Contacts of the strand formed by residues 206 - 215 (chain F) in PDB entry 1YPH
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 ALA 206 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B CYS 3.9 17.0 - - - +
2B GLY 3.5 10.5 - - - +
3B VAL* 4.1 6.3 - - + -
122D CYS* 4.0 11.4 - - - -
202F LYS* 3.3 5.9 - - - +
203F LYS* 2.8 35.3 + - - +
204F ASN* 4.4 3.6 - - + +
205F GLY* 1.3 79.3 - - - +
207F TRP* 1.3 63.9 + - - +
208F THR* 3.8 1.6 + - - +
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Residues in contact with TRP 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B GLY* 2.8 30.1 + - - -
4B PRO* 3.9 9.4 - - + +
8B PRO* 4.1 13.6 - - + +
10B LEU* 4.2 19.5 - - + -
27D TRP* 3.9 20.8 - + - -
29D TRP* 3.7 33.4 - + + -
121D VAL* 3.6 2.2 - - - +
122D CYS* 3.1 26.6 + - - +
135D THR 5.7 1.6 - - - -
136D CYS* 5.2 1.8 - - - -
137D VAL* 3.7 27.6 - - + -
200F VAL* 3.5 33.2 - - + -
201F CYS* 3.6 5.2 - - - -
202F LYS* 3.6 56.0 - - + +
205F GLY 5.8 0.2 - - - -
206F ALA* 1.3 72.9 - - - +
208F THR* 1.3 61.6 + - - +
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Residues in contact with THR 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D CYS* 3.4 14.9 - - - +
123D LEU 3.8 4.3 + - - +
124D PRO* 3.4 41.5 - - + -
128D ASP* 5.3 0.7 - - - +
130D PHE* 4.1 18.8 - - + -
200F VAL* 3.2 7.1 - - - -
201F CYS 2.9 34.6 + - - -
203F LYS* 4.3 17.9 + - + +
206F ALA* 3.8 1.9 + - - +
207F TRP* 1.3 74.7 - - - +
209F LEU* 1.4 65.3 + - - +
210F VAL* 3.2 2.9 + - - +
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Residues in contact with LEU 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D SER* 3.9 8.7 - - - +
53D VAL* 3.5 32.3 - - + -
121D VAL* 3.8 14.4 - - + +
122D CYS 2.8 18.1 + - - +
123D LEU* 4.2 14.8 - - + -
124D PRO* 3.1 25.1 - - - +
198F PRO* 3.5 29.8 - - + -
199F LEU 3.8 4.0 - - - +
200F VAL* 4.1 4.9 - - + -
208F THR* 1.4 69.8 - - - +
210F VAL* 1.3 56.7 + - - +
211F GLY 3.4 22.0 - - - +
212F ILE* 4.3 7.0 - - + -
231F VAL* 3.5 22.3 - - + +
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Residues in contact with VAL 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D PRO* 5.1 2.2 - - - -
130D PHE* 3.7 47.6 - - + -
162F LEU* 4.5 5.2 - - + -
181F ILE* 4.0 27.0 - - + +
199F LEU* 2.9 10.5 + - + +
201F CYS* 3.3 35.0 - - + -
208F THR 3.6 10.8 - - - +
209F LEU* 1.3 73.6 - - - +
211F GLY* 1.3 58.8 + - - +
229F ALA 3.7 0.7 - - - +
230F ARG* 4.0 5.0 - - + +
231F VAL* 3.1 24.7 + - - +
232F THR* 4.6 2.4 + - + +
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Residues in contact with GLY 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181F ILE* 4.4 0.9 - - - -
198F PRO 3.7 0.2 - - - -
199F LEU* 2.9 43.8 + - - +
209F LEU* 3.4 12.7 - - - +
210F VAL* 1.3 81.1 - - - +
212F ILE* 1.3 63.8 + - - -
228F TYR* 4.0 9.2 - - - -
229F ALA 3.1 10.3 - - - -
231F VAL* 3.9 1.8 - - - -
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Residues in contact with ILE 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D VAL* 4.0 12.3 - - + +
54D THR 3.8 7.0 - - - +
55D ALA* 3.8 23.3 - - + +
102D ASP 4.4 2.9 - - - +
103D ILE* 3.7 41.3 - - + -
196F GLY* 3.6 28.3 - - - +
197F GLY 3.4 4.0 - - - +
209F LEU* 4.3 9.6 - - + -
211F GLY* 1.3 78.2 - - - +
213F VAL* 1.3 67.5 + - - +
214F SER* 3.0 2.1 + - - -
228F TYR* 3.2 4.6 - - - +
229F ALA* 2.8 36.4 + - + -
231F VAL* 4.0 15.0 - - + -
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Residues in contact with VAL 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D ALA* 3.9 2.9 - - - +
57D HIS* 3.7 5.2 - - - -
138D THR* 3.6 15.7 - - - +
139D THR 5.1 1.6 - - - +
190F SER* 3.2 30.7 - - - +
194F ASP* 3.5 18.6 - - + +
195F SER* 3.7 18.7 - - - +
196F GLY* 2.9 24.2 + - - +
197F GLY 2.8 23.6 + - - +
198F PRO 4.4 0.7 - - - +
212F ILE* 1.3 69.8 - - - +
214F SER* 1.3 63.5 + - - +
215F TRP* 5.2 1.1 - - - +
227F VAL 5.2 0.7 - - - +
228F TYR* 3.6 26.8 - - + -
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Residues in contact with SER 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C TYR* 2.6 24.6 + - - -
55D ALA* 5.8 0.2 - - - -
57D HIS* 3.0 15.9 + - - -
99D ILE* 3.6 3.3 + - - +
102D ASP* 2.7 32.5 + - - +
180F MET* 5.9 1.9 - - - +
195F SER* 4.6 0.7 + - - -
212F ILE 3.0 9.8 + - - -
213F VAL* 1.3 79.4 - - - +
215F TRP* 1.3 70.6 + - - +
227F VAL* 3.1 16.9 + - - -
228F TYR* 3.8 1.1 - - - -
229F ALA* 3.7 13.2 - - - -
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Residues in contact with TRP 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C TYR* 3.4 15.7 - - + +
98D THR 4.9 2.9 - - - -
99D ILE* 3.9 15.3 - - + +
218E SER* 4.0 16.6 - - - +
219E THR* 3.8 21.8 - - + -
172F TRP* 3.5 45.1 - + - -
175F LYS* 3.7 40.4 - - + -
176F ILE* 3.9 3.4 - - + -
180F MET* 3.8 16.1 - - + +
213F VAL* 5.2 1.0 - - - +
214F SER* 1.3 100.7 + - - +
216F GLY* 1.3 73.7 + - - +
226F GLY* 4.2 0.7 - - - -
227F VAL* 2.8 69.5 + - + +
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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