Contacts of the strand formed by residues 208 - 216 (chain C) in PDB entry 4EE5
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 ASP 208 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166C ARG* 4.8 8.3 + - - -
167C TYR 3.3 5.3 - - - +
168C ALA* 3.6 23.3 - - + +
174C SER* 3.8 13.7 + - - +
176C HIS 3.0 16.8 + - - +
177C LYS* 3.1 13.5 - - + +
178C VAL 2.8 24.8 + - - -
207C LEU* 1.3 69.0 - - - +
209C TYR* 1.3 59.9 + - - +
239C TYR* 2.5 41.7 + - - -
241C TYR* 4.4 2.9 - - - -
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Residues in contact with TYR 209 (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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161C VAL* 3.9 1.7 - - - +
165C GLY 4.4 2.7 - - - -
166C ARG* 3.4 10.8 + - - -
167C TYR* 2.9 67.3 + + + +
178C VAL* 3.1 15.3 - - + +
180C ILE* 4.1 10.8 - - + -
199C HIS* 2.8 43.7 + + - -
202C LEU* 3.5 29.8 - - + -
203C GLN* 3.6 7.8 - - - +
207C LEU* 3.5 27.6 - - + -
208C ASP* 1.3 75.6 + - - +
210C GLY* 1.3 61.4 + - - +
211C ILE* 3.7 30.7 - - + -
241C TYR* 4.3 3.1 - - - -
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Residues in contact with GLY 210 (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 GLY 5.3 0.2 - - - -
165C GLY 3.3 9.2 - - - -
166C ARG* 3.6 6.3 - - - -
178C VAL 3.2 5.9 + - - -
179C ALA* 3.7 0.3 - - - -
180C ILE* 2.8 28.6 + - - +
209C TYR* 1.3 76.1 - - - +
211C ILE* 1.3 64.8 + - - -
212C TYR* 3.7 7.9 - - - -
241C TYR* 3.6 19.0 - - - -
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Residues in contact with ILE 211 (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 GLY 3.7 3.2 + - - +
165C GLY 3.1 10.8 + - - +
180C ILE* 3.7 10.1 - - + +
182C ILE* 4.3 12.3 - - + -
194C TRP* 3.8 39.9 - - + -
195C LEU* 4.3 2.9 - - + -
199C HIS* 3.6 26.2 - - + +
202C LEU* 3.9 7.6 - - + -
209C TYR* 3.7 24.9 - - + -
210C GLY* 1.3 73.7 - - - -
212C TYR* 1.3 66.0 + - - +
213C VAL* 4.7 2.5 - - + -
386C LEU 3.9 9.6 - - - +
387C TYR* 3.9 14.6 - - + -
388C THR* 3.0 27.1 + - - -
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Residues in contact with TYR 212 (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 GLY 5.9 0.9 - - - -
166C ARG* 4.6 3.7 - - - -
179C ALA* 4.2 5.6 - - + -
180C ILE 2.8 15.8 + - - +
181C ILE* 3.5 8.7 - - + -
182C ILE* 2.8 26.8 + - - -
210C GLY* 3.7 18.4 - - - -
211C ILE* 1.3 73.2 - - - +
213C VAL* 1.3 65.2 + - - +
214C ILE* 3.6 16.9 + - + +
231C GLY* 5.4 0.9 - - - -
234C GLU 5.2 0.2 - - - -
235C ALA* 3.7 31.4 - - + -
238C ASP* 2.6 39.6 + - - +
241C TYR* 2.7 33.0 + + - -
383C ARG* 5.1 0.2 - - - -
388C THR* 3.3 27.6 - - + +
390C ILE* 4.0 18.4 - - + -
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Residues in contact with VAL 213 (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* 3.6 15.7 - - + +
184C PHE* 3.6 39.3 - - + -
191C LEU* 3.6 25.6 - - + -
211C ILE* 4.7 1.3 - - + -
212C TYR* 1.3 73.2 - - - +
214C ILE* 1.3 58.7 + - - +
215C ASN 3.3 2.5 + - - +
387C TYR* 3.4 35.9 - - + -
388C THR 2.8 8.1 + - - +
389C GLN* 3.5 17.6 - - + +
390C ILE 3.0 24.1 + - - -
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Residues in contact with ILE 214 (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* 3.9 11.2 - - + -
182C ILE 2.6 18.8 + - - +
183C PRO* 3.9 0.2 - - - +
184C PHE* 2.9 28.1 + - - +
212C TYR* 4.0 17.9 - - + +
213C VAL* 1.3 76.6 - - - +
215C ASN* 1.3 57.6 + - - +
216C GLN 3.6 0.3 + - - -
227C LEU* 3.6 43.1 - - + +
230C VAL* 4.1 7.9 - - + -
231C GLY* 3.7 22.9 - - - -
390C ILE* 3.7 21.3 - - + +
392C VAL* 3.7 26.9 - - + -
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Residues in contact with ASN 215 (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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184C PHE* 3.3 30.3 - - + +
185C ARG* 3.7 8.5 - - - +
186C ASN 4.6 1.0 + - - -
213C VAL 3.3 1.0 + - - -
214C ILE* 1.3 71.8 - - - +
216C GLN* 1.3 67.6 + - - +
217C ALA* 5.5 0.2 - - - +
389C GLN* 4.0 25.4 - - + +
390C ILE 2.9 10.8 + - - +
391C THR* 3.0 35.9 + - - +
392C VAL* 2.9 29.5 + - - +
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Residues in contact with GLN 216 (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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184C PHE 2.9 16.0 + - - +
185C ARG* 3.3 42.6 - - + +
214C ILE 3.6 1.8 + - - -
215C ASN* 1.3 73.3 + - - +
217C ALA* 1.3 75.6 + - - +
218C GLY 3.6 0.9 + - - -
220C THR* 3.4 9.7 + - - -
221C ILE 3.0 24.7 + - - -
222C PHE* 3.4 13.4 - - + -
223C ASN 3.1 22.7 + - - -
227C LEU* 3.7 17.8 - - + +
392C VAL 3.8 3.1 - - - +
394C ILE* 3.7 29.1 - - + +
395C GLY 5.1 1.6 + - - -
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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