Contacts of the strand formed by residues 188 - 196 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79L GLU* 5.3 0.8 + - - -
83L PHE* 3.7 27.7 - + - -
127L TYR* 3.2 49.2 - + - -
131L TRP* 4.4 5.5 + + - -
173L ALA* 4.6 2.4 - - - +
186L PRO* 4.3 0.3 - - - +
187L CYS* 1.3 76.5 - - - +
189L MET* 1.3 61.7 + - - +
190L PHE 3.4 3.2 + - - -
213L MET* 3.5 31.2 - - + -
214L TYR 3.8 7.0 - - - -
215L GLN* 3.9 1.8 - - + +
227L ASN* 3.4 9.5 + - - +
230L SER* 5.8 0.7 - - - -
231L TYR* 2.6 37.5 + + - +
500L UMP 3.0 27.6 + - - -
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Residues in contact with MET 189 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170K ILE* 3.7 23.3 - - + -
172K SER* 5.5 0.4 - - - +
190K PHE* 3.5 39.0 - - + -
172L SER* 2.9 15.6 + - - -
173L ALA* 3.0 12.9 + - - -
174L TRP* 3.5 41.2 + - + +
186L PRO* 4.2 10.1 - - - +
187L CYS 3.1 5.6 + - - +
188L HIS* 1.3 73.8 - - - +
190L PHE* 1.3 68.2 + - + +
214L TYR* 3.3 23.8 + - + +
216L ARG* 3.7 26.2 - - - -
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Residues in contact with PHE 190 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189K MET* 3.4 26.9 - - + -
190K PHE* 2.9 37.5 - + - -
214K TYR* 3.2 43.7 - + - -
131L TRP* 6.3 0.2 - - - +
170L ILE* 4.0 2.2 - - + -
171L LEU 3.1 14.8 - - - +
172L SER* 3.5 13.9 - - - +
173L ALA 4.8 0.2 - - - +
188L HIS 3.4 3.6 - - - -
189L MET* 1.3 88.7 - - + +
191L CYS* 1.3 92.8 + - - +
192L GLN* 4.3 4.0 - - + -
212L LEU* 4.9 1.3 - - + -
213L MET* 3.5 6.2 - - - +
214L TYR* 3.0 46.3 + - + -
231L TYR* 5.1 3.6 - - - -
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Residues in contact with CYS 191 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170L ILE* 3.5 3.6 - - - -
171L LEU* 2.9 48.5 + - - -
190L PHE* 1.3 85.5 - - - +
192L GLN* 1.3 60.4 + - - +
193L PHE* 3.5 32.7 - - - -
211L CYS* 3.9 7.0 - - - -
212L LEU 3.0 13.9 - - - +
213L MET* 3.8 5.8 - - + -
231L TYR* 3.7 29.8 - - + -
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Residues in contact with GLN 192 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49K PHE* 3.5 18.8 - - + -
214K TYR* 2.7 33.9 + - - +
216K ARG* 3.1 37.7 + - - +
254K GLY* 3.5 1.9 - - - -
255K ASP* 4.3 7.1 - - - +
167L ARG* 3.7 22.0 + - - +
169L ILE 3.4 6.5 - - - +
170L ILE* 3.4 22.2 - - + +
190L PHE* 4.5 2.5 - - + -
191L CYS* 1.3 74.0 - - - +
193L PHE* 1.3 73.8 + - - +
194L PHE* 6.1 0.8 - - - -
211L CYS* 3.4 2.6 - - - -
212L LEU 2.7 33.5 + - - +
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Residues in contact with PHE 193 (chain L).
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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156L VAL* 3.8 22.2 - - + -
160L ILE* 4.5 2.7 - - + -
166L ASP 5.3 1.0 - - - +
169L ILE* 3.0 44.5 + - + +
171L LEU* 4.3 10.8 - - + -
191L CYS* 3.5 31.4 - - - -
192L GLN* 1.3 86.4 + - - +
194L PHE* 1.3 61.4 + - - +
209L LEU* 4.0 23.1 - - + -
210L SER 3.2 15.0 - - - +
211L CYS* 3.8 19.7 - - + -
234L LEU* 4.3 9.9 - - + -
235L THR* 4.0 12.6 - - - -
238L ILE* 3.4 33.7 - - + -
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Residues in contact with PHE 194 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K GLU* 4.5 4.5 - - - -
37K ARG* 3.4 36.3 - - - -
47K ALA* 5.2 5.4 - - + -
48K LEU* 5.1 2.9 - - - -
49K PHE* 3.4 63.0 - + + -
255K ASP* 3.6 30.1 - - + -
166L ASP 6.2 0.2 - - - -
169L ILE* 5.2 1.6 - - - -
192L GLN* 6.1 0.4 - - - -
193L PHE* 1.3 75.2 - - - +
195L VAL* 1.3 72.8 + - - +
196L SER* 3.4 22.7 - - - -
208L LYS 3.5 2.8 - - - +
209L LEU* 3.5 3.0 - - - +
210L SER* 2.8 36.8 + - - +
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Residues in contact with VAL 195 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37K ARG* 2.7 33.3 + - - -
160L ILE* 3.8 31.6 - - + +
164L PRO* 3.8 38.9 + - + +
169L ILE* 4.6 3.3 - - + +
194L PHE* 1.3 84.4 - - - +
196L SER* 1.3 56.8 + - - +
197L LEU* 3.7 3.7 + - + +
207L PRO* 3.5 29.2 - - + -
208L LYS 3.2 5.8 - - - +
209L LEU* 4.0 11.0 - - + -
244L THR* 4.6 7.9 - - + -
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Residues in contact with SER 196 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K GLU* 3.4 19.1 + - - -
37K ARG* 3.7 1.3 - - - +
194L PHE* 3.4 18.7 - - - -
195L VAL* 1.3 72.5 - - - +
197L LEU* 1.3 66.7 + - - +
207L PRO* 3.2 7.8 - - - +
208L LYS* 2.8 47.8 + - - +
210L SER* 5.6 1.2 + - - -
247L HIS* 5.6 4.7 - - - -
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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