Contacts of the strand formed by residues 188 - 196 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79D GLU* 5.3 1.2 + - - -
83D PHE* 3.7 29.3 - + - -
127D TYR* 3.2 49.8 - + - -
131D TRP* 4.4 3.7 + + - -
173D ALA* 4.5 2.4 - - - +
186D PRO* 4.1 0.7 - - - +
187D CYS* 1.3 76.3 - - - +
189D MET* 1.3 62.3 + - - +
190D PHE 3.4 2.2 - - - -
213D MET* 3.5 27.4 - - + -
214D TYR 3.8 7.0 - - - -
215D GLN* 4.0 2.4 - - + +
227D ASN* 3.4 11.7 + - - +
230D SER* 5.8 0.4 - - - -
231D TYR* 2.6 38.0 + + + +
500D UMP 3.3 23.6 + - - -
2501D CB3 5.8 0.2 - - - +
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Residues in contact with MET 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C ILE* 3.7 24.7 - - + -
172C SER* 5.7 0.2 - - - +
190C PHE* 3.5 40.6 - - + -
172D SER* 3.0 5.2 + - - -
173D ALA* 3.0 23.8 + - - -
174D TRP* 3.5 41.7 + - + +
186D PRO* 4.3 8.7 - - - +
187D CYS 3.0 7.6 + - - +
188D HIS* 1.3 72.8 - - - +
190D PHE* 1.3 68.3 + - + +
214D TYR* 3.3 23.5 + - + +
216D ARG* 3.6 25.4 - - - +
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Residues in contact with PHE 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C MET* 3.5 25.8 - - + -
190C PHE* 2.8 38.6 - + - -
214C TYR* 3.2 43.7 - + - -
131D TRP* 6.3 0.2 - - - +
170D ILE* 4.0 1.6 - - + -
171D LEU 3.2 14.4 - - - +
172D SER* 3.5 14.8 - - - +
173D ALA 4.8 0.2 - - - +
188D HIS 3.4 3.2 - - - -
189D MET* 1.3 88.2 - - + +
191D CYS* 1.3 81.7 + - - +
192D GLN* 4.3 3.6 - - + -
212D LEU* 4.9 1.6 - - + -
213D MET* 3.5 5.0 - - - +
214D TYR* 2.9 46.1 + - + -
231D TYR* 5.2 3.6 - - - -
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Residues in contact with CYS 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D ILE 4.0 0.3 - - - +
170D ILE* 3.5 3.6 - - - -
171D LEU* 2.9 47.2 + - - -
190D PHE* 1.3 84.8 - - - +
192D GLN* 1.3 60.6 + - - +
193D PHE* 3.5 33.2 + - - -
211D CYS* 3.9 5.4 - - - -
212D LEU 3.0 13.2 - - - +
213D MET* 3.8 6.1 - - + -
231D TYR* 3.7 29.8 - - + -
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Residues in contact with GLN 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C PHE* 3.5 19.1 - - + -
214C TYR* 2.5 35.0 + - - +
216C ARG* 3.1 36.2 + - - +
254C GLY* 3.5 1.6 - - - -
255C ASP* 4.2 7.5 - - - +
167D ARG* 3.6 22.8 + - - +
169D ILE 3.4 6.3 - - - +
170D ILE* 3.4 22.3 - - + +
190D PHE* 4.5 2.5 - - + -
191D CYS* 1.3 73.8 - - - +
193D PHE* 1.3 74.1 + - - +
194D PHE* 6.0 1.0 - - - -
211D CYS* 3.4 2.6 - - - -
212D LEU 2.7 35.2 + - - +
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Residues in contact with PHE 193 (chain D).
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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156D VAL* 3.8 22.9 - - + -
160D ILE* 4.4 2.9 - - + -
166D ASP 5.3 1.0 - - - +
169D ILE* 3.0 45.4 + - + +
171D LEU* 4.3 10.8 - - + -
191D CYS* 3.5 30.7 - - - -
192D GLN* 1.3 85.9 + - - +
194D PHE* 1.3 61.1 + - - +
209D LEU* 4.1 23.6 - - + -
210D SER 3.2 14.4 - - - +
211D CYS* 3.8 20.4 - - + -
234D LEU* 4.2 10.1 - - + -
235D THR* 3.9 13.0 - - - -
238D ILE* 3.4 34.1 - - + -
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Residues in contact with PHE 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C GLU* 4.5 4.3 - - - -
37C ARG* 3.5 35.7 - - - -
47C ALA* 5.1 5.8 - - + -
48C LEU* 5.0 3.1 - - - -
49C PHE* 3.4 66.0 - + + -
255C ASP* 3.6 29.6 - - + -
166D ASP 6.1 0.9 - - - -
169D ILE* 5.2 1.3 - - - -
192D GLN* 6.0 0.7 - - - -
193D PHE* 1.3 74.3 - - - +
195D VAL* 1.3 72.7 + - - +
196D SER* 3.5 22.2 - - - -
208D LYS 3.5 1.4 - - - +
209D LEU* 3.5 4.6 - - - +
210D SER* 2.8 36.1 + - - +
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Residues in contact with VAL 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ARG* 2.7 34.2 + - - +
160D ILE* 3.9 31.6 - - + +
164D PRO* 3.7 39.4 + - + +
169D ILE* 4.6 2.9 - - + -
193D PHE 5.5 0.2 - - - -
194D PHE* 1.3 84.9 - - - +
196D SER* 1.3 57.0 + - - +
197D LEU* 3.7 3.5 + - + +
207D PRO* 3.5 29.2 - - + -
208D LYS 3.2 5.6 - - - +
209D LEU* 4.0 10.3 - - + -
244D THR* 4.6 7.9 - - + -
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Residues in contact with SER 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C GLU* 3.5 18.8 + - - -
37C ARG* 3.8 1.6 - - - +
194D PHE* 3.5 18.2 - - - -
195D VAL* 1.3 73.0 - - - +
197D LEU* 1.3 66.4 + - - +
207D PRO* 3.2 7.3 - - - +
208D LYS* 2.8 50.9 + - - +
210D SER* 5.6 0.9 + - - -
247D HIS* 5.4 5.2 - - - -
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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