4.1 23.1 - - + -
120C PHE* 4.1 20.2 - - + -
128C ASP* 3.6 1.9 - - - -
129C MSE 2.9 64.1 + - + +
131C PHE* 4.1 12.8 - - + -
133C LEU* 5.9 0.2 - - + -
141C ILE* 4.5 11.9 - - + -
157C ALA* 4.9 0.2 - - + -
161C CYS* 4.0 1.8 - - - -
162C ASP 3.6 4.0 - - - -
163C ASN* 3.2 23.1 - - - +
185C ILE* 3.9 26.5 - - + +
186C ARG* 1.3 78.8 - - - +
188C ILE* 1.3 63.6 + - - +
189C PRO* 3.9 2.6 - - - +
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Residues in contact with ILE 188 (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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127C GLU 4.4 5.6 - - - +
128C ASP* 3.3 28.5 - - + +
161C CYS* 3.8 4.2 - - - +
162C ASP* 2.8 47.2 + - + +
186C ARG* 3.5 35.0 - - + -
187C LEU* 1.3 71.7 - - - +
189C PRO* 1.3 83.1 - - + +
190C ARG* 3.3 0.5 + - - -
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Residues in contact with PRO 189 (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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123C ILE* 3.6 32.3 - - + +
126C ILE 3.5 22.7 - - - +
127C GLU 3.3 20.9 - - - +
128C ASP* 4.0 1.6 - - - -
129C MSE 4.2 10.5 - - + -
160C PHE 3.3 9.6 - - - +
161C CYS* 3.9 2.0 - - - -
162C ASP* 5.4 0.2 - - - +
187C LEU 3.9 6.1 - - - +
188C ILE* 1.3 95.4 - - + +
190C ARG* 1.3 65.1 + - - +
191C HIS* 3.8 21.9 + - + +
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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