Contacts of the strand formed by residues 221 - 229 (chain C) in PDB entry 4I7C
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 PHE 221 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185C PHE* 3.6 33.4 - + + -
187C PHE* 3.7 34.5 - + - -
189C PHE* 3.9 22.2 - + + -
211C LEU* 4.1 19.3 - - + -
217C GLN 3.3 22.2 - - - -
218C ALA 3.1 9.7 + - - +
219C GLU 4.0 0.3 - - - +
220C ASN* 1.3 87.8 - - + +
222C ALA* 1.3 62.9 + - - +
239C THR* 3.8 9.2 + - - +
240C PRO* 3.3 26.6 - - + +
279C ILE* 4.3 1.3 - - + -
280C SER 3.4 14.6 - - - +
281C MET* 4.0 15.0 - - + -
282C CYS* 3.6 10.5 - - - -
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Residues in contact with ALA 222 (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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221C PHE* 1.3 75.8 - - - +
223C TYR* 1.3 63.3 + - - +
237C GLU* 6.5 0.4 - - + -
238C ALA 3.5 12.3 - - - +
239C THR* 5.6 0.7 - - - +
240C PRO* 4.1 2.7 - - - -
279C ILE* 3.7 5.0 - - - +
280C SER* 2.9 43.2 + - - +
282C CYS* 4.1 17.7 - - + -
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Residues in contact with TYR 223 (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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189C PHE* 6.5 0.2 - - + -
208C ILE* 3.7 21.8 - - - +
209C VAL* 3.3 46.0 - - + -
222C ALA* 1.3 76.5 - - - +
224C ARG* 1.3 59.5 + - - +
225C LEU* 3.8 25.8 - - + -
236C TRP* 3.1 29.3 + + - -
237C GLU* 3.2 7.4 - - - +
238C ALA* 2.9 72.3 + - + +
239C THR 3.7 10.7 + - - -
240C PRO* 3.6 20.9 - - + -
255C ASP 5.1 0.9 + - - -
256C CYS* 4.7 0.3 - - - +
277C VAL* 5.4 0.9 - - + -
278C THR 3.4 9.2 - - - +
279C ILE* 4.4 11.2 - - + -
280C SER* 5.3 0.2 - - - -
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Residues in contact with ARG 224 (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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162C ASP* 5.1 1.6 + - - -
223C TYR* 1.3 75.1 - - - +
225C LEU* 1.3 63.4 + - - +
226C GLU* 3.6 23.0 + - - +
235C THR* 3.4 31.9 - - + -
236C TRP 3.3 2.9 - - - -
237C GLU* 3.6 26.1 + - + +
276C ASN 3.4 4.9 - - - +
277C VAL* 3.4 2.9 - - - +
278C THR* 3.0 65.0 + - + +
115D ARG* 5.8 3.4 - - - +
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Residues in contact with LEU 225 (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 PHE* 6.3 0.2 - - + -
191C LEU* 6.2 0.2 - - + -
207C ALA* 3.6 46.7 - - + +
208C ILE 3.9 2.7 - - - +
209C VAL* 3.8 20.4 - - + -
223C TYR* 3.8 18.8 - - + -
224C ARG* 1.3 75.3 - - - +
226C GLU* 1.3 60.8 + - - +
234C LEU 3.9 0.3 - - - +
235C THR* 3.4 3.6 - - - +
236C TRP* 2.8 38.5 + - + +
257C LEU* 3.9 18.6 - - + +
275C ILE* 4.1 11.2 - - + -
276C ASN 3.4 2.5 - - - -
277C VAL* 3.5 30.1 - - + -
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Residues in contact with GLU 226 (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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224C ARG* 3.6 35.3 + - - +
225C LEU* 1.3 77.2 - - - +
227C LEU* 1.3 65.0 - - - +
228C ASN* 3.4 22.8 + - - +
233C ARG* 4.1 25.0 + - + -
234C LEU 3.2 9.9 - - - +
235C THR* 4.0 12.0 + - + +
257C LEU* 5.7 0.2 - - - -
274C GLY 4.1 0.5 - - - +
275C ILE* 3.7 4.8 - - - +
276C ASN* 3.0 56.0 + - + +
278C THR* 6.1 0.2 - - - -
115D ARG* 5.2 6.1 + - - -
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Residues in contact with LEU 227 (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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226C GLU* 1.3 75.5 - - - +
228C ASN* 1.3 63.9 + - - +
233C ARG* 3.3 6.9 - - - +
234C LEU* 2.9 44.7 + - + +
257C LEU* 4.3 11.4 - - + -
259C PHE* 4.0 35.9 - - + -
263C ILE* 4.7 0.4 - - + -
264C ALA* 5.8 0.4 - - - -
267C PHE* 3.4 37.8 - - + -
273C LEU* 4.3 13.5 - - + -
274C GLY 4.3 5.8 - - - +
275C ILE* 3.8 36.6 - - + -
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Residues in contact with ASN 228 (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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226C GLU* 3.4 23.9 + - - +
227C LEU* 1.3 78.2 + - - +
229C GLY* 1.3 61.2 + - - +
232C ARG 3.8 4.5 - - - +
233C ARG* 3.2 29.2 + - - +
267C PHE* 3.5 15.4 - - - +
274C GLY 4.7 5.3 + - - +
276C ASN* 3.3 25.2 + - - +
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Residues in contact with GLY 229 (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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228C ASN* 1.3 77.5 - - - +
230C HIS* 1.3 59.7 + - - -
231C ARG 3.1 8.1 + - - -
232C ARG* 3.1 22.5 + - - +
266C LEU 5.0 5.6 - - - -
267C PHE* 3.4 16.2 - - - -
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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