Contacts of the strand formed by residues 188 - 196 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A GLU* 5.3 0.8 + - - -
83A PHE* 3.7 27.3 - + - -
127A TYR* 3.2 48.3 - + - -
131A TRP* 4.4 4.9 + + - -
173A ALA* 4.6 2.6 - - - +
186A PRO* 4.2 0.7 - - - +
187A CYS* 1.3 75.9 - - - +
189A MET* 1.3 61.3 + - - +
190A PHE 3.4 2.6 + - - -
213A MET* 3.5 29.8 - - + -
214A TYR 3.8 7.0 - - - -
215A GLN* 4.1 2.5 - - + -
227A ASN* 3.3 12.1 + - - +
230A SER* 5.8 0.2 - - - -
231A TYR* 2.6 37.2 + + - +
350A UMP 3.2 24.9 + - - -
2351A CB3 5.8 0.4 - - - +
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Residues in contact with MET 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A SER* 2.9 14.9 + - - -
173A ALA 3.1 11.8 + - - -
174A TRP* 3.5 39.9 + - + +
186A PRO* 4.3 9.2 - - - +
187A CYS 3.1 5.6 + - - +
188A HIS* 1.3 73.9 - - - +
190A PHE* 1.3 69.4 + - + +
214A TYR* 3.3 24.7 + - + +
216A ARG* 3.7 26.5 - - - -
170B ILE* 3.6 25.4 - - + -
172B SER* 5.7 0.2 - - - +
190B PHE* 3.5 39.5 - - + -
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Residues in contact with PHE 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A TRP* 6.3 0.2 - - - +
170A ILE* 4.0 1.8 - - + -
171A LEU 3.1 14.6 - - - +
172A SER* 3.5 13.9 - - - +
174A TRP* 6.0 0.2 - - + -
188A HIS 3.4 3.2 + - - -
189A MET* 1.3 87.4 - - + +
191A CYS* 1.3 94.6 + - - +
192A GLN* 4.3 3.4 - - + -
212A LEU* 4.9 1.3 - - + -
213A MET* 3.5 5.1 - - - +
214A TYR* 3.0 44.8 + - + -
231A TYR* 5.3 3.4 - - - -
189B MET* 3.5 22.0 - - + -
190B PHE* 2.8 38.8 - + - -
214B TYR* 3.1 48.5 - + - -
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Residues in contact with CYS 191 (chain A).
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* 3.5 3.3 - - - -
171A LEU* 2.9 46.3 + - - +
190A PHE* 1.3 86.2 - - - +
192A GLN* 1.3 61.1 + - - +
193A PHE* 3.4 35.2 - - - -
211A CYS* 4.0 6.3 - - - -
212A LEU 3.0 14.1 - - - +
213A MET* 3.8 9.0 - - + -
231A TYR* 3.8 26.5 - - + -
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Residues in contact with GLN 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ARG* 3.6 21.4 + - - +
169A ILE 3.4 6.3 - - - +
170A ILE* 3.5 19.6 - - + +
190A PHE* 4.5 2.0 - - + -
191A CYS* 1.3 75.3 - - - +
193A PHE* 1.3 75.2 + - - +
194A PHE* 6.1 0.8 - - - -
211A CYS* 3.3 2.1 - - - -
212A LEU 2.7 34.9 + - - +
49B PHE* 3.5 18.7 - - + -
214B TYR* 2.5 36.0 + - - +
216B ARG* 3.0 36.3 + - - +
254B GLY* 3.5 1.6 - - - -
255B ASP* 4.1 8.3 - - - +
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Residues in contact with PHE 193 (chain A).
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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156A VAL* 3.8 22.4 - - + -
160A ILE* 4.4 2.5 - - + -
166A ASP 5.3 0.9 - - - +
169A ILE* 3.0 44.2 + - + +
171A LEU* 4.3 11.0 - - + -
191A CYS* 3.4 30.5 - - - -
192A GLN* 1.3 86.0 + - - +
194A PHE* 1.3 63.3 + - - +
209A LEU* 4.0 22.4 - - + -
210A SER 3.2 15.3 - - - +
211A CYS* 3.7 22.4 - - + -
234A LEU* 4.3 9.9 - - + -
235A THR* 3.9 12.6 - - - -
238A ILE* 3.4 33.4 - - + -
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Residues in contact with PHE 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ASP 6.1 0.9 - - - -
169A ILE* 5.2 1.6 - - - -
192A GLN* 6.1 0.7 - - - -
193A PHE* 1.3 74.9 - - - +
195A VAL* 1.3 71.7 + - - +
196A SER* 3.4 23.1 - - - -
208A LYS 3.5 1.1 - - - +
209A LEU* 3.5 4.5 - - - +
210A SER* 2.8 37.7 + - - +
35B GLU* 4.4 4.0 - - - -
37B ARG* 3.5 35.9 - - - -
47B ALA* 5.1 5.4 - - + -
48B LEU* 5.0 3.1 - - - -
49B PHE* 3.3 64.4 - + + -
255B ASP* 3.6 30.5 - - + -
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Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ILE* 3.9 31.4 - - + +
164A PRO* 3.8 39.1 + - + +
169A ILE* 4.6 3.1 - - + -
194A PHE* 1.3 84.7 - - - +
196A SER* 1.3 56.0 + - - +
197A LEU* 3.8 3.6 + - + +
207A PRO* 3.5 29.6 - - + -
208A LYS 3.2 5.2 - - - +
209A LEU* 4.0 11.0 - - + -
244A THR* 4.5 7.9 - - + -
37B ARG* 2.7 33.9 + - - +
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Residues in contact with SER 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A PHE* 3.4 15.9 - - - -
195A VAL* 1.3 72.0 - - - +
197A LEU* 1.3 65.2 + - - +
207A PRO* 3.2 6.6 - - - +
208A LYS* 2.8 51.4 + - - +
210A SER* 5.7 0.9 + - - -
247A HIS* 5.5 4.9 - - - -
35B GLU* 3.4 22.9 + - - -
37B 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