Contacts of the strand formed by residues 188 - 196 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79P GLU* 5.4 0.8 + - - -
83P PHE* 3.7 27.3 - + - -
127P TYR* 3.2 49.2 - + - -
131P TRP* 4.4 6.1 + + - -
173P ALA* 4.6 2.3 - - - +
186P PRO* 4.3 0.3 - - - +
187P CYS* 1.3 74.1 - - - +
189P MET* 1.3 63.1 + - - +
190P PHE* 3.4 3.6 + - - -
213P MET* 3.5 30.3 - - + -
214P TYR 3.7 7.2 - - - -
215P GLN* 3.9 2.7 - - + +
227P ASN* 3.4 10.3 + - - +
230P SER* 5.8 0.2 - - - -
231P TYR* 2.5 36.2 + + - +
700P UMP 3.1 25.6 + - - -
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Residues in contact with MET 189 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170O ILE* 3.7 24.9 - - + -
172O SER* 5.5 0.4 - - - +
190O PHE* 3.5 39.5 - - + -
172P SER* 2.9 15.6 + - - -
173P ALA 3.0 12.7 + - - -
174P TRP* 3.5 40.9 + - + -
186P PRO* 4.2 10.3 - - - +
187P CYS 3.0 7.7 + - - +
188P HIS* 1.3 70.8 - - - +
190P PHE* 1.3 67.8 + - + +
214P TYR* 3.3 23.8 + - + +
216P ARG* 3.7 25.4 - - - -
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Residues in contact with PHE 190 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189O MET* 3.5 25.4 - - + -
190O PHE* 2.9 36.1 - + - -
214O TYR* 3.2 44.4 - + - -
131P TRP* 6.2 0.2 - - - +
170P ILE* 4.0 2.5 - - + -
171P LEU 3.1 14.6 - - - +
172P SER* 3.5 14.6 - - - +
188P HIS 3.4 3.6 + - - -
189P MET* 1.3 88.3 - - + +
191P CYS* 1.3 90.7 + - - +
192P GLN* 4.3 4.0 - - + -
212P LEU* 4.9 1.6 - - + -
213P MET* 3.5 5.2 - - - +
214P TYR* 3.0 46.0 + - + -
231P TYR* 5.1 3.6 + - - -
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Residues in contact with CYS 191 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169P ILE 4.1 0.2 - - - +
170P ILE* 3.6 3.1 - - - -
171P LEU* 2.9 47.5 + - - -
190P PHE* 1.3 85.7 - - - +
192P GLN* 1.3 60.0 + - - +
193P PHE* 3.5 33.2 - - - -
211P CYS* 4.0 6.5 - - - -
212P LEU 3.0 14.4 - - - +
213P MET* 3.9 8.5 - - + -
231P TYR* 3.8 26.7 - - + -
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Residues in contact with GLN 192 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49O PHE* 3.6 18.6 - - + -
214O TYR* 2.5 35.5 + - - +
216O ARG* 3.1 42.8 + - - +
254O GLY* 3.6 1.7 - - - -
255O ASP* 4.3 6.5 - - - +
167P ARG* 3.7 17.4 + - - +
169P ILE 3.4 6.8 - - - +
170P ILE* 3.4 20.7 - - + +
190P PHE* 4.3 2.9 - - + -
191P CYS* 1.3 75.7 - - - +
193P PHE* 1.3 73.3 + - - +
194P PHE* 6.1 0.6 - - - -
211P CYS* 3.4 2.3 - - - -
212P LEU 2.8 34.6 + - - +
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Residues in contact with PHE 193 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156P VAL* 3.8 20.9 - - + -
160P ILE* 4.4 3.1 - - + -
166P ASP 5.3 0.9 - - - +
169P ILE* 3.0 46.5 + - + +
171P LEU* 4.3 10.8 - - + -
191P CYS* 3.5 31.4 - - - -
192P GLN* 1.3 84.7 + - - +
194P PHE* 1.3 61.8 + - - +
209P LEU* 4.1 21.5 - - + -
210P SER 3.3 14.4 - - - +
211P CYS* 3.8 19.5 - - + -
234P LEU* 4.3 9.9 - - + -
235P THR* 4.1 12.6 - - - -
238P ILE* 3.4 33.4 - - + -
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Residues in contact with PHE 194 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35O GLU* 4.6 3.8 - - - -
37O ARG* 3.5 34.5 - - - -
47O ALA* 5.2 4.3 - - + -
48O LEU* 5.0 3.1 - - - -
49O PHE* 3.4 66.0 - + + -
255O ASP* 3.5 32.5 - - + -
164P PRO 5.6 0.2 - - - -
166P ASP 6.2 0.2 - - - -
169P ILE* 5.2 0.9 - - - -
192P GLN* 4.2 0.9 + - - -
193P PHE* 1.3 75.9 - - - +
195P VAL* 1.3 72.7 + - - +
196P SER* 3.4 23.6 - - - -
208P LYS 3.5 2.6 - - - +
209P LEU* 3.5 3.3 - - - +
210P SER* 2.9 34.8 + - - +
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Residues in contact with VAL 195 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37O ARG* 2.8 26.5 + - - +
160P ILE* 3.8 32.5 - - + +
164P PRO* 3.7 39.8 + - + +
169P ILE* 4.6 3.1 - - + -
194P PHE* 1.3 83.4 - - - +
196P SER* 1.3 63.4 + - - +
197P LEU* 3.7 4.0 + - + +
207P PRO* 3.5 28.5 - - + -
208P LYS 3.3 5.4 - - - +
209P LEU* 4.0 10.8 - - + -
244P THR* 4.7 7.0 - - + -
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Residues in contact with SER 196 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35O GLU* 3.5 14.3 + - - -
37O ARG* 3.7 6.3 - - - +
194P PHE* 3.4 18.8 - - - -
195P VAL* 1.3 72.3 - - - +
197P LEU* 1.3 66.7 + - - +
207P PRO* 3.3 7.8 - - - +
208P LYS* 2.9 46.9 + - - +
210P SER* 5.6 1.2 + - - -
247P HIS* 5.6 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