Contacts of the strand formed by residues 172 - 179 (chain C) in PDB entry 1WNT
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 ILE 172 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206B LEU* 4.9 0.6 - - - +
119C ALA* 4.0 23.8 - - + +
122C LEU* 3.8 31.4 - - + -
123C ILE* 4.2 12.8 - - + -
127C VAL 4.7 1.3 - - - +
129C GLY* 3.3 24.0 - - - +
130C ALA 4.2 1.8 - - - +
131C ILE* 4.4 14.1 - - + -
164C ALA 4.9 0.5 - - - +
167C LEU* 3.4 40.8 + - + +
168C GLY* 3.7 7.1 + - - -
170C HIS* 3.0 20.8 - - + +
171C LYS* 1.3 79.3 - - - +
173C ARG* 1.3 70.7 + - - +
174C VAL* 4.1 1.2 + - - +
231C THR* 4.8 0.7 + - - -
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Residues in contact with ARG 173 (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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206B LEU* 4.0 16.8 - - + -
129C GLY 3.0 12.1 + - - +
130C ALA* 3.2 9.4 - - + +
131C ILE* 2.6 32.7 + - - +
171C LYS 3.9 3.1 + - - +
172C ILE* 1.3 74.4 - - - +
174C VAL* 1.3 56.4 + - - +
175C ASN* 3.3 11.2 - - - +
222C LEU 3.0 23.8 + - - -
223C LEU 4.0 4.8 + - - -
224C SER 2.9 30.3 + - - -
225C ASP* 4.5 2.6 - - - +
227C SER* 2.9 24.0 + - - -
228C GLY* 3.3 29.4 - - - -
230C THR 3.0 23.8 + - - +
231C THR* 3.6 14.8 - - - +
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Residues in contact with VAL 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C ILE* 3.5 14.6 - - + -
133C ASN* 3.6 22.0 - - - +
160C THR* 3.8 14.4 - - - +
163C MET* 3.7 35.4 - - + +
164C ALA* 3.8 4.0 - - - +
167C LEU* 3.4 34.5 - - + -
172C ILE 4.3 0.9 - - - +
173C ARG* 1.3 79.2 - - - +
175C ASN* 1.3 60.7 + - - +
231C THR* 3.0 6.0 + - - -
232C GLY* 2.5 36.4 + - - -
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Residues in contact with ASN 175 (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 ILE 3.1 9.1 + - - +
132C VAL* 3.1 9.2 - - - +
133C ASN* 2.6 30.6 + - - -
160C THR* 3.7 6.5 - - - -
173C ARG* 3.3 17.4 - - - +
174C VAL* 1.3 81.1 - - - +
176C ALA* 1.3 53.7 - - - +
222C LEU* 3.8 33.2 + - + +
230C THR 2.9 21.0 + - - -
231C THR* 2.8 26.0 + - - +
233C SER* 3.1 25.8 + - - +
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Residues in contact with ALA 176 (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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132C VAL* 5.5 0.2 - - - -
133C ASN* 3.1 16.6 - - + +
135C SER* 4.2 4.7 - - - -
156C LEU* 5.4 0.2 - - + -
157C ASP* 4.2 15.7 - - - +
160C THR* 3.7 19.5 - - + +
175C ASN* 1.3 76.0 - - - +
177C VAL* 1.3 54.8 + - - +
178C ASN* 3.7 9.2 - - - +
222C LEU* 4.2 4.4 - - - +
233C SER* 2.6 20.8 + - - +
234C THR* 3.1 2.2 - - + -
235C LEU* 2.8 30.1 + - - +
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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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132C VAL* 4.2 5.6 - - + -
133C ASN 3.1 10.0 + - - +
134C VAL* 3.7 26.5 - - + -
135C SER* 2.8 31.2 + - - -
176C ALA* 1.3 71.6 - - - +
178C ASN* 1.3 66.3 + - - +
179C PRO* 3.4 14.1 - - + +
215C VAL* 4.5 7.2 - - + -
218C ALA* 4.3 14.8 - - + -
219C ILE* 4.1 14.1 - - + -
222C LEU* 4.8 6.1 - - + -
235C LEU* 3.3 7.9 - - - +
237C VAL* 3.5 27.6 - - + -
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Residues in contact with ASN 178 (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 SER* 3.7 3.0 + - - -
136C SER 3.1 25.9 + - - +
137C GLN* 4.0 1.0 - - - +
139C SER* 3.4 14.1 + - - -
157C ASP* 3.5 15.4 + - - -
176C ALA* 3.7 1.9 - - - +
177C VAL* 1.3 85.5 + - - +
179C PRO* 1.3 62.8 - - - +
234C THR* 3.4 23.7 - - - -
235C LEU 2.9 8.1 + - - -
236C PRO* 3.3 5.7 - - + +
237C VAL* 2.8 24.8 + - - -
238C GLU* 3.9 7.1 - - - +
242C TRP* 3.2 30.3 - - + -
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Residues in contact with PRO 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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19C ILE* 5.6 0.9 - - + -
134C VAL* 4.6 7.4 - - + -
135C SER 3.6 14.8 - - - +
136C SER* 3.8 0.7 - - - -
137C GLN* 3.0 21.0 + - - +
177C VAL* 3.4 19.0 - - + +
178C ASN* 1.3 89.9 - - - +
180C THR* 1.3 69.7 + - - +
182C VAL* 4.6 5.6 - - + -
210C ALA* 5.5 2.0 - - + -
215C VAL* 4.2 25.6 - - + -
237C VAL* 3.3 20.4 - - + +
2245C NAP 3.7 17.7 - - + +
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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