Contacts of the strand formed by residues 177 - 184 (chain C) in PDB entry 4EEM
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C SER 4.7 7.0 - - - +
175C PRO* 3.7 10.5 + - - +
176C HIS* 1.3 73.5 - - - +
178C VAL* 1.3 59.4 + - - +
208C ASP* 3.2 19.7 - - + +
239C TYR* 3.9 25.4 - - + +
240C ASP* 2.6 39.2 + - + +
241C TYR* 3.7 10.1 - - - -
242C THR* 3.0 31.6 + - - +
243C CYS* 3.0 27.7 + - - +
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Residues in contact with VAL 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C HIS* 3.8 27.1 - - + +
177C LYS* 1.3 74.6 - - - +
179C ALA* 1.3 64.5 + - - +
180C ILE* 3.7 14.8 - - + -
207C LEU* 4.5 6.3 - - + -
208C ASP 2.8 9.7 + - - +
209C TYR* 3.1 32.1 - - + +
210C GLY 3.1 5.5 + - - -
241C TYR* 3.4 4.1 - - - -
243C CYS* 3.3 15.0 - - - +
245C VAL* 3.6 31.4 - - + -
260C TYR 3.7 6.7 - - - +
261C ARG* 3.8 16.4 - - + -
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Residues in contact with ALA 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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178C VAL* 1.3 73.7 - - - +
180C ILE* 1.3 62.5 + - - +
181C ILE* 3.8 4.1 + - + +
210C GLY 3.8 4.7 - - - -
212C TYR* 4.1 4.5 - - + -
235C ALA* 3.8 20.2 - - + -
241C TYR* 3.4 23.6 - - + -
243C CYS 2.9 6.9 + - - -
244C PHE* 3.4 27.0 - - + +
245C VAL 2.9 23.9 + - - +
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Residues in contact with ILE 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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178C VAL* 3.7 20.4 + - + -
179C ALA* 1.3 75.2 - - - +
181C ILE* 1.3 63.4 + - - +
182C ILE* 4.0 2.6 + - + -
194C TRP* 3.7 29.4 - - + -
202C LEU* 3.6 40.4 - - + -
207C LEU* 5.2 0.2 - - + -
209C TYR* 4.1 19.7 - - + -
210C GLY 2.9 13.8 + - - +
211C ILE* 3.7 7.1 - - + +
212C TYR* 2.8 31.9 + - - +
245C VAL* 3.5 25.4 - - + +
247C SER* 4.6 6.1 - - - -
260C TYR* 5.1 2.9 - - + -
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Residues in contact with ILE 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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179C ALA* 4.2 11.0 - - + +
180C ILE* 1.3 79.3 - - - +
182C ILE* 1.3 63.6 + - - +
183C PRO* 3.8 3.3 - - - +
212C TYR* 3.5 11.7 - - + -
214C ILE* 3.9 22.0 - - + -
228C LEU* 4.1 21.4 - - + +
231C GLY* 3.5 33.9 - - - +
232C PHE 3.5 4.9 - - - +
244C PHE* 3.7 26.7 - - + -
245C VAL 2.7 13.1 + - - +
246C PHE* 3.5 20.0 - - + -
247C SER 3.0 22.5 + - - -
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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
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180C ILE* 4.7 2.9 - - + +
181C ILE* 1.3 79.0 - - - +
183C PRO* 1.3 70.4 - - - +
184C PHE* 3.9 6.7 - - + +
191C LEU* 4.2 15.0 - - + -
194C TRP* 3.7 52.5 - - + -
211C ILE* 4.2 10.5 - - + -
212C TYR 2.9 12.4 + - - +
213C VAL* 3.6 6.5 - - + -
214C ILE 2.8 28.5 + - - -
247C SER* 3.4 17.3 - - - +
249C VAL* 3.5 32.8 - - + -
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Residues in contact with PRO 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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181C ILE 3.8 0.9 - - - +
182C ILE* 1.3 86.4 - - + +
184C PHE* 1.3 59.0 + - - +
214C ILE* 4.0 4.9 - - + +
222C PHE* 4.2 7.4 - - + -
224C ARG* 4.0 26.5 - - + +
227C LEU* 4.2 11.0 - - + -
228C LEU* 3.5 29.7 - - + -
247C SER 3.2 17.7 - - - +
248C ASP* 3.8 13.9 - - - +
403C UDP 2.7 40.8 + - - +
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Residues in contact with PHE 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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182C ILE* 3.9 3.4 - - + +
183C PRO* 1.3 74.2 - - - +
185C ARG* 1.3 57.0 + - - +
186C ASN* 3.8 13.5 - - - -
187C ARG* 3.3 50.0 - - + -
188C GLN* 3.7 19.1 - - + -
191C LEU* 4.0 15.3 - - + -
213C VAL* 3.4 28.3 - - + -
214C ILE 2.9 18.1 + - - +
215C ASN* 3.2 20.2 - - - -
216C GLN* 2.9 30.3 + - - +
222C PHE* 3.8 11.8 - - - -
227C LEU* 4.1 0.6 - - - +
249C VAL* 4.4 12.6 - - + -
389C GLN* 4.1 11.4 - - - -
403C UDP 3.5 4.7 - - - -
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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