Contacts of the strand formed by residues 177 - 182 (chain C) in PDB entry 3AP3
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 LYS 177 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70C LEU 2.6 14.7 + - - +
71C ILE* 3.5 4.5 - - + +
72C PHE* 3.0 26.9 + - - +
175C ASN 4.6 6.1 - - - +
176C SER* 1.3 76.5 - - - +
178C PHE* 1.3 65.4 + - - +
231C GLU* 3.2 28.5 - - - +
232C LYS* 3.6 10.3 - - + +
255C PHE* 2.9 41.4 + - + -
256C LEU* 3.6 37.6 + - + +
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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
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72C PHE* 3.4 38.8 - + + -
163C LEU* 4.3 11.9 - - + -
166C SER* 3.6 25.4 - - - -
169C LEU* 3.3 37.7 - - + -
170C SER* 3.6 22.9 - - - -
176C SER* 3.4 21.3 - - - -
177C LYS* 1.3 76.6 - - - +
179C LEU* 1.3 63.6 + - - +
180C LEU 4.0 0.2 - - - -
228C VAL* 4.8 6.3 - - + -
232C LYS* 2.8 21.9 + - + +
233C CYS* 3.4 17.3 - - - -
234C LEU* 2.8 32.1 + - - +
255C PHE* 4.2 1.3 - - - -
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Residues in contact with LEU 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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71C ILE* 3.9 26.2 - - + -
72C PHE 2.9 12.7 + - - +
73C VAL* 3.3 15.4 - - + +
74C GLY 2.9 27.0 + - - +
84C MET* 4.6 9.2 - - + -
88C LEU* 4.0 22.2 - - + -
163C LEU* 4.2 2.5 - - - -
178C PHE* 1.3 77.7 - - - +
180C LEU* 1.3 59.6 + - - +
181C MET* 3.9 0.9 - - - -
234C LEU* 3.7 28.7 - - + -
236C VAL* 3.9 17.9 - - + -
252C ILE* 4.2 20.0 - - + -
255C PHE* 4.1 9.9 - - + -
256C LEU* 4.6 5.8 - - + -
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Residues in contact with LEU 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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74C GLY 3.3 2.7 - - - -
75C GLY* 3.6 26.2 - - - +
163C LEU* 3.6 17.3 - - + -
178C PHE 4.0 1.2 - - - -
179C LEU* 1.3 70.2 - - - +
181C MET* 1.3 65.8 + - - +
182C VAL* 3.4 14.1 + - + +
218C ILE* 4.7 6.7 - - + -
221C MET* 3.3 50.0 - - + +
222C TYR* 4.1 14.8 - - + +
225C CYS* 3.9 16.4 - - + -
233C CYS* 4.5 5.2 - - - -
234C LEU 3.2 11.3 + - - +
235C PRO* 3.7 2.9 - - + +
236C VAL* 3.1 22.2 + - - -
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Residues in contact with MET 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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73C VAL* 4.2 5.8 - - + -
74C GLY 2.7 12.3 + - - +
75C GLY* 4.0 10.2 - - - -
76C VAL 4.7 1.0 + - - -
79C SER* 3.2 39.1 + - - +
80C GLY* 3.7 14.4 - - - +
81C THR* 3.6 33.9 - - + -
84C MET* 3.5 29.4 - - + +
179C LEU 3.7 1.1 + - - +
180C LEU* 1.3 72.7 - - - +
182C VAL* 1.3 62.5 + - - +
183C ARG 4.1 0.4 - - - -
218C ILE* 5.1 3.3 - - - +
236C VAL* 3.5 22.7 - - + +
238C TYR* 4.4 10.8 - - + -
241C LEU* 3.9 24.5 - - + -
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Residues in contact with VAL 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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180C LEU* 3.7 18.8 - - + +
181C MET* 1.3 77.4 - - - +
183C ARG* 1.3 57.0 + - - +
218C ILE* 4.1 20.2 - - + -
222C TYR* 5.5 1.1 - - + -
235C PRO* 4.8 12.8 - - + -
236C VAL 2.7 13.4 + - - +
237C TYR* 3.3 30.3 - - + -
238C TYR* 2.9 12.4 + - - +
239C GLU* 2.6 26.2 - - - +
323C LEU* 3.8 24.9 - - + -
325C TYR* 3.1 17.0 + - + -
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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