Contacts of the strand formed by residues 176 - 187 (chain C) in PDB entry 4A12
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 LEU 176 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141C ILE* 3.3 44.7 - - + +
142C GLU* 3.6 9.0 - - - +
169C LYS* 3.8 25.4 - - + -
170C SER 3.6 8.7 - - - +
171C TYR* 3.5 28.0 - - + +
175C THR* 1.3 70.2 - - - +
177C VAL* 1.3 58.9 + - - +
178C PHE 3.4 22.2 - - - +
179C LYS* 4.4 15.0 - - + -
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Residues in contact with VAL 177 (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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114C LEU* 5.8 0.2 - - - +
140C PHE* 3.6 5.0 - - - +
141C ILE* 2.9 25.9 + - - -
142C GLU* 3.2 34.0 + - + +
143C LYS 5.1 2.7 - - - +
144C VAL* 3.7 29.4 - - + +
150C VAL* 4.5 3.4 - - + -
170C SER* 3.0 25.4 + - - +
171C TYR* 4.1 0.9 - - - -
172C VAL* 3.9 27.6 - - + -
175C THR* 3.4 16.8 - - + +
176C LEU* 1.3 72.8 - - - +
178C PHE* 1.3 63.7 + - + +
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Residues in contact with PHE 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C LEU* 4.1 21.1 - - + -
115C PHE* 4.3 10.5 - - - -
118C ALA* 3.7 29.4 - - + -
138C ILE* 3.5 38.8 - - + -
139C GLN 3.3 14.8 - - - -
140C PHE* 3.8 33.0 - + + -
141C ILE* 3.7 3.8 - - - -
168C VAL* 4.5 4.3 - - + -
169C LYS* 3.6 0.2 - - - -
170C SER* 2.9 54.4 + - - -
176C LEU* 3.4 9.4 - - - +
177C VAL* 1.3 80.5 - - - +
179C LYS* 1.3 60.4 + - - +
180C GLY* 3.9 17.0 - - - -
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Residues in contact with LYS 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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138C ILE* 3.4 2.6 - - - +
139C GLN* 2.7 65.3 + - + +
141C ILE* 3.5 14.6 - - + +
167C GLU* 6.5 1.1 - - + -
168C VAL 3.4 10.8 - - - +
169C LYS* 4.3 23.3 - - + +
176C LEU* 4.4 15.0 - - + -
178C PHE* 1.3 77.5 - - - +
180C GLY* 1.3 59.5 + - - +
181C ASN* 4.8 15.5 - - - +
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Residues in contact with GLY 180 (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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137C SER 3.3 8.5 - - - -
138C ILE* 3.9 13.0 - - - -
167C GLU* 3.5 2.6 - - - -
168C VAL* 2.7 43.4 + - - +
178C PHE* 3.9 7.4 - - - -
179C LYS* 1.3 76.1 - - - +
181C ASN* 1.3 65.0 + - - -
182C PHE* 3.7 7.2 - - - -
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Residues in contact with ASN 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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135C GLU 4.6 0.2 - - - -
136C SER* 3.2 8.5 + - - -
137C SER* 2.8 51.3 + - - +
139C GLN* 5.7 1.0 + - - -
157C VAL* 5.8 0.2 - - - +
166C VAL 3.4 4.0 - - - +
167C GLU* 3.3 29.2 - - - +
179C LYS* 4.8 16.4 - - - +
180C GLY* 1.3 79.3 - - - +
182C PHE* 1.3 60.4 + - - +
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Residues in contact with PHE 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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115C PHE* 3.5 24.9 - + - -
118C ALA* 3.7 22.2 - - + -
119C ASN* 3.7 22.2 - - - -
122C CYS* 3.7 18.4 - - - -
133C THR* 4.0 18.4 - - + -
135C GLU 3.7 1.6 - - - -
136C SER* 3.4 21.5 - - - -
138C ILE* 4.3 1.8 - - + -
164C TYR 3.5 1.2 - - - +
165C TYR* 3.4 7.7 - - - +
166C VAL* 2.7 42.3 + - + +
168C VAL* 3.8 25.6 - - + -
180C GLY* 3.7 21.3 - - - -
181C ASN* 1.3 78.1 - - - +
183C LYS* 1.3 59.1 + - - +
184C MSE 3.8 9.4 - - - -
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Residues in contact with LYS 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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133C THR* 3.8 1.0 - - - -
134C HIS* 2.8 37.9 + - + +
135C GLU* 2.9 57.6 + - + +
163C HIS* 3.6 32.4 - - + +
164C TYR 3.8 2.5 - - - -
165C TYR* 3.3 40.6 + - + -
182C PHE* 1.3 70.0 - - - +
184C MSE 1.3 55.7 - - - +
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Residues in contact with MSE 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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119C ASN 4.7 0.7 - - - +
122C CYS* 3.8 25.1 - - + -
123C VAL* 3.8 16.2 - - + +
126C ILE* 3.7 28.0 - - + -
131C VAL* 3.7 26.2 - - + -
132C LEU 3.6 2.5 - - - +
133C THR* 3.4 44.9 - - - +
163C HIS* 3.3 3.6 - - - -
164C TYR* 2.7 47.2 + - + +
166C VAL* 4.0 10.8 - - + -
182C PHE* 4.0 12.3 - - + -
183C LYS* 1.3 71.8 - - - +
185C PHE* 1.3 63.4 + - - +
186C TYR* 3.7 0.4 + - + -
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Residues in contact with PHE 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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130C THR* 5.1 5.6 - - - -
131C VAL* 3.4 7.1 - - - +
132C LEU* 2.7 59.0 + - + +
134C HIS* 3.4 42.2 - + + +
162C LYS* 3.2 47.3 - - + -
163C HIS* 3.7 8.9 - + + -
183C LYS 3.8 0.8 + - - -
184C MSE 1.3 72.9 - - - +
186C TYR* 1.3 68.5 + - - +
187C ASP* 3.9 29.2 - - + -
143D LYS* 6.0 2.5 - - - -
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Residues in contact with TYR 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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126C ILE* 4.5 4.5 - - + -
128C GLN* 3.7 33.9 - - + -
130C THR 3.4 7.0 - - - +
131C VAL* 5.0 0.4 - - + -
159C GLN* 3.2 18.2 + - - -
160C THR 2.7 30.0 + - - -
161C ALA* 3.1 22.4 + - - +
162C LYS* 3.1 26.9 + - - +
163C HIS 3.4 18.8 - - - -
164C TYR* 3.4 31.9 - + + -
184C MSE 6.2 0.2 - - + -
185C PHE* 1.3 85.7 - - - +
187C ASP* 1.3 63.1 + - - +
188C LYS* 3.8 31.3 + - + -
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Residues in contact with ASP 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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128C GLN* 4.5 1.3 - - - +
129C PRO* 3.4 15.5 - - - +
130C THR* 3.0 33.3 + - - +
185C PHE* 3.9 20.0 - - + -
186C TYR* 1.3 75.1 - - - +
188C LYS* 1.3 65.3 + - - +
189C ARG* 3.0 31.0 + - - +
190C GLY 4.2 0.9 + - - -
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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