Contacts of the strand formed by residues 180 - 186 (chain C) in PDB entry 3H3B
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 GLU 180 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104C PHE* 4.6 0.4 - - - -
171C VAL* 3.3 5.3 - - - -
172C LYS* 2.8 64.5 + - + +
174C ASN* 4.7 5.9 + - - -
177C LYS* 5.9 3.2 - - - +
178C SER* 4.1 9.0 - - - +
179C PRO* 1.3 76.7 - - - +
181C TRP* 1.3 61.7 + - - +
182C ILE* 3.2 2.9 + - - +
195C ASN* 5.5 3.6 - - - +
197C LYS* 2.7 40.6 + - - +
198C PHE* 4.1 20.0 - - + -
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Residues in contact with TRP 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C TYR* 3.5 26.0 - + + -
101C PRO* 3.7 25.4 - - + -
102C TRP* 3.0 55.8 + + + +
103C THR* 5.7 0.4 - - - +
104C PHE* 4.2 11.3 - - + -
169C ASN* 3.0 31.8 - - + +
170C TRP 3.9 4.9 - - - -
171C VAL* 4.4 6.3 - - + -
179C PRO 4.2 0.6 - - - -
180C GLU* 1.3 68.1 - - - +
182C ILE* 1.3 64.9 + - - +
183C GLY* 3.5 25.1 + - - -
184C HIS* 3.4 35.0 - + - -
193C THR* 4.0 9.2 - - + -
194C TYR 4.4 2.0 - - - -
195C ASN* 3.2 37.1 + - + +
198C PHE* 4.4 0.6 - - - -
241C MET* 4.4 9.9 - - + -
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Residues in contact with ILE 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C TRP* 2.8 18.9 + - + +
171C VAL 3.9 4.5 - - - +
172C LYS* 3.8 22.0 - - + +
180C GLU 3.9 1.3 - - - +
181C TRP* 1.3 73.0 - - - +
183C GLY* 1.3 57.5 + - - +
194C TYR* 3.7 5.6 - - + +
195C ASN* 2.9 23.5 + - - +
198C PHE* 3.7 33.7 - - + +
202C ALA* 3.6 29.2 - - + -
204C PHE* 4.0 9.4 - - + -
215C MET* 3.8 15.0 - - + -
217C LEU* 5.2 0.9 - - + -
228C TYR* 3.6 36.8 - - + -
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Residues in contact with GLY 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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169C ASN* 3.4 2.8 - - - -
170C TRP* 2.8 25.8 + - - +
181C TRP* 3.3 24.6 + - - -
182C ILE* 1.3 79.8 - - - +
184C HIS* 1.3 59.0 + - - -
193C THR 3.1 14.1 - - - -
204C PHE* 3.6 9.1 - - - -
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Residues in contact with HIS 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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102A ASN* 5.3 0.9 - - + -
103A ASN* 3.9 13.3 + - - -
167A SER 6.1 0.4 - - - -
100C TYR* 2.8 41.2 + + - -
102C TRP* 4.0 11.6 - + - -
167C PHE* 4.6 20.0 - + + -
168C ILE 3.2 15.7 - - - +
169C ASN* 3.2 32.5 - - - +
181C TRP* 3.4 9.5 - + - -
183C GLY* 1.3 73.3 - - - +
185C ILE* 1.3 63.6 + - - +
186C SER 5.2 0.2 + - - -
191C THR 3.9 1.7 + - - +
192C SER* 3.5 1.7 - - - -
193C THR* 2.9 40.9 + - - +
204C PHE* 3.6 6.3 - - - -
233C SER* 4.8 3.4 - - - -
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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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161B LEU* 4.9 2.2 - - + -
167C PHE* 3.4 8.5 - - - +
168C ILE* 2.9 50.6 + - + +
170C TRP* 4.9 3.4 - - - +
184C HIS* 1.3 75.8 - - - +
186C SER* 1.3 74.9 + - - +
187C SER 3.5 0.6 + - - +
190C ALA* 4.1 13.7 - - + +
191C THR 3.3 7.9 - - - +
192C SER* 3.4 24.2 - - - +
204C PHE* 3.8 31.6 - - + +
205C THR* 4.2 5.2 - - - +
206C VAL* 3.9 33.7 - - + -
213C ALA* 5.0 1.1 - - + -
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Residues in contact with SER 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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166A ARG 2.5 30.6 + - - -
167A SER* 3.8 20.2 - - - -
167C PHE* 3.8 16.7 - - - -
184C HIS* 5.2 0.2 + - - -
185C ILE* 1.3 76.4 - - - +
187C SER* 1.3 59.6 + - - +
188C SER* 3.9 1.6 + - - -
189C TYR 3.5 9.2 + - - -
190C ALA* 3.0 28.6 + - - -
191C THR* 2.8 22.9 + - - -
206C VAL* 4.6 0.3 - - - +
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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