Contacts of the strand formed by residues 178 - 187 (chain C) in PDB entry 5T78
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 TYR 178 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110C GLU* 4.4 18.4 + - - +
143C ASN* 3.0 5.6 + - - -
144C PHE* 2.8 55.4 + - + +
145C TYR* 3.8 27.4 - + - -
147C LYS* 3.7 55.1 - - + +
168C TRP* 5.0 1.3 - - + -
169C THR* 3.7 22.2 - - - +
170C ASP* 4.2 0.7 - - - -
171C GLN* 3.6 48.0 + - + +
177C THR* 1.3 75.6 - - - +
179C SER* 1.3 64.5 + - - +
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Residues in contact with SER 179 (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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141C LEU 3.2 11.2 - - - -
142C ASN* 3.2 17.8 + - - +
143C ASN* 2.8 28.9 + - - -
144C PHE* 3.7 4.9 - - - -
168C TRP* 3.6 5.2 - - - +
169C THR* 3.0 44.1 + - - -
177C THR* 5.1 0.2 + - - -
178C TYR* 1.3 73.6 + - - +
180C MET* 1.3 63.4 + - - +
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Residues in contact with MET 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C PHE* 3.8 1.9 - - - -
141C LEU* 2.8 55.7 + - + +
142C ASN* 4.7 1.5 - - - +
144C PHE* 3.8 2.0 - - + -
149C ILE* 3.9 23.8 - - + +
151C VAL* 4.3 9.0 - - + -
166C ASN* 3.6 24.5 - - + +
167C SER 3.2 13.2 - - - +
168C TRP* 3.3 50.7 - - + -
169C THR* 4.8 0.9 - - - +
179C SER* 1.3 76.8 - - - +
181C SER* 1.3 73.7 + - - +
182C SER* 4.0 8.1 - - - -
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Residues in contact with SER 181 (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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138C VAL* 4.9 2.7 - - - -
139C CYS 3.4 4.3 - - - -
140C PHE* 3.7 28.7 - - - -
165C LEU 3.8 1.7 + - - +
166C ASN* 3.4 4.0 - - - -
167C SER* 3.0 40.7 + - - -
180C MET* 1.3 78.0 - - - +
182C SER* 1.3 61.0 + - - +
183C THR* 4.8 5.5 + - - -
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Residues in contact with SER 182 (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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138C VAL* 3.4 3.3 - - - +
139C CYS* 2.9 38.4 + - - -
141C LEU* 5.3 0.9 - - - -
151C VAL* 3.7 20.2 - - - +
153C TRP* 2.8 34.8 + - - -
164C VAL* 3.7 3.6 - - - +
165C LEU 3.6 0.4 - - - -
166C ASN* 2.8 23.4 + - - -
180C MET* 4.0 4.7 - - - -
181C SER* 1.3 73.4 - - - +
183C THR* 1.3 60.8 + - - +
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Residues in contact with THR 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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136C SER* 4.0 20.4 - - - +
137C VAL 3.4 5.6 - - - +
138C VAL* 3.8 17.0 - - + +
163C GLY 3.4 4.0 - - - +
164C VAL* 3.5 1.5 - - - -
165C LEU* 3.0 46.6 + - + +
181C SER* 4.8 6.1 + - - -
182C SER* 1.3 77.1 + - - +
184C LEU* 1.3 59.3 + - - +
185C THR* 3.7 18.7 + - - +
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Residues in contact with LEU 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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135C ALA 3.8 1.2 - - - +
136C SER* 3.4 1.6 - - - -
137C VAL* 2.9 45.1 + - + +
153C TRP* 3.9 48.2 - - + +
155C ILE* 3.9 28.5 - - + -
160C ARG* 3.8 13.9 - - + -
162C ASN 3.7 23.3 - - - +
163C GLY 3.5 5.6 - - - +
164C VAL* 3.9 9.9 - - + +
183C THR* 1.3 71.9 - - - +
185C THR* 1.3 63.8 + - - +
186C LEU* 4.0 19.9 + - + -
197C TYR* 5.1 1.3 - - + -
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Residues in contact with THR 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 GLN* 5.3 1.3 - - - +
134C GLY* 6.1 0.9 - - - -
135C ALA 3.7 5.2 - - - +
136C SER* 3.5 21.3 + - - +
160C ARG* 4.7 2.6 + - - -
163C GLY* 3.1 25.8 + - - +
165C LEU* 6.1 0.5 - - - +
183C THR* 3.7 11.4 + - - +
184C LEU* 1.3 73.2 - - - +
186C LEU* 1.3 77.3 + - - +
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Residues in contact with LEU 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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134C GLY* 3.9 2.3 - - - -
135C ALA 2.8 34.0 + - - +
137C VAL* 4.6 6.3 - - + -
155C ILE* 4.0 9.6 - - + -
160C ARG* 3.4 38.1 - - - +
184C LEU* 4.2 17.5 - - + +
185C THR* 1.3 85.0 - - - +
187C THR* 1.3 68.9 + - - +
190C GLU* 3.5 13.9 - - - +
191C TYR* 4.2 21.5 - - + +
197C TYR* 3.7 29.6 - - + +
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Residues in contact with THR 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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133C GLY 4.1 6.1 - - - -
134C GLY* 4.8 0.7 - - - -
135C ALA* 4.2 1.1 - - - -
186C LEU* 1.3 78.9 - - - +
188C LYS* 1.3 65.1 + - - +
189C ASP* 3.5 8.5 + - - +
190C GLU* 3.0 29.6 + - + +
191C TYR* 3.0 22.9 + - - +
193C ARG* 5.3 0.2 + - - -
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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