Contacts of the strand formed by residues 188 - 196 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79H GLU* 5.2 0.8 + - - -
83H PHE* 3.6 30.2 - + - -
127H TYR* 3.2 49.5 - + - -
131H TRP* 4.4 3.9 + + - -
173H ALA* 4.6 2.6 - - - +
186H PRO* 4.2 0.3 - - - +
187H CYS* 1.3 76.6 - - - +
189H MET* 1.3 60.5 + - - +
190H PHE 3.4 2.8 + - - -
213H MET* 3.6 29.4 - - + -
214H TYR 3.8 7.0 - - - -
215H GLN* 4.1 2.0 - - + -
227H ASN* 3.4 10.4 + - - +
230H SER* 5.7 0.2 - - - -
231H TYR* 2.5 39.0 + + - +
700H UMP 3.2 24.4 + - - -
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Residues in contact with MET 189 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170G ILE* 3.7 24.2 - - + -
172G SER* 5.5 0.4 - - - +
190G PHE* 3.5 40.2 - - + -
172H SER* 2.9 14.9 + - - -
173H ALA 3.0 13.1 + - - -
174H TRP* 3.5 35.5 + - + -
186H PRO* 4.3 9.4 - - - +
187H CYS 4.0 6.3 - - - +
188H HIS* 1.3 74.4 - - - +
190H PHE* 1.3 69.2 + - + +
214H TYR* 3.3 23.3 + - + +
216H ARG* 3.7 30.7 - - - +
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Residues in contact with PHE 190 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G MET* 3.5 24.0 - - + -
190G PHE* 2.8 37.0 - + - -
214G TYR* 3.2 44.2 - + - -
131H TRP* 6.3 0.2 - - - +
170H ILE* 4.1 1.3 - - + -
171H LEU 3.1 14.8 - - - +
172H SER* 3.5 14.8 - - - +
188H HIS 3.4 2.8 + - - -
189H MET* 1.3 87.8 - - + +
191H CYS* 1.3 91.7 + - - +
192H GLN* 4.3 3.8 - - + -
212H LEU* 4.9 2.2 - - + -
213H MET* 3.5 5.3 - - - +
214H TYR* 3.0 46.6 + - + -
231H TYR* 5.2 3.1 - - - -
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Residues in contact with CYS 191 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169H ILE 4.0 0.2 - - - +
170H ILE* 3.5 2.9 - - - -
171H LEU* 2.9 47.9 + - - -
190H PHE* 1.3 85.0 - - - +
192H GLN* 1.3 61.1 + - - +
193H PHE* 3.5 33.6 - - - -
211H CYS* 4.0 5.8 - - - -
212H LEU 3.0 13.7 - - - +
213H MET* 3.9 5.6 - - + -
231H TYR* 3.8 29.2 - - + -
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Residues in contact with GLN 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G PHE* 3.6 18.4 - - + -
214G TYR* 2.5 39.7 + - - +
216G ARG* 3.0 32.4 + - - +
254G GLY* 3.5 2.4 - - - -
255G ASP* 4.2 7.7 - - - +
167H ARG* 3.7 21.6 + - - +
169H ILE 3.4 5.8 - - - +
170H ILE* 3.5 20.5 - - + +
190H PHE* 4.3 2.7 - - + -
191H CYS* 1.3 74.8 - - - +
193H PHE* 1.3 75.0 + - - +
194H PHE* 6.0 0.8 - - - -
211H CYS* 3.4 2.3 - - - -
212H LEU 2.7 35.8 + - - +
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Residues in contact with PHE 193 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156H VAL* 3.8 20.9 - - + -
160H ILE* 4.4 3.6 - - + -
166H ASP 5.3 0.9 - - - +
169H ILE* 3.0 46.0 + - + +
171H LEU* 4.3 10.8 - - + -
191H CYS* 3.5 31.0 - - - -
192H GLN* 1.3 84.6 + - - +
194H PHE* 1.3 62.2 + - - +
209H LEU* 4.1 21.3 - - + -
210H SER 3.2 14.6 - - - +
211H CYS* 3.8 20.0 - - + -
234H LEU* 4.3 10.1 - - + -
235H THR* 4.0 13.2 - - - -
238H ILE* 3.4 32.3 - - + -
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Residues in contact with PHE 194 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G GLU* 4.5 4.0 - - - -
37G ARG* 3.6 34.1 - - - -
47G ALA* 5.1 4.9 - - + -
48G LEU* 4.9 2.9 - - - -
49G PHE* 3.4 65.3 - + + -
255G ASP* 3.5 31.4 - - + -
166H ASP 6.1 0.7 - - - -
169H ILE* 5.2 1.6 - - - -
192H GLN* 6.0 0.9 - - - -
193H PHE* 1.3 76.4 - - - +
195H VAL* 1.3 72.6 + - - +
196H SER* 3.5 23.3 - - - -
208H LYS 3.5 2.6 - - - +
209H LEU* 3.5 3.3 - - - +
210H SER* 2.9 35.2 + - - +
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Residues in contact with VAL 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G ARG* 2.8 26.9 + - - -
160H ILE* 3.9 32.8 - - + +
164H PRO* 3.8 39.5 + - + +
169H ILE* 4.6 3.4 - - + -
194H PHE* 1.3 83.4 - - - +
196H SER* 1.3 63.4 + - - +
197H LEU* 3.7 3.3 + - + +
207H PRO* 3.5 28.7 - - + -
208H LYS 3.3 6.3 - - - +
209H LEU* 4.1 10.5 - - + -
244H THR* 4.7 5.8 - - + -
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Residues in contact with SER 196 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G GLU* 3.5 18.7 + - - -
37G ARG* 3.8 1.8 - - - +
194H PHE* 3.5 18.7 - - - -
195H VAL* 1.3 72.8 - - - +
197H LEU* 1.3 65.8 + - - +
207H PRO* 3.3 8.3 - - - +
208H LYS* 2.8 47.6 + - - +
210H SER* 5.7 0.7 + - - -
247H HIS* 5.5 4.9 - - - -
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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