Contacts of the strand formed by residues 188 - 196 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79B GLU* 5.3 0.8 + - - -
83B PHE* 3.7 29.9 - + - -
127B TYR* 3.1 49.6 - + - -
131B TRP* 4.4 3.9 + + - -
173B ALA* 4.5 2.4 - - - +
186B PRO* 4.2 0.7 - - - +
187B CYS* 1.3 76.1 - - - +
189B MET* 1.3 61.9 + - - +
190B PHE 3.4 2.2 + - - -
213B MET* 3.5 30.1 - - + -
214B TYR 3.8 7.2 - - - -
215B GLN* 4.0 2.4 - - + +
227B ASN* 3.4 10.6 + - - +
230B SER* 6.5 0.2 - - - -
231B TYR* 2.6 36.5 + + - +
400B UMP 3.2 24.6 + - - -
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Residues in contact with MET 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A ILE* 3.6 24.0 - - + -
172A SER* 5.7 0.2 - - - +
190A PHE* 3.5 41.1 - - + -
172B SER* 2.9 5.4 + - - -
173B ALA* 2.9 23.8 + - - -
174B TRP* 3.5 41.1 + - + +
186B PRO* 4.3 8.5 - - - +
187B CYS 3.0 7.6 + - - +
188B HIS* 1.3 72.8 - - - +
190B PHE* 1.3 68.1 + - + +
214B TYR* 3.3 24.0 + - + +
216B ARG* 3.7 25.1 - - - +
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Residues in contact with PHE 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A MET* 3.5 25.6 - - + -
190A PHE* 2.8 38.8 - + - -
214A TYR* 3.2 44.2 - + - -
131B TRP* 6.3 0.2 - - - +
170B ILE* 4.1 1.6 - - + -
171B LEU 3.1 14.8 - - - +
172B SER* 3.5 14.6 - - - +
173B ALA 4.8 0.2 - - - +
188B HIS 3.4 3.0 - - - -
189B MET* 1.3 87.6 - - + +
191B CYS* 1.3 93.3 + - - +
192B GLN* 4.2 3.6 - - + -
212B LEU* 4.9 1.3 - - + -
213B MET* 3.5 5.4 - - - +
214B TYR* 3.0 46.7 + - + -
231B TYR* 5.2 3.6 - - - -
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Residues in contact with CYS 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B ILE 4.0 0.2 - - - +
170B ILE* 3.5 3.5 - - - -
171B LEU* 2.9 47.0 + - - -
190B PHE* 1.3 86.0 - - - +
192B GLN* 1.3 60.0 + - - +
193B PHE* 3.5 32.9 + - - -
211B CYS* 3.9 6.1 - - - -
212B LEU 3.0 13.5 - - - +
213B MET* 3.8 5.8 - - + -
231B TYR* 3.7 29.8 - - + -
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Residues in contact with GLN 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A PHE* 3.5 19.4 - - + -
214A TYR* 2.5 35.8 + - - +
216A ARG* 3.1 35.0 + - - +
254A GLY* 3.5 2.1 - - - -
255A ASP* 4.2 7.7 - - - +
167B ARG* 3.6 23.0 + - - +
169B ILE 3.4 5.8 - - - +
170B ILE* 3.5 19.4 - - + +
190B PHE* 4.5 2.7 - - + -
191B CYS* 1.3 74.9 - - - +
193B PHE* 1.3 74.9 + - - +
194B PHE* 6.0 1.0 - - - -
211B CYS* 3.4 2.5 - - - -
212B LEU 2.7 34.3 + - - +
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Residues in contact with PHE 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B VAL* 3.8 22.9 - - + -
160B ILE* 4.5 2.9 - - + -
166B ASP 5.3 1.0 - - - +
169B ILE* 3.0 44.5 + - + +
171B LEU* 4.3 11.0 - - + -
191B CYS* 3.5 31.2 - - - -
192B GLN* 1.3 85.0 + - - +
194B PHE* 1.3 61.9 + - - +
209B LEU* 4.1 23.1 - - + -
210B SER 3.2 15.7 - - - +
211B CYS* 3.8 20.4 - - + -
234B LEU* 4.3 10.1 - - + -
235B THR* 4.0 12.1 - - - -
238B ILE* 3.4 33.0 - - + -
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Residues in contact with PHE 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLU* 4.5 4.0 - - - -
37A ARG* 3.5 36.6 - - - -
47A ALA* 5.1 5.4 - - + -
48A LEU* 5.0 3.1 - - - -
49A PHE* 3.4 66.2 - + + -
255A ASP* 3.5 29.6 - - + -
166B ASP 6.1 0.9 - - - -
169B ILE* 5.2 1.6 - - - -
192B GLN* 6.0 0.7 - - - -
193B PHE* 1.3 74.5 - - - +
195B VAL* 1.3 72.7 + - - +
196B SER* 3.4 23.1 - - - -
208B LYS 3.5 1.3 - - - +
209B LEU* 3.5 4.6 - - - +
210B SER* 2.8 36.4 + - - +
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Residues in contact with VAL 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ARG* 2.8 26.9 + - - -
160B ILE* 3.9 31.6 - - + +
164B PRO* 3.8 39.1 + - + +
169B ILE* 4.6 2.9 - - + -
194B PHE* 1.3 84.7 - - - +
196B SER* 1.3 63.1 + - - +
197B LEU* 3.7 3.7 + - + +
207B PRO* 3.5 30.1 - - + -
208B LYS 3.2 5.6 - - - +
209B LEU* 4.0 10.3 - - + -
244B THR* 4.6 7.6 - - + -
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Residues in contact with SER 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLU* 3.4 18.8 + - - -
37A ARG* 3.8 1.3 - - - +
194B PHE* 3.4 19.3 - - - -
195B VAL* 1.3 72.4 - - - +
197B LEU* 1.3 67.5 + - - +
207B PRO* 3.3 7.6 - - - +
208B LYS* 2.8 50.8 + - - +
210B SER* 5.7 0.9 + - - -
247B HIS* 5.5 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