Contacts of the strand formed by residues 188 - 196 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79N GLU* 5.4 1.0 + - - -
83N PHE* 3.7 27.1 - + - -
127N TYR* 3.2 48.4 - + - -
131N TRP* 4.4 6.2 + + - -
173N ALA* 4.6 2.3 - - - +
186N PRO* 4.3 0.3 - - - +
187N CYS* 1.3 74.4 - - - +
189N MET* 1.3 63.2 + - - +
190N PHE* 3.4 3.8 + - - -
213N MET* 3.5 31.6 - - + -
214N TYR 3.7 7.2 - - - -
215N GLN* 4.1 1.8 - - + -
227N ASN* 3.4 10.6 + - - +
230N SER* 5.8 0.2 - - - -
231N TYR* 2.5 38.8 + + - +
600N UMP 3.1 24.8 + - - -
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Residues in contact with MET 189 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170M ILE* 3.8 23.1 - - + -
172M SER* 5.5 0.2 - - - -
190M PHE* 3.5 40.6 - - + -
172N SER* 2.9 15.6 + - - -
173N ALA 3.0 12.5 + - - -
174N TRP* 3.5 40.3 + - + -
186N PRO* 4.2 10.5 - - - +
187N CYS 3.0 5.8 + - - +
188N HIS* 1.3 72.8 - - - +
190N PHE* 1.3 68.0 + - + +
214N TYR* 3.3 24.7 + - + +
216N ARG* 3.7 26.0 - - - -
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Residues in contact with PHE 190 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189M MET* 3.5 24.9 - - + -
190M PHE* 2.9 35.9 - + - -
214M TYR* 3.2 44.2 - + - -
131N TRP* 6.2 0.2 - - - +
170N ILE* 4.0 2.0 - - + -
171N LEU 3.1 14.6 - - - +
172N SER* 3.5 14.4 - - - +
174N TRP* 6.0 0.2 - - + -
188N HIS 3.4 3.4 + - - -
189N MET* 1.3 87.1 - - + +
191N CYS* 1.3 92.0 + - - +
192N GLN* 4.3 4.7 - - + -
212N LEU* 4.8 1.6 - - + -
213N MET* 3.4 5.4 - - - +
214N TYR* 3.0 46.6 + - + -
231N TYR* 5.1 3.6 + - - -
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Residues in contact with CYS 191 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169N ILE 4.1 0.2 - - - +
170N ILE* 3.6 3.1 - - - -
171N LEU* 2.9 47.4 + - - -
190N PHE* 1.3 85.7 - - - +
192N GLN* 1.3 61.1 + - - +
193N PHE* 3.5 33.4 - - - -
211N CYS* 3.9 10.5 - - - -
212N LEU 2.9 14.6 - - - +
213N MET* 3.8 7.4 - - - -
231N TYR* 3.8 23.8 - - + -
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Residues in contact with GLN 192 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49M PHE* 3.5 20.3 - - + -
214M TYR* 2.6 34.8 + - - +
216M ARG* 3.1 35.8 + - - +
254M GLY* 3.5 3.3 - - - -
255M ASP* 4.2 7.3 - - - +
167N ARG* 3.7 22.0 + - - +
169N ILE 3.4 6.7 - - - +
170N ILE* 3.4 21.1 - - + +
190N PHE* 4.3 2.9 - - + -
191N CYS* 1.3 74.3 - - - +
193N PHE* 1.3 74.7 + - - +
194N PHE* 6.1 0.6 - - - -
211N CYS* 3.4 3.7 - - - -
212N LEU 2.7 33.5 + - - +
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Residues in contact with PHE 193 (chain N).
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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156N VAL* 3.8 21.1 - - + -
160N ILE* 4.4 3.6 - - + -
166N ASP 5.3 0.9 - - - +
169N ILE* 3.0 46.0 + - + +
171N LEU* 4.3 11.0 - - + -
191N CYS* 3.5 31.6 - - - -
192N GLN* 1.3 84.9 + - - +
194N PHE* 1.3 62.7 + - - +
209N LEU* 4.0 21.8 - - + -
210N SER 3.2 14.6 - - - +
211N CYS* 3.8 19.7 - - + -
234N LEU* 4.4 9.6 - - + -
235N THR* 4.1 12.8 - - - -
238N ILE* 3.4 32.1 - - + -
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Residues in contact with PHE 194 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35M GLU* 4.4 4.5 - - - -
37M ARG* 3.4 36.8 - - - -
47M ALA* 5.2 4.5 - - + -
48M LEU* 5.1 3.4 - - - -
49M PHE* 3.4 63.5 - + + -
255M ASP* 3.7 30.1 - - + -
164N PRO 5.6 0.2 - - - -
166N ASP 6.2 0.2 - - - -
169N ILE* 5.2 1.1 - - - -
192N GLN* 6.1 0.7 - - - -
193N PHE* 1.3 75.8 - - - +
195N VAL* 1.3 72.7 + - - +
196N SER* 3.4 23.8 - - - -
208N LYS 3.4 2.8 - - - +
209N LEU* 3.4 3.3 - - - +
210N SER* 2.9 36.1 + - - -
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Residues in contact with VAL 195 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37M ARG* 2.7 33.6 + - - -
160N ILE* 3.8 32.3 - - + +
164N PRO* 3.7 40.4 + - + +
169N ILE* 4.6 3.4 - - + -
194N PHE* 1.3 82.3 - - - +
196N SER* 1.3 57.4 + - - +
197N LEU* 3.7 4.0 + - + +
207N PRO* 3.5 29.4 - - + -
208N LYS 3.2 5.2 - - - +
209N LEU* 4.1 10.8 - - + -
244N THR* 4.7 6.7 - - + -
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Residues in contact with SER 196 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35M GLU* 3.4 18.9 + - - -
37M ARG* 3.8 1.8 - - - +
194N PHE* 3.4 18.4 - - - -
195N VAL* 1.3 71.7 - - - +
197N LEU* 1.3 67.3 + - - +
207N PRO* 3.2 8.0 - - - +
208N LYS* 2.8 47.5 + - - +
210N SER* 5.7 0.7 + - - -
247N 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