Contacts of the strand formed by residues 207 - 220 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173D LEU* 4.2 13.7 - - + -
176D VAL* 4.0 3.8 - - + -
177D HIS* 3.9 27.4 - + + -
180D LEU* 3.7 12.1 - - + -
186D VAL* 3.3 44.6 - - + -
188D PHE* 4.3 11.7 - + - -
203D ILE* 3.1 42.7 + - + +
204D GLU* 4.4 3.6 - - - +
206D TYR* 1.3 99.2 - - + +
208D GLY* 1.3 59.5 + - - +
210D LEU* 3.6 18.5 - - + +
244D ARG 3.3 10.3 - - - +
245D LYS* 3.6 20.9 - - + -
246D LEU* 3.6 7.8 - - - +
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Residues in contact with GLY 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C GLU* 3.4 19.3 - - - -
56C TYR* 3.5 7.4 - - - -
207D PHE* 1.3 74.3 - - - +
209D ASN* 1.3 66.5 + - - -
210D LEU* 3.2 7.0 + - - -
243D GLY* 3.3 3.3 - - - -
244D ARG 2.8 32.2 + - - -
246D LEU* 3.5 7.4 - - - +
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Residues in contact with ASN 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU* 3.2 29.8 - - - +
13C ARG* 2.9 46.3 + - - +
18C LYS* 3.3 13.5 - - - +
54C GLU* 2.8 11.9 + - - -
56C TYR* 3.6 19.3 - - + -
62C GLU* 3.4 11.5 + - - -
208D GLY* 1.3 73.0 - - - +
210D LEU* 1.3 62.6 + - - +
211D GLU* 3.7 9.7 + - - +
242D PHE 3.8 4.9 - - - +
243D GLY* 3.8 4.5 - - - -
244D ARG* 3.8 20.6 - - + +
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Residues in contact with LEU 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ARG* 2.8 30.0 + - - +
222C THR* 3.9 27.5 - - + +
200D LEU* 4.1 15.5 - - + +
203D ILE* 3.8 44.0 - - + -
204D GLU* 5.9 1.3 - - - -
207D PHE 3.6 25.1 - - - +
208D GLY* 3.9 9.4 - - - +
209D ASN* 1.3 76.0 - - - +
211D GLU* 1.3 60.9 + - - +
241D VAL* 5.3 4.5 - - + -
242D PHE 3.3 10.1 - - - +
243D GLY* 4.1 3.6 - - - -
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Residues in contact with GLU 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ARG* 4.4 1.1 - - - +
18C LYS* 2.8 31.0 + - - +
61C GLU* 4.2 2.8 - - - +
62C GLU* 4.4 0.7 - - - +
219C HIS* 4.2 24.5 - - + +
220C TYR 5.6 0.2 - - - -
222C THR* 4.0 2.9 - - - -
82D TYR* 5.0 0.3 + - - -
86D LYS* 2.7 36.8 + - - -
209D ASN* 3.9 10.1 + - - +
210D LEU* 1.3 80.7 - - - +
212D VAL* 1.3 64.9 + - - +
213D VAL* 4.3 0.9 - - + -
240D LEU 3.8 0.4 - - - +
241D VAL* 3.4 3.8 - - - +
242D PHE* 2.8 47.0 + - + +
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Residues in contact with VAL 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C HIS* 3.3 8.2 + - - +
220C TYR* 2.8 54.6 + - + -
222C THR* 3.6 21.1 - - + +
227C PHE* 3.9 17.5 - - + -
196D VAL* 4.3 11.4 - - + -
200D LEU* 4.7 5.6 - - + -
211D GLU* 1.3 79.2 - - - +
213D VAL* 1.3 64.6 + - - +
239D TYR* 4.4 16.4 - - + -
240D LEU 3.2 8.5 - - - +
241D VAL* 4.0 21.8 - - + -
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Residues in contact with VAL 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C HIS* 3.9 21.3 - - + +
218C ARG 3.4 10.5 - - - +
219C HIS* 3.7 32.1 - - + +
220C TYR* 4.8 1.3 - - - -
82D TYR* 4.2 13.7 - - + +
211D GLU* 5.8 1.3 - - + -
212D VAL* 1.3 78.7 - - - +
214D GLU* 1.3 71.5 + - - +
215D ILE* 4.8 1.6 - - + -
239D TYR* 3.9 1.3 - - - -
240D LEU* 2.9 43.5 + - + +
242D PHE* 4.0 29.4 - - + -
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Residues in contact with GLU 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B ARG* 2.8 30.0 + - - -
216C LEU 3.8 0.5 - - - +
217C HIS* 3.4 5.4 - - - -
218C ARG* 2.7 85.4 + - + +
220C TYR* 3.0 21.1 + - + -
213D VAL* 1.3 75.0 - - - +
215D ILE* 1.3 63.5 + - - +
216D LEU* 4.0 12.1 - - + +
236D HIS* 4.7 6.2 + - - +
238D ALA 4.5 12.1 - - - +
239D TYR* 4.1 12.2 - - + -
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Residues in contact with ILE 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C ILE* 4.1 2.0 - - + -
216C LEU 3.5 2.2 - - - -
217C HIS* 3.6 29.4 - - + +
78D LYS* 2.8 54.3 + - + +
79D ASP* 3.8 12.4 + - - +
82D TYR* 3.6 37.9 - - + -
213D VAL* 4.8 3.4 - - + -
214D GLU* 1.3 75.8 - - - +
216D LEU* 1.3 69.9 + - - +
217D HIS* 3.9 16.8 - - + +
236D HIS* 6.0 1.2 - - - -
238D ALA 5.1 2.2 + - - -
240D LEU* 3.7 25.7 - - + +
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Residues in contact with LEU 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B ARG* 3.9 19.5 - - - +
233B MET* 4.8 4.7 - - - -
214C GLU 3.7 0.7 - - - +
215C ILE* 3.4 4.7 - - - -
216C LEU* 2.8 57.9 + - + +
218C ARG* 5.9 1.8 - - + -
78D LYS* 4.6 1.3 - - - -
214D GLU* 4.0 23.1 - - + +
215D ILE* 1.3 81.7 - - - +
217D HIS* 1.3 62.0 + - - +
218D ARG 4.2 0.2 + - - -
233D MET* 3.6 28.5 - - + -
234D VAL 3.7 9.9 - - - +
235D ALA* 3.2 24.5 - - - +
236D HIS* 5.5 0.7 - - - -
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Residues in contact with HIS 217 (chain D).
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* 3.5 38.6 - + + -
213C VAL* 3.9 21.3 - - + -
214C GLU 3.5 2.9 - - - -
215C ILE* 3.4 33.2 - - + +
61D GLU* 5.6 0.2 - - - -
78D LYS* 3.7 45.5 - - + +
215D ILE* 3.9 5.1 - - + +
216D LEU* 1.3 80.4 + - - +
218D ARG* 1.3 60.0 + - - +
219D HIS* 4.2 15.0 - - + +
233D MET* 3.3 22.1 - - - +
234D VAL* 4.4 6.2 + - - +
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Residues in contact with ARG 218 (chain D).
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* 3.4 3.2 - - - +
214B GLU* 3.0 37.6 + - - +
216B LEU* 3.6 19.8 - - - +
235B ALA* 2.6 36.7 + - + +
236B HIS* 4.0 9.1 + - - +
213C VAL* 3.3 3.6 - - - -
214C GLU* 2.8 68.1 + - + +
216C LEU* 5.3 3.8 - - + +
216D LEU 4.2 0.4 - - - -
217D HIS* 1.3 75.6 - - - +
219D HIS* 1.3 67.0 + - - +
220D TYR* 3.4 15.6 + - - -
229D PRO* 3.5 23.7 - - + +
230D GLU* 6.2 0.2 - - + -
233D MET* 4.0 25.3 - - + -
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Residues in contact with HIS 219 (chain D).
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* 5.2 4.9 - - - -
211C GLU* 4.3 24.5 + - + +
212C VAL 3.1 10.3 + - - +
213C VAL* 3.6 32.8 - - + +
217D HIS* 4.5 18.5 - + + +
218D ARG* 1.3 79.2 - - - +
220D TYR* 1.3 64.7 + - - +
229D PRO* 3.5 5.0 - - - +
230D GLU* 3.0 39.1 + - + +
232D GLN 5.8 1.0 + - - -
233D MET* 5.6 1.6 - - - +
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Residues in contact with TYR 220 (chain D).
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* 3.7 3.5 + - - -
220A TYR* 4.3 3.3 + - - -
239B TYR* 4.0 8.2 + - - -
212C VAL* 2.7 31.0 + - + +
214C GLU* 2.8 48.4 + - + -
239C TYR* 3.5 25.9 + + - -
218D ARG* 3.4 20.5 + - - -
219D HIS* 1.3 81.3 - - - +
221D LYS* 1.3 64.4 + - - +
222D THR* 3.5 12.0 + - - +
227D PHE* 3.3 35.9 - + + -
228D ARG 3.3 20.2 - - - +
229D PRO* 3.5 20.5 - - + +
230D GLU* 3.5 12.0 - - - +
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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