Contacts of the strand formed by residues 188 - 196 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79M GLU* 5.4 1.2 + - - -
83M PHE* 3.8 26.4 - + - -
127M TYR* 3.2 47.6 - + - -
131M TRP* 4.4 5.9 + + - -
173M ALA* 4.6 1.9 - - - +
186M PRO* 4.3 0.3 - - - +
187M CYS* 1.3 75.4 - - - +
189M MET* 1.3 63.0 + - - +
190M PHE 3.4 3.6 + - - -
213M MET* 3.5 31.4 - - + -
214M TYR 3.7 6.7 - - - -
215M GLN* 3.9 2.4 - - + +
227M ASN* 3.4 10.6 + - - +
231M TYR* 2.6 34.8 + + - +
550M UMP 3.0 27.4 + - - -
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Residues in contact with MET 189 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172M SER* 2.9 15.4 + - - -
173M ALA 3.0 12.2 + - - -
174M TRP* 3.5 35.6 + - + -
186M PRO* 4.2 10.1 - - - +
187M CYS 3.1 6.1 + - - +
188M HIS* 1.3 73.9 - - - +
190M PHE* 1.3 68.6 + - + +
214M TYR* 3.3 24.5 + - + +
216M ARG* 3.7 30.1 - - - -
170N ILE* 3.8 24.5 - - + -
172N SER* 5.6 0.2 - - - -
190N PHE* 3.5 39.5 - - + -
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Residues in contact with PHE 190 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131M TRP* 6.3 0.7 - - - +
170M ILE* 4.0 2.9 - - + -
171M LEU 3.1 14.4 - - - +
172M SER* 3.5 14.8 - - - +
188M HIS 3.4 3.2 - - - -
189M MET* 1.3 89.5 - - + +
191M CYS* 1.3 91.3 + - - +
192M GLN* 4.3 3.4 - - + -
212M LEU* 4.9 1.8 - - + -
213M MET* 3.5 6.0 - - - +
214M TYR* 3.0 45.0 + - + -
231M TYR* 5.1 3.4 - - - -
189N MET* 3.5 24.5 - - + -
190N PHE* 2.9 36.8 - + - -
214N TYR* 3.1 45.5 - + - -
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Residues in contact with CYS 191 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169M ILE 4.1 0.2 - - - +
170M ILE* 3.6 3.6 - - - -
171M LEU* 2.9 46.2 + - - -
190M PHE* 1.3 84.0 - - - +
192M GLN* 1.3 61.6 + - - +
193M PHE* 3.5 33.5 - - - -
211M CYS* 3.9 5.6 - - - -
212M LEU 2.9 14.6 - - - +
213M MET* 3.8 13.7 - - + -
231M TYR* 3.7 22.4 - - + -
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Residues in contact with GLN 192 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167M ARG* 3.7 22.0 + - - +
169M ILE 3.4 6.2 - - - +
170M ILE* 3.4 21.4 - - + +
190M PHE* 4.3 2.7 - - + -
191M CYS* 1.3 73.9 - - - +
193M PHE* 1.3 74.3 + - - +
194M PHE* 6.1 0.2 - - - -
211M CYS* 3.4 2.0 - - - -
212M LEU 2.7 34.3 + - - +
49N PHE* 3.5 19.4 - - + -
214N TYR* 2.5 41.5 + - - +
216N ARG* 3.1 24.6 + - - +
254N GLY* 3.4 8.7 - - - -
255N ASP* 4.2 7.3 - - - +
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Residues in contact with PHE 193 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156M VAL* 3.8 25.4 - - + -
160M ILE* 4.5 3.4 - - + -
166M ASP 5.3 1.0 - - - +
169M ILE* 3.0 44.7 + - + +
171M LEU* 4.3 10.8 - - + -
191M CYS* 3.5 30.7 - - - -
192M GLN* 1.3 86.4 + - - +
194M PHE* 1.3 62.3 + - - +
209M LEU* 4.1 21.8 - - + -
210M SER 3.2 14.1 - - - +
211M CYS* 3.8 21.1 - - + -
234M LEU* 4.3 10.3 - - + -
235M THR* 4.0 12.3 - - - -
238M ILE* 3.4 29.2 - - + -
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Residues in contact with PHE 194 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169M ILE* 5.2 0.9 - - - -
192M GLN* 6.1 0.7 - - - -
193M PHE* 1.3 75.3 - - - +
195M VAL* 1.3 73.9 + - - +
196M SER* 3.4 23.1 - - - -
208M LYS 3.5 1.4 - - - +
209M LEU* 3.5 3.5 - - - +
210M SER* 2.8 37.0 + - - +
35N GLU* 4.4 4.5 - - - -
37N ARG* 3.5 34.8 - - - -
47N ALA* 5.2 5.2 - - + -
48N LEU* 5.0 2.9 - - - -
49N PHE* 3.4 64.4 - + + -
255N ASP* 3.7 30.1 - - + -
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Residues in contact with VAL 195 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160M ILE* 3.8 32.3 - - + +
164M PRO* 3.8 37.8 + - + +
169M ILE* 4.6 3.1 - - + -
194M PHE* 1.3 84.9 - - - +
196M SER* 1.3 55.5 + - - +
197M LEU* 3.7 3.6 + - + +
207M PRO* 3.5 28.9 - - + -
208M LYS 3.2 5.4 - - - +
209M LEU* 4.0 11.0 - - + -
244M THR* 4.6 7.9 - - + -
37N ARG* 2.8 32.9 + - - +
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Residues in contact with SER 196 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194M PHE* 3.4 18.6 - - - -
195M VAL* 1.3 72.6 - - - +
197M LEU* 1.3 66.8 + - - +
207M PRO* 3.2 6.8 - - - +
208M LYS* 2.8 52.4 + - - +
210M SER* 5.5 1.4 + - - -
247M HIS* 5.5 4.9 - - - -
35N GLU* 3.5 18.8 + - - -
37N ARG* 3.8 0.9 - - - +
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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