Contacts of the strand formed by residues 188 - 196 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79K GLU* 5.4 0.8 + - - -
83K PHE* 3.8 27.4 - + - -
127K TYR* 3.2 48.1 - + - -
131K TRP* 4.4 5.9 + + - -
173K ALA* 4.6 2.6 - - - +
186K PRO* 4.3 0.2 - - - +
187K CYS* 1.3 74.5 - - - +
189K MET* 1.3 63.0 + - - +
190K PHE 3.4 3.4 + - - -
213K MET* 3.5 30.5 - - + -
214K TYR 3.7 7.4 - - - -
215K GLN* 4.0 3.6 - - + -
227K ASN* 3.4 9.4 + - - -
230K SER* 5.9 0.2 - - - -
231K TYR* 2.6 37.2 + + - +
450K UMP 3.0 26.8 + - - -
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Residues in contact with MET 189 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172K SER* 2.9 15.6 + - - -
173K ALA 3.0 11.3 + - - -
174K TRP* 3.5 35.3 + - + +
186K PRO* 4.2 9.6 - - - +
187K CYS 3.0 7.8 + - - +
188K HIS* 1.3 71.7 - - - +
190K PHE* 1.3 68.3 + - + +
214K TYR* 3.3 24.3 + - + +
216K ARG* 3.7 30.1 - - - -
170L ILE* 3.7 24.0 - - + -
172L SER* 5.7 0.4 - - - +
190L PHE* 3.4 40.2 - - + -
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Residues in contact with PHE 190 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131K TRP* 6.2 0.4 - - - +
170K ILE* 4.0 2.0 - - + -
171K LEU 3.1 15.3 - - - +
172K SER* 3.5 14.6 - - - +
188K HIS 3.4 3.8 + - - -
189K MET* 1.3 88.3 - - + +
191K CYS* 1.3 93.1 + - - +
192K GLN* 4.3 3.6 - - + -
212K LEU* 4.9 1.1 - - + -
213K MET* 3.5 5.2 - - - +
214K TYR* 3.0 45.3 + - + -
231K TYR* 5.2 3.6 - - - -
189L MET* 3.5 23.6 - - + -
190L PHE* 2.9 37.2 - + - -
214L TYR* 3.1 48.5 - + - -
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Residues in contact with CYS 191 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169K ILE 4.1 0.3 - - - +
170K ILE* 3.6 3.5 - - - -
171K LEU* 2.9 46.8 + - - -
190K PHE* 1.3 83.9 - - - +
192K GLN* 1.3 60.7 + - - +
193K PHE* 3.5 33.7 - - - -
211K CYS* 4.0 6.5 - - - -
212K LEU 3.0 13.9 - - - +
213K MET* 3.8 13.9 - - + -
231K TYR* 3.7 21.5 - - + -
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Residues in contact with GLN 192 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167K ARG* 3.7 22.2 + - - +
169K ILE 3.4 5.6 - - - +
170K ILE* 3.4 21.8 - - + +
190K PHE* 4.5 2.5 - - + -
191K CYS* 1.3 73.6 - - - +
193K PHE* 1.3 76.5 + - - +
194K PHE* 6.1 0.6 - - - -
211K CYS* 3.4 2.0 - - - -
212K LEU 2.7 33.3 + - - +
49L PHE* 3.4 20.1 - - + -
214L TYR* 2.5 37.4 + - - +
216L ARG* 3.1 27.1 + - - +
254L GLY* 3.4 9.2 - - - -
255L ASP* 4.2 7.5 - - - +
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Residues in contact with PHE 193 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156K VAL* 3.8 26.5 - - + -
160K ILE* 4.4 2.5 - - + -
166K ASP 5.3 0.9 - - - +
169K ILE* 3.0 44.9 + - + +
171K LEU* 4.3 11.0 - - + -
191K CYS* 3.5 30.5 - - - -
192K GLN* 1.3 85.0 + - - +
194K PHE* 1.3 62.6 + - - +
209K LEU* 4.1 22.4 - - + -
210K SER 3.3 15.5 - - - +
211K CYS* 3.8 20.4 - - + -
234K LEU* 4.3 9.9 - - + -
235K THR* 4.1 12.3 - - - -
238K ILE* 3.4 30.5 - - + -
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Residues in contact with PHE 194 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164K PRO 5.6 0.2 - - - -
169K ILE* 5.2 1.1 - - - -
192K GLN* 6.1 0.7 - - - -
193K PHE* 1.3 76.3 - - - +
195K VAL* 1.3 72.5 + - - +
196K SER* 3.4 23.1 - - - -
208K LYS 3.5 1.1 - - - +
209K LEU* 3.5 4.7 - - - +
210K SER* 2.8 37.3 + - - +
35L GLU* 4.4 4.0 - - - -
37L ARG* 3.5 36.1 - - - -
47L ALA* 5.2 4.9 - - + -
48L LEU* 5.0 3.6 - - - -
49L PHE* 3.4 63.0 - + + -
255L ASP* 3.6 30.3 - - + -
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Residues in contact with VAL 195 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160K ILE* 3.8 32.5 - - + +
164K PRO* 3.7 39.3 + - + +
169K ILE* 4.6 2.9 - - + -
194K PHE* 1.3 85.1 - - - +
196K SER* 1.3 56.6 + - - +
197K LEU* 3.7 3.9 + - + +
207K PRO* 3.6 29.4 - - + -
208K LYS 3.2 6.1 - - - +
209K LEU* 4.0 11.0 - - + -
244K THR* 4.7 6.7 - - + -
37L ARG* 2.8 32.8 + - - +
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Residues in contact with SER 196 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194K PHE* 3.4 19.1 - - - -
195K VAL* 1.3 72.4 - - - +
197K LEU* 1.3 66.2 + - - +
207K PRO* 3.3 7.1 - - - +
208K LYS* 2.8 52.0 + - - +
210K SER* 5.6 1.4 + - - -
247K HIS* 5.5 4.5 - - - -
35L GLU* 3.5 18.2 + - - -
37L ARG* 3.8 2.0 - - - +
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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