Contacts of the strand formed by residues 162 - 168 (chain C) in PDB entry 5EWL
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 HIS 162 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160C TRP* 4.7 0.9 - - - -
161C ASN* 1.3 94.7 + - + +
163C VAL* 1.4 65.7 + - - +
211C LYS* 3.4 10.4 + - + +
213C ASP* 2.8 36.4 + - - +
237C ALA* 3.7 17.8 - - + +
238C ARG 4.9 0.2 + - - -
239C VAL* 4.0 12.6 - - - +
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Residues in contact with VAL 163 (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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155C MET* 3.8 38.8 - - + -
160C TRP* 4.1 6.3 - - + +
162C HIS* 1.4 80.2 - - - +
164C ILE* 1.3 64.6 + - - +
165C LEU 5.2 0.4 - - - +
180C LEU* 5.0 4.3 - - + -
184C LEU* 5.0 0.2 - - + -
211C LYS 3.1 13.6 + - - +
212C ALA* 3.3 20.4 - - + +
213C ASP* 2.9 26.9 + - - +
214C LYS 3.8 0.3 + - - -
237C ALA* 4.3 1.8 - - - -
239C VAL* 3.5 28.9 - - + +
241C ILE* 3.8 20.9 - - + -
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Residues in contact with ILE 164 (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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163C VAL* 1.3 73.3 - - - +
165C LEU* 1.3 62.0 + - - +
166C ILE* 4.0 10.5 + - + -
213C ASP* 5.2 0.9 - - + -
214C LYS* 3.5 11.7 - - + +
216C LEU* 4.3 25.4 - - + -
232C ALA* 3.4 30.3 - - + +
235C LEU* 3.9 20.2 - - + -
237C ALA* 3.1 42.0 - - + +
239C VAL 2.8 10.3 + - - +
240C ILE* 3.4 18.2 - - + +
241C ILE* 2.8 28.4 + - - +
266C TYR* 6.1 0.7 - - + -
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Residues in contact with LEU 165 (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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151C TRP* 4.7 7.0 - - + -
163C VAL* 4.1 1.7 - - + -
164C ILE* 1.3 73.0 - - - +
166C ILE* 1.3 54.7 + - - +
167C VAL* 3.8 17.0 - - + -
176C ALA* 5.8 0.7 - - + -
177C GLN* 3.8 43.1 - - + +
180C LEU* 3.8 25.4 - - + -
181C GLU* 5.4 2.0 - - + -
212C ALA* 5.0 5.4 - - + -
214C LYS 2.9 12.1 + - - +
215C VAL* 3.2 17.3 - - + +
216C LEU* 2.7 33.8 + - - +
241C ILE* 3.5 34.5 - - + +
242C LEU* 4.9 0.9 - - - +
243C SER 5.3 0.7 - - - +
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Residues in contact with ILE 166 (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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164C ILE* 4.4 9.6 - - + -
165C LEU* 1.3 74.6 - - - +
167C VAL* 1.3 64.8 + - - +
216C LEU* 3.3 16.2 - - + +
218C PHE* 3.8 17.0 - - + -
228C LEU* 3.8 26.2 - - + -
229C LEU* 4.5 23.6 - - + -
232C ALA* 4.7 11.7 - - + -
240C ILE* 3.4 29.6 - - + -
241C ILE 2.8 12.3 + - - +
242C LEU* 3.3 14.7 - - + +
243C SER 2.9 25.1 + - - -
252C VAL* 4.8 8.3 - - + -
268C TRP* 5.0 0.2 - - + -
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Residues in contact with VAL 167 (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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165C LEU* 3.8 25.8 - - + -
166C ILE* 1.3 80.1 - - - +
168C SER* 1.3 64.2 + - - +
173C GLY* 3.4 29.6 - - - +
174C ARG 4.9 0.2 - - - +
176C ALA* 4.6 0.2 - - + -
177C GLN* 4.0 21.3 - - + +
215C VAL* 4.3 4.7 - - + -
216C LEU 2.8 13.9 + - - +
217C GLN* 3.1 39.5 - - + +
218C PHE* 3.1 11.8 + - - -
243C SER* 3.3 19.5 - - - -
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Residues in contact with SER 168 (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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167C VAL* 1.3 79.5 - - - +
169C ASP* 1.3 58.5 + - - +
170C ASP* 2.7 43.0 + - - +
173C GLY* 3.4 17.2 + - - -
174C ARG* 3.9 1.6 + - - +
218C PHE* 3.7 29.1 - - - -
220C PRO* 4.2 6.5 - - - -
243C SER 3.0 14.5 + - - -
244C ALA* 3.6 11.7 - - - -
245C SER 4.6 0.5 + - - -
248C ASP* 4.6 4.0 - - - -
273C ARG* 5.1 1.2 + - - -
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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