Contacts of the strand formed by residues 207 - 220 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173B LEU* 4.0 22.7 - - + -
176B VAL* 4.2 8.1 - - + -
177B HIS* 3.9 24.7 - - + -
180B LEU* 3.5 27.6 - - + -
186B VAL* 3.5 24.0 - - + -
188B PHE* 4.7 2.0 - + - -
203B ILE* 3.1 44.8 + - + +
204B GLU* 4.3 2.4 - - - +
206B TYR* 1.3 92.7 - - + +
208B GLY* 1.3 59.4 + - - +
210B LEU* 3.7 16.4 - - + +
244B ARG 3.2 11.2 - - - +
245B LYS* 3.5 29.4 - - + -
246B LEU* 3.5 8.3 - - - +
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Residues in contact with GLY 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLU* 3.5 12.8 - - - -
56A TYR* 3.4 13.0 - - - -
207B PHE* 1.3 74.1 - - - +
209B ASN* 1.3 69.3 + - - -
210B LEU* 3.2 8.0 + - - +
243B GLY* 3.3 3.8 - - - -
244B ARG 2.8 29.4 + - - -
246B LEU* 3.4 7.9 - - - +
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Residues in contact with ASN 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 3.6 12.4 - - - +
13A ARG* 2.8 43.8 + - + +
18A LYS* 3.4 14.3 - - - +
54A GLU* 2.7 16.1 + - - +
56A TYR* 3.5 20.6 - - + -
62A GLU* 3.2 24.7 + - - -
208B GLY* 1.3 72.9 - - - +
210B LEU* 1.3 64.7 + - - +
211B GLU* 3.7 8.8 + - - +
242B PHE 3.7 5.4 - - - +
243B GLY* 3.9 4.0 - - - -
244B ARG* 4.0 18.5 - - + +
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Residues in contact with LEU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ARG* 3.0 29.9 + - - +
222A THR* 3.9 29.6 - - + +
200B LEU* 3.9 20.0 - - + +
203B ILE* 3.7 38.1 - - + -
204B GLU* 6.0 1.3 - - - -
207B PHE 3.7 23.6 - - - +
208B GLY* 3.9 10.1 - - - +
209B ASN* 1.3 75.8 - - - +
211B GLU* 1.3 60.1 + - - +
241B VAL* 5.3 4.7 - - + -
242B PHE 3.4 10.5 - - - +
243B GLY* 4.2 4.7 - - - -
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Residues in contact with GLU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 4.5 1.3 - - - +
18A LYS* 2.9 31.3 + - - -
61A GLU* 4.1 3.6 - - - +
62A GLU* 4.6 0.3 - - - +
219A HIS* 4.3 24.0 - - + +
220A TYR 5.8 0.2 - - - -
222A THR* 4.0 2.5 - - - -
82B TYR* 5.2 0.2 + - - -
86B LYS* 2.7 37.9 + - - -
209B ASN* 4.0 11.1 + - - +
210B LEU* 1.3 81.3 - - - +
212B VAL* 1.3 65.0 + - - +
213B VAL* 4.2 1.8 - - + -
240B LEU 3.7 0.7 - - - +
241B VAL* 3.5 3.8 - - - +
242B PHE* 2.9 46.6 + - + +
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Residues in contact with VAL 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A HIS* 3.3 7.6 + - - +
220A TYR* 2.8 55.3 + - + -
222A THR* 3.7 21.6 - - + +
227A PHE* 4.0 17.0 - - + -
196B VAL* 4.2 15.9 - - + -
200B LEU* 4.5 6.3 - - + -
211B GLU* 1.3 78.6 - - - +
213B VAL* 1.3 63.2 + - - +
239B TYR* 4.3 15.0 - - + -
240B LEU 3.3 8.5 - - - +
241B VAL* 4.2 21.5 - - + -
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Residues in contact with VAL 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A HIS* 3.8 21.1 - - + +
218A ARG 3.3 12.6 - - - +
219A HIS* 3.6 32.5 - - + +
220A TYR* 4.7 1.3 - - - -
82B TYR* 4.4 13.7 - - + +
86B LYS* 6.3 0.2 - - - -
211B GLU* 5.7 1.6 - - + -
212B VAL* 1.3 78.7 - - - +
214B GLU* 1.3 73.4 + - - +
215B ILE* 4.7 2.2 - - + -
239B TYR* 3.9 1.3 - - - -
240B LEU* 2.9 53.7 + - + +
242B PHE* 4.2 16.2 - - + -
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Residues in contact with GLU 214 (chain B).
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 3.7 0.9 - - - +
217A HIS* 3.5 5.2 - - - -
218A ARG* 2.7 83.3 + - + +
220A TYR* 2.9 19.8 + - + -
213B VAL* 1.3 75.8 - - - +
215B ILE* 1.3 62.1 + - - +
216B LEU* 4.0 11.2 + - + +
236B HIS* 4.4 5.7 + - - +
238B ALA 4.5 13.5 - - - +
239B TYR* 4.1 12.7 - - + -
240B LEU* 5.6 0.4 - - - -
218D ARG* 3.0 32.2 + - - +
229D PRO* 4.7 0.3 - - - +
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Residues in contact with ILE 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ILE* 4.1 1.6 - - + -
216A LEU 3.5 2.0 - - - -
217A HIS* 3.4 35.4 - - + +
78B LYS* 2.8 55.1 + - + +
79B ASP* 3.7 13.0 + - - +
82B TYR* 3.7 32.1 - - + -
213B VAL* 4.7 4.3 - - + -
214B GLU* 1.3 77.5 - - - +
216B LEU* 1.3 68.2 + - - +
217B HIS* 3.8 15.0 - - + +
235B ALA 6.1 0.2 - - - -
236B HIS* 6.0 1.0 - - - -
237B THR 5.8 0.3 + - - -
238B ALA 5.0 2.2 + - - -
240B LEU* 3.8 24.6 - - + +
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Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A GLU 3.7 0.7 - - - +
215A ILE* 3.5 0.7 - - - -
216A LEU* 2.8 60.9 + - + +
218A ARG* 5.9 1.6 - - + +
78B LYS* 4.4 0.9 - - - +
214B GLU* 4.0 21.8 - - + +
215B ILE* 1.3 81.5 - - - +
217B HIS* 1.3 67.0 + - - +
218B ARG 4.2 0.4 + - - -
233B MET* 4.1 22.9 - - + -
234B VAL 5.0 2.2 - - - +
235B ALA 4.1 10.5 - - - +
236B HIS* 5.9 0.4 - - - -
216C LEU* 5.8 7.9 - - + -
218D ARG* 3.6 30.7 - - - +
233D MET* 4.9 9.6 - - + -
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Residues in contact with HIS 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A TYR* 3.6 40.9 + + - +
213A VAL* 3.8 19.4 - - + +
214A GLU 3.5 2.9 - - - -
215A ILE* 3.4 35.5 - - + +
78B LYS* 3.6 44.8 + - + +
215B ILE* 3.8 4.1 - - + +
216B LEU* 1.3 82.6 - - - +
218B ARG* 1.3 59.7 + - - +
219B HIS* 4.1 16.7 + - + -
233B MET* 3.4 22.1 - - - +
234B VAL* 4.5 6.6 + - - +
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Residues in contact with ARG 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A VAL* 3.4 2.5 - - - -
214A GLU* 2.7 69.0 + - + +
216A LEU* 5.8 2.2 - - + +
216B LEU 4.2 0.6 - - - -
217B HIS* 1.3 73.1 - - - +
219B HIS* 1.3 71.2 + - - +
220B TYR* 3.3 11.2 + - + -
229B PRO* 3.6 25.0 - - + +
233B MET* 3.9 20.9 - - + -
218C ARG* 3.2 5.4 - - - +
220C TYR* 3.9 0.4 + - - -
214D GLU* 2.8 39.0 + - - +
216D LEU* 3.9 14.0 - - - +
235D ALA* 2.7 51.3 + - + -
236D HIS* 4.1 3.8 + - - +
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Residues in contact with HIS 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A TYR* 5.1 6.0 + - - -
211A GLU* 4.2 24.9 + - + -
212A VAL 3.3 16.4 - - - +
213A VAL* 3.7 25.8 - - + +
217B HIS* 4.3 18.3 + - + +
218B ARG* 1.3 79.2 - - - +
220B TYR* 1.3 58.7 + - - +
229B PRO* 3.5 5.2 - - - +
230B GLU* 2.8 44.7 + - + +
232B GLN 5.9 0.4 + - - -
233B MET* 5.5 1.8 - - - +
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Residues in contact with TYR 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A VAL* 2.8 27.8 + - + +
214A GLU* 2.7 48.4 + - + -
239A TYR* 3.5 26.6 + + - -
218B ARG* 3.3 18.0 + - - -
219B HIS* 1.3 81.0 - - - +
221B LYS* 1.3 62.9 + - - +
222B THR* 3.5 11.3 + - - +
227B PHE* 3.4 36.1 - + + -
228B ARG 3.3 19.7 - - - -
229B PRO* 3.5 26.5 - - + +
230B GLU* 4.1 10.1 - - - +
218C ARG* 4.0 1.6 + - - -
220C TYR* 4.3 3.1 + - - -
239D TYR* 4.0 8.2 + - - -
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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