Contacts of the strand formed by residues 185 - 198 (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 THR 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A THR* 2.9 44.4 + - - +
183A PRO 3.4 1.2 - - - -
184A PRO* 1.3 91.0 - - + +
186A ALA* 1.3 63.4 + - - +
187A GLN* 3.4 9.0 + - - -
215A SER* 4.3 13.1 + - - +
216A VAL 3.2 14.6 - - - +
217A GLN* 3.9 12.8 - - + +
218A VAL* 3.6 8.4 - - - +
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Residues in contact with ALA 186 (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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179A PHE* 4.7 3.6 - - + -
180A THR 3.2 17.7 - - - +
181A ILE* 4.3 2.9 - - - -
182A THR* 4.1 0.7 - - - -
185A THR* 1.3 76.0 - - - +
187A GLN* 1.3 68.0 + - - +
188A VAL* 3.7 0.6 + - + -
215A SER* 3.2 5.4 - - - -
216A VAL* 2.7 34.2 + - + +
218A VAL* 3.4 19.1 - - + -
228A PHE* 4.2 19.3 - - + -
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Residues in contact with GLN 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LYS 3.5 1.6 - - - +
179A PHE* 3.4 3.8 - - - -
180A THR* 2.9 42.4 + - - +
182A THR* 2.4 41.4 + - - +
185A THR* 3.4 16.5 + - - -
186A ALA* 1.3 70.9 - - - +
188A VAL* 1.3 60.9 + - - +
214A ASP 3.7 6.7 - - - +
215A SER* 3.5 13.5 + - - +
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Residues in contact with VAL 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A TRP* 3.4 39.5 - - + -
178A LYS 3.4 4.3 - - - +
179A PHE* 3.7 31.4 - - + -
186A ALA 4.1 8.5 - - - +
187A GLN* 1.3 77.4 - - - +
189A ALA* 1.3 62.4 + - - +
190A ALA 4.3 0.4 - - - +
212A ILE* 4.5 1.3 - - + -
213A GLN* 3.4 6.8 - - - +
214A ASP* 2.8 51.7 + - + +
215A SER 4.4 0.7 - - - +
216A VAL* 4.2 18.6 - - + -
231A ILE* 4.7 4.7 - - + -
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Residues in contact with ALA 189 (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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176A GLU 4.1 0.2 - - - +
178A LYS* 2.8 46.5 + - + +
187A GLN 4.1 0.2 - - - -
188A VAL* 1.3 75.4 - - - +
190A ALA* 1.3 61.5 + - - +
212A ILE 3.4 7.9 - - - +
213A GLN* 5.6 1.1 - - + -
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Residues in contact with ALA 190 (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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176A GLU 3.1 14.8 - - - +
177A TRP* 3.3 42.4 - - + +
189A ALA* 1.3 76.5 - - - +
191A VAL* 1.3 65.8 + - - +
192A LEU* 4.8 0.2 - - + -
211A ASP* 3.5 4.7 - - - +
212A ILE* 2.9 41.3 + - + +
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Residues in contact with VAL 191 (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 ARG 4.1 0.2 - - - +
175A SER* 3.3 2.8 - - - -
176A GLU* 2.9 51.3 + - + +
190A ALA* 1.3 77.4 - - - +
192A LEU* 1.3 70.9 + - - +
193A LYS* 4.0 30.3 - - + +
209A HIS* 4.3 9.2 - - + -
210A LYS 3.3 9.0 - - - +
211A ASP* 3.5 20.6 - - - +
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Residues in contact with LEU 192 (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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173A TRP* 4.7 2.0 - - + -
174A ARG 3.6 4.5 - - - -
175A SER* 3.5 23.1 - - - -
177A TRP* 3.6 26.5 - - + +
190A ALA* 4.8 0.2 - - + -
191A VAL* 1.3 77.2 - - - +
193A LYS* 1.3 60.5 - - - +
209A HIS* 3.0 8.4 - - - +
210A LYS* 2.9 37.6 + - + +
212A ILE* 4.2 20.6 - - + -
235A ALA 4.2 9.4 - - - +
236A GLU* 3.7 12.6 - - + +
239A TYR* 3.5 51.5 + - + -
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Residues in contact with LYS 193 (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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172A ARG 4.0 0.4 - - - +
173A TRP* 3.4 2.5 - - - -
174A ARG* 2.8 83.8 + - + +
191A VAL* 4.0 29.2 - - + +
192A LEU* 1.3 80.8 - - - +
194A ILE* 1.3 68.6 + - - +
208A SER 3.2 9.0 - - - +
209A HIS* 4.0 13.2 - - + -
239A TYR* 4.2 1.0 + - - -
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Residues in contact with ILE 194 (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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172A ARG 3.4 7.6 - - - +
173A TRP* 3.7 28.3 - - + -
174A ARG* 5.4 2.1 + - - -
193A LYS* 1.3 81.4 - - - +
195A GLN* 1.3 64.7 + - - +
196A VAL* 4.0 14.8 - - + -
206A LEU* 3.8 20.6 - - + +
207A VAL* 3.5 5.2 - - - +
208A SER* 2.9 36.3 + - - +
239A TYR* 3.5 17.7 - - + +
240A GLN* 6.0 0.2 - - - -
243A ILE* 3.3 34.1 - - + -
240B VAL* 4.1 16.2 - - + -
243B LEU* 4.1 9.2 - - + -
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Residues in contact with GLN 195 (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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23A HIS 5.3 0.4 + - - -
24A ALA 5.0 2.0 + - - +
25A PRO* 3.9 10.2 - - + +
26A PRO* 3.3 34.1 - - + +
61A GLN* 4.7 11.1 + - - +
171A GLY* 3.3 2.4 - - - -
172A ARG* 2.9 35.5 + - + +
174A ARG* 4.7 14.2 + - - +
194A ILE* 1.3 76.0 - - - +
196A VAL* 1.3 68.9 + - - +
205A GLN* 2.9 28.2 + - - +
206A LEU 3.2 10.1 - - - +
207A VAL* 4.5 12.7 - - + +
17B PRO* 4.1 13.1 - - - +
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Residues in contact with VAL 196 (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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26A PRO* 5.7 0.2 - - - -
170A ASN 3.5 4.5 - - - +
194A ILE* 4.0 9.0 - - + -
195A GLN* 1.3 83.4 - - - +
197A HIS* 1.3 65.4 + - - +
205A GLN* 3.0 9.4 - - - +
206A LEU* 3.0 39.2 + - + -
236B THR* 4.0 20.0 - - + -
239B ILE* 3.7 49.8 - - + -
240B VAL* 3.8 26.9 - - + +
243B LEU* 4.3 4.5 - - + -
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Residues in contact with HIS 197 (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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25A PRO* 3.6 13.0 - - + +
26A PRO* 5.3 2.0 - - + +
28A GLU* 2.6 41.3 + - - +
169A TRP* 3.1 7.7 - - - +
170A ASN* 2.8 36.1 + - + +
195A GLN* 5.7 0.2 - - - +
196A VAL* 1.3 76.9 - - - +
198A TYR* 1.3 66.0 + - - +
199A TYR* 3.3 19.9 - + - +
203A ASN* 2.9 20.3 + - - -
204A VAL 3.4 2.9 - - - -
205A GLN* 3.4 19.0 + - + +
14B ARG 2.9 29.1 + - - -
15B ARG* 3.7 9.9 - - + -
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Residues in contact with TYR 198 (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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167A ASN 4.5 9.4 - - - -
168A PHE 3.4 9.4 - - - -
169A TRP* 4.2 9.6 - + + -
196A VAL* 4.3 0.6 - - - +
197A HIS* 1.3 73.6 - - - +
199A TYR* 1.3 61.8 + - - +
200A GLU* 3.2 53.8 + - + +
203A ASN* 3.6 0.9 + - - -
204A VAL* 2.9 38.0 + - + +
193B LEU* 4.3 10.8 - - + -
231B ILE* 3.4 47.1 - - + +
235B LYS* 3.3 38.1 + - + -
236B THR* 4.5 11.9 - - + -
239B ILE* 5.1 2.2 - - + -
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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