Contacts of the strand formed by residues 207 - 220 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A LEU* 4.3 22.2 - - + -
176A VAL* 4.3 6.7 - - + -
177A HIS* 4.0 26.0 - - + -
180A LEU* 3.6 27.1 - - + -
186A VAL* 3.5 25.8 - - + -
188A PHE* 4.6 2.7 - + - -
203A ILE* 3.1 44.3 + - + +
204A GLU* 4.1 3.1 - - - +
206A TYR* 1.3 94.0 - - + +
208A GLY* 1.3 59.7 + - - +
210A LEU* 3.7 14.4 - - + +
243A GLY* 4.4 3.4 - - - -
244A ARG 3.3 9.0 - - - +
245A LYS* 3.6 28.7 - - + -
246A LEU* 3.6 6.1 - - - +
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Residues in contact with GLY 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A PHE* 1.3 74.6 - - - +
209A ASN* 1.3 68.8 + - - -
210A LEU* 3.2 7.6 + - - -
243A GLY* 3.2 4.0 - - - -
244A ARG 2.8 28.4 + - - -
246A LEU* 3.5 12.0 - - - +
54B GLU* 3.4 14.4 - - - -
56B TYR* 3.4 7.9 - - - -
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Residues in contact with ASN 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A GLY* 1.3 72.8 - - - +
210A LEU* 1.3 63.2 + - - +
211A GLU* 3.7 9.5 + - - +
242A PHE 3.8 4.7 - - - +
243A GLY* 3.8 4.7 - - - -
244A ARG* 3.8 20.5 - - + +
11B LEU* 3.5 17.4 - - - +
13B ARG* 2.9 39.7 + - + +
18B LYS* 3.4 15.2 - - - +
54B GLU* 2.8 14.9 + - - -
56B TYR* 3.6 19.0 - - + -
62B GLU* 3.2 25.3 + - - -
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Residues in contact with LEU 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A LEU* 4.1 19.1 - - + +
203A ILE* 3.9 38.6 - - + -
204A GLU* 5.9 1.3 - - - -
207A PHE 3.7 24.0 - - - +
208A GLY* 4.0 8.5 - - - +
209A ASN* 1.3 75.7 - - - +
211A GLU* 1.3 60.2 + - - +
241A VAL* 5.1 3.1 - - + -
242A PHE 3.3 11.9 - - - +
243A GLY* 4.1 5.4 - - - -
13B ARG* 3.1 28.8 + - - +
222B THR* 3.8 30.1 - - + +
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Residues in contact with GLU 211 (chain A).
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 0.7 + - - -
86A LYS* 2.7 34.9 + - - -
209A ASN* 4.1 9.5 + - - +
210A LEU* 1.3 80.5 - - - +
212A VAL* 1.3 64.3 + - - +
213A VAL* 5.9 0.7 - - + -
240A LEU 3.6 0.7 - - - +
241A VAL* 3.3 4.7 - - - +
242A PHE* 2.7 53.4 + - + +
13B ARG* 4.5 1.8 - - - +
18B LYS* 2.8 30.7 + - - -
61B GLU* 4.1 4.0 - - - +
62B GLU* 4.6 0.2 - - - +
219B HIS* 4.2 24.3 + - + -
222B THR* 4.0 1.8 - - - -
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Residues in contact with VAL 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A VAL* 4.3 13.5 - - + -
200A LEU* 4.4 5.4 - - + -
211A GLU* 1.3 77.9 - - - +
213A VAL* 1.3 64.6 + - - +
239A TYR* 4.3 17.0 - - + -
240A LEU 3.1 9.2 - - - +
241A VAL* 4.1 19.5 - - + -
219B HIS* 3.3 7.8 - - - +
220B TYR* 2.8 45.6 + - + +
222B THR* 3.7 22.1 - - + +
227B PHE* 3.9 26.9 - - + -
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Residues in contact with VAL 213 (chain A).
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* 4.3 14.1 - - + +
211A GLU* 5.7 1.3 - - + -
212A VAL* 1.3 77.9 - - - +
214A GLU* 1.3 73.5 + - - +
215A ILE* 4.7 2.0 - - + -
239A TYR* 3.9 1.5 - - - -
240A LEU* 2.9 51.9 + - + +
242A PHE* 4.2 16.6 - - + -
217B HIS* 3.8 19.7 - - + +
218B ARG 3.4 12.3 - - - +
219B HIS* 3.7 31.0 - - + +
220B TYR* 4.7 1.8 - - - -
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Residues in contact with GLU 214 (chain A).
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* 1.3 75.1 - - - +
215A ILE* 1.3 62.7 + - - +
216A LEU* 4.1 10.6 + - + +
236A HIS* 4.4 5.9 + - - +
238A ALA 4.5 13.0 - - - +
239A TYR* 4.2 12.4 - - + -
240A LEU* 5.5 0.4 - - - -
216B LEU 3.7 1.2 - - - +
217B HIS* 3.5 5.7 - - - -
218B ARG* 2.7 78.8 + - + +
220B TYR* 2.7 26.1 + - + -
218C ARG* 2.8 31.3 + - - -
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Residues in contact with ILE 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LYS* 2.8 62.5 + - + +
79A ASP* 3.9 11.9 + - - +
82A TYR* 3.7 25.1 - - + -
213A VAL* 4.7 3.6 - - + -
214A GLU* 1.3 77.9 - - - +
216A LEU* 1.3 67.2 + - - +
217A HIS* 3.7 16.8 - - + +
235A ALA 5.6 0.3 - - - +
236A HIS* 6.0 1.4 - - - -
237A THR 5.7 0.2 + - - -
238A ALA 5.1 2.0 + - - -
240A LEU* 3.7 28.7 - - + +
215B ILE* 4.1 1.8 - - + -
216B LEU 3.5 2.2 - - - -
217B HIS* 3.4 31.9 - - + +
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Residues in contact with LEU 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LYS* 4.6 0.7 - - - +
214A GLU* 4.2 22.2 - - + +
215A ILE* 1.3 80.3 - - - +
217A HIS* 1.3 66.9 + - - +
218A ARG 4.1 0.2 - - - -
233A MET* 4.0 23.8 - - + -
234A VAL 5.0 2.7 - - - +
235A ALA 4.2 11.2 - - - +
236A HIS* 6.1 0.4 - - - -
214B GLU 3.7 0.9 - - - +
215B ILE* 3.5 0.7 - - - -
216B LEU* 2.8 59.7 + - + +
218B ARG* 5.8 2.7 - - + +
216C LEU* 5.7 4.5 - - + -
218C ARG* 3.8 28.0 - - - +
233C MET* 4.9 11.7 - - + -
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Residues in contact with HIS 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LYS* 3.7 44.3 + - + +
215A ILE* 3.7 4.9 - - + +
216A LEU* 1.3 81.0 - - - +
218A ARG* 1.3 61.4 + - - +
219A HIS* 4.1 15.3 + - + +
233A MET* 3.4 21.4 - - - +
234A VAL* 4.5 5.9 + - - +
82B TYR* 3.6 40.8 + + - +
213B VAL* 3.8 18.8 - - + +
214B GLU 3.5 2.7 - - - -
215B ILE* 3.4 36.0 - - + +
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Residues in contact with ARG 218 (chain A).
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 4.1 0.8 - - - -
217A HIS* 1.3 73.7 - - - +
219A HIS* 1.3 71.3 + - - +
220A TYR* 3.3 13.5 + - + -
229A PRO* 3.6 26.8 - - + +
232A GLN 5.9 0.2 - - - +
233A MET* 3.9 21.5 - - + -
213B VAL* 3.3 2.5 - - - -
214B GLU* 2.7 69.3 + - + +
216B LEU* 5.9 2.0 - - + +
214C GLU* 2.9 43.3 + - - -
216C LEU* 4.3 14.3 - - - +
235C ALA* 2.8 48.7 + - + -
236C HIS* 4.1 4.0 + - - +
218D ARG* 3.4 2.6 - - - +
220D TYR* 3.7 0.8 + - - -
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Residues in contact with HIS 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLU* 6.1 0.2 - - - -
217A HIS* 4.4 18.2 + - + +
218A ARG* 1.3 79.6 - - - +
220A TYR* 1.3 64.3 + - - +
229A PRO* 3.5 4.3 - - - +
230A GLU* 2.9 38.7 + - + +
232A GLN 5.8 1.0 + - - +
233A MET* 5.4 2.8 - - + +
82B TYR* 5.1 7.6 + - - -
211B GLU* 4.3 23.8 + - + +
212B VAL 3.3 9.1 + - - +
213B VAL* 3.6 33.9 - - + +
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Residues in contact with TYR 220 (chain A).
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* 3.3 17.6 + - - -
219A HIS* 1.3 82.8 - - - +
221A LYS* 1.3 63.8 + - - +
222A THR* 3.6 10.7 + - - +
227A PHE* 3.4 36.1 - + + -
228A ARG 3.4 20.2 - - - +
229A PRO* 3.5 25.7 - - + +
230A GLU* 3.6 13.2 - - - +
212B VAL* 2.8 30.6 + - + +
214B GLU* 2.9 46.4 + - + -
239B TYR* 3.5 26.3 + + - -
239C TYR* 4.0 8.6 + - - -
220D TYR* 4.3 4.2 + - - -
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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