Contacts of the strand formed by residues 188 - 196 (chain F) in PDB entry 2AAZ
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 HIS 188 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79F GLU* 5.3 1.2 + - - -
83F PHE* 3.6 30.0 - + - -
127F TYR* 3.2 49.1 - + - -
131F TRP* 4.4 3.9 + + - -
173F ALA* 4.6 2.4 - - - +
186F PRO* 4.1 0.5 - - - +
187F CYS* 1.3 77.0 - - - +
189F MET* 1.3 60.3 + - - +
190F PHE 3.4 3.0 + - - -
213F MET* 3.6 29.8 - - + -
214F TYR 3.8 6.7 - - - -
215F GLN* 4.0 2.2 - - + -
227F ASN* 3.4 10.1 + - - +
230F SER* 5.8 0.2 - - - -
231F TYR* 2.5 35.4 + + - +
600F UMP 3.3 23.8 + - - -
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Residues in contact with MET 189 (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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170E ILE* 3.7 23.6 - - + -
172E SER* 5.5 0.4 - - - +
190E PHE* 3.5 40.2 - - + -
172F SER* 3.0 15.1 + - - -
173F ALA 3.0 12.8 + - - -
174F TRP* 3.5 40.3 + - + -
186F PRO* 4.3 9.2 - - - +
187F CYS 3.1 6.2 + - - +
188F HIS* 1.3 74.4 - - - +
190F PHE* 1.3 69.0 + - + +
214F TYR* 3.2 24.4 + - + +
216F ARG* 3.7 25.6 - - - +
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Residues in contact with PHE 190 (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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189E MET* 3.5 24.5 - - + -
190E PHE* 2.8 36.8 - + - -
214E TYR* 3.2 44.4 - + - -
131F TRP* 6.3 0.2 - - - +
170F ILE* 4.1 1.8 - - + -
171F LEU 3.1 15.0 - - - +
172F SER* 3.6 14.6 - - - +
174F TRP* 6.0 0.2 - - + -
188F HIS 3.4 3.0 + - - -
189F MET* 1.3 87.6 - - + +
191F CYS* 1.3 92.9 + - - +
192F GLN* 4.3 4.5 - - + -
212F LEU* 4.8 2.0 - - + -
213F MET* 3.5 5.0 - - - +
214F TYR* 3.0 46.5 + - + -
231F TYR* 5.3 3.1 - - - -
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Residues in contact with CYS 191 (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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169F ILE 4.1 0.2 - - - +
170F ILE* 3.5 3.5 - - - -
171F LEU* 2.9 47.1 + - - -
190F PHE* 1.3 85.4 - - - +
192F GLN* 1.3 60.3 + - - +
193F PHE* 3.5 32.7 - - - -
211F CYS* 3.9 6.5 - - - -
212F LEU 3.0 14.1 - - - +
213F MET* 3.8 9.0 - - + -
231F TYR* 3.8 27.6 - - + -
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Residues in contact with GLN 192 (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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49E PHE* 3.5 19.5 - - + -
214E TYR* 2.5 35.5 + - - +
216E ARG* 3.1 35.0 + - - +
254E GLY* 3.4 3.1 - - - -
255E ASP* 4.2 8.3 - - - +
167F ARG* 3.6 22.0 + - - +
169F ILE 3.4 6.3 - - - +
170F ILE* 3.5 20.3 - - + +
190F PHE* 4.3 3.1 - - + -
191F CYS* 1.3 74.9 - - - +
193F PHE* 1.3 75.3 + - - +
194F PHE* 6.0 0.8 - - - -
211F CYS* 3.4 3.3 - - - +
212F LEU 2.7 34.0 + - - +
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Residues in contact with PHE 193 (chain F).
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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156F VAL* 3.7 21.5 - - + -
160F ILE* 4.4 3.4 - - + -
166F ASP 5.3 0.9 - - - +
169F ILE* 3.0 45.2 + - + +
171F LEU* 4.3 11.4 - - + -
191F CYS* 3.5 29.6 - - - -
192F GLN* 1.3 85.2 + - - +
194F PHE* 1.3 63.0 + - - +
209F LEU* 4.1 20.9 - - + -
210F SER 3.2 14.6 - - - +
211F CYS* 3.8 20.2 - - + -
234F LEU* 4.3 10.1 - - + -
235F THR* 4.0 13.0 - - + -
238F ILE* 3.3 33.2 - - + -
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Residues in contact with PHE 194 (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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35E GLU* 4.4 5.4 - - - -
37E ARG* 3.5 33.9 - - - -
47E ALA* 5.1 4.9 - - + -
48E LEU 5.0 2.9 - - - -
49E PHE* 3.4 64.6 - + + -
255E ASP* 3.6 31.0 - - + -
166F ASP 6.1 0.7 - - - -
169F ILE* 5.1 2.0 - - - -
192F GLN* 6.0 0.9 - - - -
193F PHE* 1.3 75.9 - - - +
195F VAL* 1.3 72.9 + - - +
196F SER* 3.4 24.0 - - - -
208F LYS 3.5 1.2 - - - +
209F LEU* 3.5 4.7 - - - +
210F SER* 2.9 35.8 + - - +
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Residues in contact with VAL 195 (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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37E ARG* 2.4 34.6 + - - +
160F ILE* 3.8 32.1 - - + +
164F PRO* 3.7 40.4 + - + +
169F ILE* 4.6 3.4 - - + -
194F PHE* 1.3 83.2 - - - +
196F SER* 1.3 56.7 + - - +
197F LEU* 3.7 3.1 + - + +
207F PRO* 3.5 28.7 - - + -
208F LYS 3.2 5.4 - - - +
209F LEU* 4.0 10.5 - - + -
244F THR* 4.6 6.7 - - + -
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Residues in contact with SER 196 (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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35E GLU* 3.4 14.7 + - - -
37E ARG* 3.7 5.6 - - - +
194F PHE* 3.4 19.2 - - - -
195F VAL* 1.3 73.1 - - - +
197F LEU* 1.3 66.8 + - - +
207F PRO* 3.2 8.0 - - - +
208F LYS* 2.8 50.3 + - - +
210F SER* 5.6 1.2 + - - -
247F HIS* 5.6 4.5 - - - -
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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