Contacts of the strand formed by residues 188 - 196 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79C GLU* 5.3 0.8 + - - -
83C PHE* 3.7 27.6 - + - -
127C TYR* 3.2 49.0 - + - -
131C TRP* 4.4 4.8 + + - -
173C ALA* 4.5 2.8 - - - +
186C PRO* 4.2 0.5 - - - +
187C CYS* 1.3 75.0 - - - +
189C MET* 1.3 61.4 + - - +
190C PHE 3.4 2.6 + - - -
213C MET* 3.5 30.5 - - + -
214C TYR 3.8 7.2 - - - -
215C GLN* 4.0 2.5 - - + -
227C ASN* 3.4 11.2 + - - +
230C SER* 5.8 0.2 - - - -
231C TYR* 2.6 37.0 + + - +
450C UMP 3.2 25.0 + - - -
2451C CB3 5.9 0.2 - - - +
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Residues in contact with MET 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C SER* 2.9 15.1 + - - -
173C ALA 3.0 12.5 + - - -
174C TRP* 3.5 40.4 + - + +
186C PRO* 4.3 9.2 - - - +
187C CYS 3.1 7.6 + - - +
188C HIS* 1.3 72.4 - - - +
190C PHE* 1.3 68.2 + - + +
214C TYR* 3.2 24.8 + - + +
216C ARG* 3.7 25.1 - - - -
170D ILE* 3.7 25.4 - - + -
172D SER* 5.7 0.2 - - - +
190D PHE* 3.5 39.3 - - + -
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Residues in contact with PHE 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C TRP* 6.3 0.2 - - - +
170C ILE* 4.0 2.0 - - + -
171C LEU 3.1 15.0 - - - +
172C SER* 3.5 14.6 - - - +
174C TRP* 6.0 0.2 - - + -
188C HIS 3.4 2.6 - - - -
189C MET* 1.3 88.1 - - + +
191C CYS* 1.3 94.2 + - - +
192C GLN* 4.3 3.4 - - + -
212C LEU* 4.9 1.3 - - + -
213C MET* 3.5 4.8 - - - +
214C TYR* 3.0 43.7 + - + -
231C TYR* 5.3 3.4 - - - -
189D MET* 3.5 21.8 - - + -
190D PHE* 2.8 38.8 - + - -
214D TYR* 3.1 48.7 - + - -
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Residues in contact with CYS 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C ILE* 3.5 3.3 - - - -
171C LEU* 2.9 46.4 + - - +
190C PHE* 1.3 84.8 - - - +
192C GLN* 1.3 61.1 + - - +
193C PHE* 3.5 34.5 - - - -
211C CYS* 4.0 6.1 - - - -
212C LEU 3.0 14.6 - - - +
213C MET* 3.8 9.0 - - + -
231C TYR* 3.8 25.8 - - + -
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Residues in contact with GLN 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C ARG* 3.7 22.0 + - - +
169C ILE 3.4 5.8 - - - +
170C ILE* 3.5 19.9 - - + +
190C PHE* 4.5 2.2 - - + -
191C CYS* 1.3 75.1 - - - +
193C PHE* 1.3 76.4 + - - +
194C PHE* 6.0 0.8 - - - -
211C CYS* 3.4 2.3 - - - -
212C LEU 2.7 34.3 + - - +
49D PHE* 3.5 18.7 - - + -
214D TYR* 2.5 35.2 + - - +
216D ARG* 3.0 36.0 + - - +
254D GLY* 3.5 1.6 - - - -
255D ASP* 4.1 8.9 - - - +
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Residues in contact with PHE 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C VAL* 3.7 23.3 - - + -
160C ILE* 4.5 2.7 - - + -
166C ASP 5.3 0.7 - - - +
169C ILE* 3.0 44.3 + - + +
171C LEU* 4.3 11.0 - - + -
191C CYS* 3.5 29.6 - - - -
192C GLN* 1.3 85.7 + - - +
194C PHE* 1.3 63.0 + - - +
209C LEU* 4.1 22.0 - - + -
210C SER 3.2 15.3 - - - +
211C CYS* 3.7 21.1 - - + -
234C LEU* 4.3 10.5 - - + -
235C THR* 4.0 12.3 - - - -
238C ILE* 3.4 32.5 - - + -
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Residues in contact with PHE 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C ASP 6.1 0.9 - - - -
169C ILE* 5.2 2.0 - - - -
192C GLN* 6.0 0.7 - - - -
193C PHE* 1.3 76.4 - - - +
195C VAL* 1.3 72.6 + - - +
196C SER* 3.5 23.1 - - - -
208C LYS 3.5 2.3 - - - +
209C LEU* 3.5 3.3 - - - +
210C SER* 2.8 37.1 + - - +
35D GLU* 4.4 5.2 - - - -
37D ARG* 3.5 34.3 - - - -
47D ALA* 5.1 5.6 - - + -
48D LEU* 5.0 3.4 - - - -
49D PHE* 3.4 61.9 - + + -
255D ASP* 3.5 31.4 - - + -
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Residues in contact with VAL 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C ILE* 3.8 32.1 - - + +
164C PRO* 3.8 39.0 + - + +
169C ILE* 4.6 3.1 - - + -
194C PHE* 1.3 84.7 - - - +
196C SER* 1.3 56.4 + - - +
197C LEU* 3.7 3.3 + - + +
207C PRO* 3.5 29.4 - - + -
208C LYS 3.2 5.6 - - - +
209C LEU* 4.0 10.8 - - + -
244C THR* 4.5 8.1 - - + -
37D ARG* 2.4 33.3 + - - +
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Residues in contact with SER 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C PHE* 3.5 15.2 - - - -
195C VAL* 1.3 72.1 - - - +
197C LEU* 1.3 66.0 + - - +
207C PRO* 3.2 6.6 - - - +
208C LYS* 2.8 51.4 + - - +
210C SER* 5.7 0.7 + - - -
247C HIS* 5.6 4.5 - - - -
35D GLU* 3.3 22.8 + - - -
37D ARG* 3.7 1.6 - - - +
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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