Contacts of the strand formed by residues 202 - 217 (chain A) in PDB entry 3AA6
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 GLY 202 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A TYR* 4.3 0.4 - - - -
199A TYR* 3.1 20.4 - - - +
200A GLU 3.1 2.9 + - - -
201A ASP* 1.3 78.7 - - - +
203A ASN* 1.3 61.6 + - - +
204A VAL 4.2 0.2 - - - -
14B ARG* 2.9 29.2 + - - +
192B SER* 3.3 14.4 - - - -
193B LEU* 4.1 5.6 - - - -
194B THR* 4.7 2.5 - - - -
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Residues in contact with ASN 203 (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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197A HIS* 2.9 21.7 + - - -
198A TYR 3.6 3.6 - - - -
202A GLY* 1.3 76.8 - - - +
204A VAL* 1.3 60.2 - - - +
205A GLN* 3.2 10.2 + - - +
13B MET 2.9 24.9 + - - +
14B ARG* 3.1 24.5 + - - +
16B LEU 2.9 22.0 + - - -
18B PRO* 3.6 13.8 - - + +
191B GLY* 3.1 21.8 - - - -
192B SER* 3.0 16.8 + - - +
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Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A VAL 3.8 0.2 - - - +
197A HIS* 3.4 0.7 - - - -
198A TYR* 2.9 39.5 + - + +
203A ASN* 1.3 76.9 - - - +
205A GLN* 1.3 70.4 + - - +
189B LEU* 4.6 4.9 - - + -
190B GLY 3.4 5.4 - - - +
192B SER 3.7 15.5 - - - +
193B LEU* 4.0 15.9 - - + -
231B ILE* 4.3 9.6 - - + -
232B TYR* 3.5 52.7 - - + +
236B THR* 4.4 20.2 - - + +
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Residues in contact with GLN 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PRO* 4.5 1.3 - - - +
195A GLN* 2.9 29.7 + - - -
196A VAL 3.0 10.5 - - - +
197A HIS* 3.4 19.6 - - + -
203A ASN* 3.2 15.4 + - - -
204A VAL* 1.3 81.7 - - - +
206A LEU* 1.3 61.6 + - - +
207A VAL* 4.7 1.2 - - + +
15B ARG 2.9 27.3 + - - -
16B LEU 3.6 0.2 + - - -
17B PRO* 3.5 20.0 - - - +
18B PRO* 3.6 18.1 - - + +
19B GLN* 3.0 25.9 + - - +
188B ASN 3.5 0.2 - - - +
189B LEU* 3.5 5.5 - - - -
190B GLY 2.9 21.8 + - - -
236B THR* 6.0 0.4 - - - -
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Residues in contact with LEU 206 (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 ILE* 4.0 17.0 - - + -
195A GLN* 3.2 7.4 - - - +
196A VAL* 3.0 40.4 + - + +
204A VAL* 5.4 0.2 - - - +
205A GLN* 1.3 72.9 - - - +
207A VAL* 1.3 70.8 + - - +
208A SER* 4.5 7.0 - - - -
243A ILE* 5.1 3.6 - - + -
247A TYR* 3.7 9.9 - - + +
187B MET* 3.6 38.8 - - + -
188B ASN 3.5 15.5 - - - +
189B LEU* 3.8 19.4 - - + +
236B THR* 5.0 2.1 - - - +
240B VAL* 3.5 32.1 - - + -
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Residues in contact with VAL 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ILE 3.5 5.8 - - - +
195A GLN* 4.5 19.5 - - + +
205A GLN* 4.7 4.5 - - + +
206A LEU* 1.3 79.6 - - - +
208A SER* 1.3 66.3 - - - +
209A HIS* 6.0 2.7 - - + +
17B PRO* 5.2 4.5 - - + -
19B GLN* 3.8 28.7 - - + +
186B THR* 4.1 2.3 - - - +
187B MET* 3.8 0.7 - - - -
188B ASN* 2.9 38.2 + - + +
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Residues in contact with SER 208 (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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193A LYS* 3.2 3.5 - - - +
194A ILE* 2.9 39.7 + - - +
206A LEU* 4.5 12.3 - - - -
207A VAL* 1.3 80.3 - - - +
209A HIS* 1.3 67.0 + - - +
239A TYR* 2.7 31.9 + - - -
243A ILE* 4.3 7.9 - - - +
184B SER 4.0 1.9 + - - -
186B THR* 3.1 14.7 + - - -
187B MET* 4.3 8.2 - - - +
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Residues in contact with HIS 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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191A VAL* 4.3 6.1 - - + -
192A LEU 3.0 13.9 - - - +
193A LYS* 4.0 15.5 - - + -
207A VAL* 6.0 2.8 - - + +
208A SER* 1.3 78.7 + - - +
210A LYS* 1.3 63.8 + - - +
211A ASP* 3.9 26.8 + - - -
239A TYR* 3.8 3.8 - - - -
184B SER 4.4 0.7 - - - -
185B GLY* 3.5 1.4 - - - -
186B THR* 3.0 54.9 + - + +
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Residues in contact with LYS 210 (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 VAL* 3.3 5.8 - - - +
192A LEU* 2.9 37.4 + - + +
209A HIS* 1.3 76.3 - - - +
211A ASP* 1.3 76.4 + - - +
212A ILE* 3.9 25.1 - - + +
235A ALA* 5.0 1.4 + - - +
238A GLU* 4.3 21.0 + - - +
239A TYR* 3.8 31.4 + - + +
182B THR 3.0 22.8 + - - +
183B GLY* 2.8 29.9 + - - +
184B SER 3.9 1.8 - - - +
185B GLY* 4.0 13.0 - - - +
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Residues in contact with ASP 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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190A ALA 3.5 5.2 - - - +
191A VAL* 3.5 22.3 - - - +
209A HIS* 3.9 17.7 + - - -
210A LYS* 1.3 87.4 - - - +
212A ILE* 1.3 63.5 + - - +
213A GLN 4.6 0.2 + - - -
185B GLY* 5.5 0.2 - - - -
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Residues in contact with ILE 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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177A TRP* 3.9 29.6 - - + -
188A VAL* 5.2 1.3 - - + -
189A ALA* 3.4 5.5 - - - +
190A ALA* 2.9 43.7 + - + +
192A LEU* 4.2 17.7 - - + -
210A LYS* 3.9 33.9 - - + +
211A ASP* 1.3 76.3 - - - +
213A GLN* 1.3 72.2 + - - +
214A ASP* 4.7 8.1 - - + +
231A ILE* 5.8 1.1 - - + -
235A ALA* 3.9 21.8 - - + -
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Residues in contact with GLN 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 VAL 3.4 7.6 - - - +
189A ALA* 4.8 1.8 - - + +
212A ILE* 1.3 77.2 - - - +
214A ASP* 1.3 71.3 + - - +
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Residues in contact with ASP 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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187A GLN* 3.7 3.3 - - - +
188A VAL* 2.8 45.1 + - + +
212A ILE* 4.7 8.9 - - + +
213A GLN* 1.3 82.1 - - - +
215A SER* 1.3 78.4 + - - +
216A VAL* 4.4 12.4 - - - +
231A ILE* 4.4 14.7 - - + +
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Residues in contact with SER 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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185A THR* 4.3 11.4 - - - +
186A ALA 3.2 8.4 + - - -
187A GLN* 3.5 22.1 + - - -
188A VAL* 4.7 0.2 - - - -
214A ASP* 1.3 92.0 + - - +
216A VAL* 1.3 66.4 + - - +
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Residues in contact with VAL 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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185A THR* 3.2 7.2 - - - -
186A ALA* 2.7 41.2 + - + +
188A VAL* 4.2 8.7 - - + -
214A ASP* 4.4 8.5 - - - +
215A SER* 1.3 85.9 - - - +
217A GLN* 1.3 64.6 + - - +
227A GLU* 5.7 4.0 - - + +
228A PHE* 3.9 24.7 - - + -
231A ILE* 2.9 40.6 - - + -
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Residues in contact with GLN 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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184A PRO* 3.4 31.9 + - - +
185A THR* 3.9 12.6 - - + +
216A VAL* 1.3 82.6 - - - +
218A VAL* 1.3 64.9 + - - +
224A THR* 4.9 2.8 - - - +
227A GLU* 4.8 15.6 - - - +
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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