Contacts of the strand formed by residues 208 - 219 (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 LYS 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A PHE* 3.5 1.4 - - - +
195A VAL* 3.2 6.8 - - - -
196A SER* 2.8 51.0 + - - +
199A PRO* 6.3 4.5 - - - -
206A LYS 4.3 7.5 + - - +
207A PRO* 1.3 75.3 - - - +
209A LEU* 1.3 59.9 + - - +
210A SER* 4.1 1.1 + - - -
245A GLU* 3.4 22.4 - - + +
246A PRO 5.8 0.4 + - - -
247A HIS* 3.7 41.1 + - + +
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Residues in contact with LEU 209 (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* 3.8 24.7 - - + -
193A PHE* 4.0 11.2 - - + -
194A PHE 3.5 12.6 - - - +
195A VAL* 4.0 10.8 - - + +
207A PRO 3.9 0.4 + - - -
208A LYS* 1.3 72.8 - - - +
210A SER* 1.3 68.9 + - - +
235A THR* 3.6 38.8 - - + +
238A ILE* 3.8 21.3 - - + -
239A ALA* 3.8 3.4 - - + +
244A THR* 3.7 24.2 - - + +
245A GLU 2.8 16.2 + - - +
246A PRO* 3.6 2.2 - - + +
247A HIS 2.7 27.9 + - - -
248A GLU 3.7 0.5 + - - -
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Residues in contact with SER 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A PHE* 3.2 10.3 - - - +
194A PHE* 2.8 38.5 + - - -
196A SER* 5.7 0.9 + - - -
208A LYS 5.1 0.9 + - - -
209A LEU* 1.3 73.8 - - - +
211A CYS* 1.3 63.8 + - - +
235A THR* 4.9 0.7 - - - -
247A HIS* 3.5 27.9 - - - -
248A GLU* 3.2 19.8 + - - +
250A ILE* 4.8 1.1 - - - -
49B PHE* 3.9 24.2 - - - -
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Residues in contact with CYS 211 (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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191A CYS* 4.0 22.9 - - - -
192A GLN 3.3 5.4 - - - -
193A PHE* 3.7 25.1 - - + -
210A SER* 1.3 76.2 - - - +
212A LEU* 1.3 57.9 + - - +
231A TYR* 4.1 11.4 - - - -
234A LEU* 6.0 0.2 - - - -
235A THR* 3.3 24.9 - - + +
248A GLU 3.0 7.2 + - - +
249A PHE* 3.3 19.6 - - + -
250A ILE* 2.8 33.1 + - - +
49B PHE* 4.2 3.6 - - - -
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Residues in contact with LEU 212 (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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190A PHE* 5.2 0.9 - - + -
191A CYS* 3.0 4.1 - - - -
192A GLN* 2.7 35.9 + - - +
211A CYS* 1.3 74.2 - - - +
213A MET* 1.3 77.4 + - - +
214A TYR* 4.3 2.7 - - + +
250A ILE* 3.2 18.6 - - + +
252A GLN* 4.6 9.6 - - + -
49B PHE* 3.7 19.4 - - + -
50B ALA* 3.4 26.7 - - + -
214B TYR* 3.6 39.9 - - + +
252B GLN* 3.6 18.8 - - - +
253B MET 3.9 2.2 - - - +
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Residues in contact with MET 213 (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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188A HIS* 3.5 22.9 - - + -
190A PHE 3.5 11.4 - - - +
191A CYS* 3.8 5.6 - - + -
211A CYS 4.1 0.6 - - - -
212A LEU* 1.3 79.1 - - - +
214A TYR* 1.3 79.6 + - - +
215A GLN* 3.5 20.4 - - - +
227A ASN* 4.0 11.0 - - + +
231A TYR* 3.7 39.3 - - + -
249A PHE* 3.8 18.8 - - + -
250A ILE 2.8 7.3 + - - -
251A LEU* 3.4 26.6 - - + +
252A GLN 3.0 25.3 + - - -
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Residues in contact with TYR 214 (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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49A PHE* 4.6 0.2 - - - -
189A MET* 3.3 29.0 + - + +
190A PHE* 3.0 32.7 + - + +
212A LEU* 4.3 3.5 - - + +
213A MET* 1.3 79.3 - - - +
215A GLN* 1.3 59.7 + - - +
216A ARG* 3.8 14.4 - - + -
252A GLN* 3.4 26.9 - - + -
253A MET 4.3 1.8 - - - -
254A GLY* 3.4 14.5 - - - -
190B PHE* 3.2 33.9 - + - -
192B GLN* 2.5 37.2 + - - +
212B LEU* 3.5 39.8 - - + +
214B TYR* 5.1 6.5 - + + -
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Residues in contact with GLN 215 (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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187A CYS 3.2 18.2 - - - +
188A HIS* 4.0 3.1 - - - +
213A MET* 3.5 13.6 - - - +
214A TYR* 1.3 73.9 - - - +
216A ARG* 1.3 61.9 + - - +
217A SER 3.1 17.7 + - - +
218A CYS* 3.4 24.3 - - - +
224A VAL* 4.4 5.1 - - - +
227A ASN* 2.8 45.1 + - - +
251A LEU* 4.1 11.7 - - + +
252A GLN 2.9 12.0 + - - +
253A MET* 3.5 0.5 - - - -
254A GLY 2.8 26.0 + - - -
350A UMP 3.1 23.0 + - - -
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Residues in contact with ARG 216 (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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174A TRP* 3.8 22.8 - - - -
185A PRO* 2.9 30.5 + - - +
186A PRO 2.6 18.6 + - - +
187A CYS* 3.0 25.2 + - - +
189A MET* 3.7 17.0 - - - +
214A TYR* 3.8 5.3 + - - -
215A GLN* 1.3 71.5 - - - +
217A SER* 1.3 72.6 + - - +
255A ASP* 2.8 26.2 + - - +
350A UMP 2.7 44.4 + - - -
167B ARG* 3.0 27.5 + - - +
168B ARG* 3.8 10.0 - - - +
170B ILE* 4.3 2.9 - - + -
192B GLN* 3.1 34.8 + - - +
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Residues in contact with SER 217 (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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187A CYS* 3.7 5.8 + - - +
215A GLN* 3.1 17.7 + - - +
216A ARG* 1.3 98.3 - - - +
218A CYS* 1.3 61.7 + - - +
255A ASP* 3.5 5.2 - - - -
257A HIS* 3.1 10.9 - - - -
350A UMP 2.6 57.0 + - - +
167B ARG* 3.1 9.0 - - - -
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Residues in contact with CYS 218 (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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215A GLN* 3.4 43.3 - - - +
217A SER* 1.3 78.9 - - - +
219A ASP* 1.3 59.9 + - - +
220A LEU* 3.2 3.0 + - + +
224A VAL* 3.8 14.6 - - + -
253A MET* 3.5 36.8 - - - -
254A GLY 4.3 0.4 - - - -
255A ASP 2.8 16.1 + - - +
256A ALA* 4.2 2.2 - - - -
257A HIS* 3.0 35.7 + - - +
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Residues in contact with ASP 219 (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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218A CYS* 1.3 68.6 - - - +
220A LEU* 1.3 59.1 + - - +
221A GLY 3.3 5.4 + - - -
222A LEU* 3.2 25.6 + - - +
223A GLY 2.8 26.5 + - - -
224A VAL* 3.0 7.6 + - - +
257A HIS* 3.8 9.8 + - - +
259A TYR* 3.4 20.9 + - - -
262A HIS* 3.6 14.2 + - - -
315A MET* 5.5 0.3 - - - -
316A SER 5.5 0.2 + - - -
350A UMP 3.0 17.9 + - - +
2351A CB3 2.7 42.7 + - - +
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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