Contacts of the strand formed by residues 207 - 220 (chain C) in PDB entry 2YVL
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 207 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173C LEU* 3.9 23.8 - - + -
176C VAL* 4.2 7.2 - - + -
177C HIS* 3.9 25.8 - - + -
180C LEU* 3.5 29.4 - - + -
186C VAL* 3.5 28.0 - - + -
188C PHE* 4.4 2.7 - + - -
203C ILE* 2.8 42.5 + - + +
204C GLU* 3.5 15.2 - - - +
206C TYR* 1.3 91.0 - - + +
208C GLY* 1.3 59.4 + - - +
210C LEU* 3.8 12.0 - - + +
243C GLY* 4.6 0.2 - - - -
244C ARG 3.2 10.8 - - - +
245C LYS* 3.6 26.5 - - + -
246C LEU* 3.6 6.2 - - - +
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Residues in contact with GLY 208 (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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204C GLU* 5.5 2.2 - - - -
207C PHE* 1.3 72.3 - - - +
209C ASN* 1.3 68.6 + - - -
210C LEU* 3.2 8.0 + - - +
243C GLY* 3.3 4.3 - - - -
244C ARG 2.8 29.5 + - - -
246C LEU* 3.5 9.7 - - - +
54D GLU* 3.5 10.3 - - - -
56D TYR* 3.4 13.5 - - - -
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Residues in contact with ASN 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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208C GLY* 1.3 73.3 - - - +
210C LEU* 1.3 63.5 + - - +
211C GLU* 3.7 10.0 + - - +
242C PHE 3.7 5.5 - - - +
243C GLY* 3.8 4.2 - - - -
244C ARG* 3.9 18.9 + - + +
11D LEU* 3.2 14.0 - - - +
13D ARG* 3.0 41.1 + - - +
18D LYS* 3.4 18.7 + - - +
54D GLU* 2.8 15.2 + - - -
56D TYR* 3.6 21.1 - - + -
62D GLU* 3.2 21.5 - - - +
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Residues in contact with LEU 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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200C LEU* 4.1 13.7 - - + -
203C ILE* 3.7 41.7 - - + -
204C GLU* 3.4 30.1 - - + +
207C PHE 3.8 21.5 - - - +
208C GLY* 3.9 10.3 - - - +
209C ASN* 1.3 76.6 - - - +
211C GLU* 1.3 61.4 + - - +
241C VAL* 5.2 3.1 - - + -
242C PHE 3.3 10.8 - - - +
243C GLY* 4.2 2.9 - - - -
13D ARG* 3.0 30.6 + - - +
222D THR* 3.8 25.6 - - + +
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Residues in contact with GLU 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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82C TYR* 5.0 1.0 + - - -
86C LYS* 2.7 39.4 + - - -
209C ASN* 4.0 11.2 - - - +
210C LEU* 1.3 80.1 - - - +
212C VAL* 1.3 65.2 + - - +
213C VAL* 4.2 1.1 - - + -
240C LEU 3.8 0.6 - - - +
241C VAL* 3.2 4.5 - - - +
242C PHE* 2.7 47.5 + - + +
13D ARG* 4.5 5.2 - - - +
18D LYS* 2.9 26.1 + - - +
61D GLU* 4.2 2.1 - - - +
62D GLU* 4.6 0.7 - - - +
219D HIS* 4.3 23.8 - - + +
220D TYR 5.6 0.2 - - - -
222D THR* 4.0 2.5 - - - -
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Residues in contact with VAL 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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196C VAL* 4.3 13.9 - - + -
200C LEU* 4.7 7.4 - - + -
211C GLU* 1.3 78.5 - - - +
213C VAL* 1.3 64.7 + - - +
239C TYR* 4.4 15.3 - - + -
240C LEU 3.3 9.2 - - - +
241C VAL* 3.8 18.8 - - + -
219D HIS* 3.1 8.1 + - - +
220D TYR* 2.7 53.1 + - + -
222D THR* 3.8 20.6 - - + +
227D PHE* 3.8 20.0 - - + -
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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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82C TYR* 4.4 13.7 - - + +
211C GLU* 5.6 2.0 - - + -
212C VAL* 1.3 78.5 - - - +
214C GLU* 1.3 72.7 + - - +
215C ILE* 4.7 1.8 - - + -
239C TYR* 3.9 1.8 - - - -
240C LEU* 2.9 47.2 + - + +
242C PHE* 4.2 23.3 - - + -
217D HIS* 3.9 17.7 - - + -
218D ARG 3.3 14.1 - - - +
219D HIS* 3.6 32.3 - - + +
220D TYR* 4.8 1.8 - - - -
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Residues in contact with GLU 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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218A ARG* 2.9 30.0 + - - +
213C VAL* 1.3 76.8 - - - +
215C ILE* 1.3 62.2 + - - +
216C LEU* 3.9 13.9 - - + +
236C HIS* 4.3 6.5 + - - +
238C ALA 4.4 14.8 - - - +
239C TYR* 3.9 12.4 - - + -
240C LEU* 5.5 0.7 - - - -
216D LEU 3.7 0.9 - - - +
217D HIS* 3.5 5.4 - - - -
218D ARG* 2.8 69.4 + - + +
220D TYR* 2.8 31.1 + - + -
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Residues in contact with ILE 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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78C LYS* 2.6 57.7 + - + +
79C ASP* 3.9 11.7 + - - +
82C TYR* 3.7 34.5 - - + -
213C VAL* 4.7 3.8 - - + -
214C GLU* 1.3 78.6 - - - +
216C LEU* 1.3 65.8 + - - +
217C HIS* 3.7 16.2 - - + +
235C ALA 5.6 0.5 - - - +
236C HIS* 6.1 0.7 - - - -
238C ALA 5.1 1.6 + - - -
240C LEU* 3.7 25.7 - - + +
215D ILE* 4.1 2.7 - - + -
216D LEU 3.4 2.5 - - - -
217D HIS* 3.4 33.0 - - + +
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Residues in contact with LEU 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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216A LEU* 5.7 5.4 - - + -
218A ARG* 4.3 12.3 - - - +
233A MET* 4.9 9.4 - - + -
216B LEU* 5.8 7.6 - - + -
78C LYS* 4.4 0.9 - - - +
214C GLU* 3.9 33.4 - - + +
215C ILE* 1.3 80.8 - - - +
217C HIS* 1.3 66.6 + - - +
218C ARG 4.2 0.4 + - - -
233C MET* 3.9 25.1 - - + -
234C VAL 5.1 2.2 - - - +
235C ALA 4.1 17.9 - - - +
214D GLU 3.8 0.5 - - - +
215D ILE* 3.5 0.2 - - - -
216D LEU* 2.8 55.2 + - + +
218D ARG* 5.3 4.0 - - + -
233D MET* 6.3 0.7 - - + -
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Residues in contact with HIS 217 (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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78C LYS* 3.5 44.8 + - + +
215C ILE* 3.7 9.2 - - + +
216C LEU* 1.3 82.2 - - - +
218C ARG* 1.3 60.0 + - - +
219C HIS* 4.1 14.4 + - + +
233C MET* 3.6 22.2 - - - +
234C VAL* 4.5 5.9 + - - +
82D TYR* 3.6 41.9 + + - +
213D VAL* 3.9 19.3 - - + +
214D GLU 3.4 2.9 - - - -
215D ILE* 3.6 29.5 - - + +
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Residues in contact with ARG 218 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A GLU* 2.8 40.4 + - - -
216A LEU* 3.8 17.4 - - - +
235A ALA* 2.7 48.1 + - + -
236A HIS* 4.1 3.8 + - - +
218B ARG* 3.2 5.7 - - - +
220B TYR* 4.0 0.4 + - - -
216C LEU 4.2 0.4 - - - -
217C HIS* 1.3 74.1 - - - +
219C HIS* 1.3 71.0 + - - +
220C TYR* 3.4 13.4 + - + -
229C PRO* 3.7 23.1 - - + +
230C GLU* 6.0 0.2 - - + -
233C MET* 3.8 26.9 - - + -
213D VAL* 3.4 1.7 - - - -
214D GLU* 2.7 68.9 + - + +
216D LEU* 5.9 2.0 - - + +
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Residues in contact with HIS 219 (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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61C GLU* 6.1 0.7 - - - -
217C HIS* 4.4 17.8 + - + +
218C ARG* 1.3 77.8 - - - +
220C TYR* 1.3 62.3 + - - +
229C PRO* 3.5 4.7 - - - +
230C GLU* 2.9 40.7 + - + +
232C GLN 5.9 0.6 + - - -
233C MET* 5.6 2.2 - - - +
82D TYR* 5.0 7.8 + - - -
211D GLU* 4.2 24.0 + - + +
212D VAL 3.3 13.8 + - - +
213D VAL* 3.7 27.4 - - + +
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Residues in contact with TYR 220 (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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239A TYR* 4.1 7.6 - - - -
218B ARG* 3.9 2.4 + - - -
220B TYR* 4.3 2.9 + - - -
218C ARG* 3.4 21.0 + - - -
219C HIS* 1.3 81.3 - - - +
221C LYS* 1.3 63.5 + - - +
222C THR* 3.4 12.1 + - - +
227C PHE* 3.4 35.4 - + + -
228C ARG 3.4 19.5 - - - -
229C PRO* 3.5 25.9 - - + +
230C GLU* 3.8 10.7 - - - +
212D VAL* 2.8 28.2 + - + +
214D GLU* 3.0 44.8 + - + -
239D TYR* 3.5 25.6 + + - -
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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