Contacts of the strand formed by residues 192 - 203 (chain A) in PDB entry 2BGY
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 ALA 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A THR* 3.8 21.5 - - + -
185A VAL 3.4 4.9 - - - -
186A TYR* 3.8 13.2 - - + +
190A GLY 3.6 2.6 + - - -
191A ASN* 1.3 72.1 - - - +
193A HIS* 1.3 60.8 + - - +
194A ASP* 4.1 4.5 - - - +
215A SER* 3.6 8.2 + - - -
250A ILE* 3.2 17.0 - - - +
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Residues in contact with HIS 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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184A THR* 3.4 0.6 - - - -
185A VAL* 2.8 45.8 + - + +
186A TYR 4.6 1.3 - - - -
187A ASP* 2.8 37.5 + - + +
191A ASN 3.4 16.2 - - - -
192A ALA* 1.3 74.4 - - - +
194A ASP* 1.3 60.7 + - - +
195A MET* 3.2 6.8 + - - -
213A ASP* 2.5 32.0 + - - +
215A SER* 3.6 4.3 - - - -
247A THR* 3.4 15.9 - - + -
248A GLY 3.2 23.1 - - - -
249A THR* 4.3 2.2 - - - -
250A ILE* 3.5 24.1 - - + +
255A ALA* 5.0 0.7 - - - -
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Residues in contact with ASP 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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182A THR* 4.3 13.7 - - + -
183A VAL 4.1 3.4 - - - -
184A THR* 2.8 32.1 + - - +
192A ALA* 4.7 4.5 - - - +
193A HIS* 1.3 68.4 - - - +
195A MET* 1.3 63.6 + - - +
196A ASN* 4.3 0.8 + - - +
214A SER* 2.7 49.3 + - - +
215A SER* 2.9 18.1 + - - +
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Residues in contact with MET 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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182A THR* 3.3 4.5 - - - -
183A VAL* 2.9 56.4 + - + +
185A VAL* 3.8 22.0 - - + -
193A HIS* 3.9 2.5 - - - +
194A ASP* 1.3 68.7 - - - +
196A ASN* 1.3 63.4 + - - +
197A VAL* 4.0 3.6 + - + +
211A THR* 4.6 4.9 - - + -
212A HIS 3.5 26.0 - - - +
213A ASP* 3.7 29.2 - - + +
245A ILE* 3.9 26.9 - - + -
246A THR 5.1 0.9 - - - +
247A THR* 3.9 17.9 - - - -
258A PHE* 4.2 9.9 - - + -
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Residues in contact with ASN 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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180A LYS* 3.8 17.8 + - - +
181A GLY 3.5 3.3 + - - +
182A THR* 2.9 34.1 + - - +
194A ASP* 3.4 2.4 + - - +
195A MET* 1.3 72.3 - - - +
197A VAL* 1.3 60.4 - - - +
198A TYR* 3.6 30.5 + - + +
210A TYR 3.8 0.3 - - - +
211A THR* 3.2 7.6 - - - -
212A HIS* 2.9 38.2 + - + +
214A SER* 3.4 25.1 + - - -
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Residues in contact with VAL 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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153A MET* 3.6 29.6 - - + -
179A LYS 4.0 0.3 - - - +
180A LYS* 3.3 4.0 - - - +
181A GLY 2.8 33.5 + - - +
183A VAL* 4.6 8.3 - - + -
195A MET* 4.1 12.1 - - + +
196A ASN* 1.3 78.2 - - - +
198A TYR* 1.3 62.5 + - - +
199A PHE* 3.8 21.3 - - + -
209A VAL* 3.6 26.7 - - + -
210A TYR 3.4 3.8 - - - +
211A THR* 4.4 11.2 - - + -
260A LEU* 4.8 8.3 - - + -
262A PHE* 4.2 7.9 - - + -
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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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169A PHE* 3.4 28.9 - + + -
171A VAL* 3.5 40.2 + - + +
177A TYR* 3.8 36.8 - + + -
179A LYS 3.4 3.1 - - - +
180A LYS* 3.4 37.4 + - + +
196A ASN* 3.6 37.1 + - + +
197A VAL* 1.3 74.9 - - - +
199A PHE* 1.3 62.3 + - - +
200A VAL* 4.9 0.4 - - - -
208A ALA 3.5 1.4 - - - +
209A VAL* 3.2 7.7 - - - +
210A TYR* 2.8 46.3 + - + +
212A HIS* 4.7 5.6 - - + +
222A PRO* 5.5 0.2 - - + -
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Residues in contact with PHE 199 (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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153A MET* 3.9 14.6 - - - -
155A ILE* 3.6 46.4 - - + -
157A LEU* 4.3 13.0 - - + -
177A TYR* 3.8 0.7 - - - +
178A ASN* 2.8 33.6 + - - +
179A LYS* 2.9 29.8 + - + +
197A VAL* 3.8 22.2 - - + -
198A TYR* 1.3 73.2 - - - +
200A VAL* 1.3 55.6 + - - +
201A LYS 4.2 0.7 - - - -
207A TRP* 4.3 14.6 - - + -
208A ALA 3.4 5.4 - - - +
209A VAL* 4.0 16.2 - - + -
229A LEU* 4.0 14.4 - - + -
262A PHE* 3.8 25.1 - + - -
275A ILE* 4.8 4.5 - - + -
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Residues in contact with VAL 200 (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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164A PRO* 4.1 11.7 - - + -
169A PHE* 3.8 22.7 - - + -
176A SER 3.8 12.1 - - - +
177A TYR* 3.6 22.2 - - + -
178A ASN* 3.4 2.2 - - - -
199A PHE* 1.3 76.1 - - - +
201A LYS* 1.3 76.8 + - - +
202A THR* 3.2 6.9 + - + +
207A TRP* 4.2 2.4 - - - -
208A ALA* 2.8 39.0 + - + +
210A TYR* 3.9 22.2 - - + +
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Residues in contact with LYS 201 (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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159A SER* 2.7 33.1 + - - +
161A ASP 2.9 27.2 + - - +
162A PRO 4.0 8.7 - - - +
163A VAL* 3.7 16.7 - - + +
164A PRO* 3.7 15.1 - - - +
178A ASN* 2.9 20.0 + - - +
200A VAL* 1.3 75.5 - - - +
202A THR* 1.3 61.8 + - - +
203A LYS 3.6 28.3 - - - +
204A ASP* 4.4 12.1 + - - +
205A ASN 4.9 2.8 - - - +
206A GLU 3.6 7.9 - - - +
207A TRP* 3.6 33.0 - - + -
267A GLN* 5.3 0.8 + - - -
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Residues in contact with THR 202 (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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163A VAL* 3.9 15.0 - - - +
200A VAL* 3.5 17.7 - - + +
201A LYS* 1.3 74.2 - - - +
203A LYS* 1.3 74.2 + - - +
206A GLU* 3.0 29.3 + - - +
207A TRP 4.9 0.2 - - - -
208A ALA* 3.7 22.7 - - + +
228A THR* 5.0 3.9 - - + +
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Residues in contact with LYS 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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163A VAL* 4.3 8.7 - - - -
201A LYS* 3.6 15.4 - - - +
202A THR* 1.3 89.8 + - - +
204A ASP* 1.3 78.9 + - - +
205A ASN 3.1 2.4 + - - -
206A GLU* 3.2 40.4 + - + +
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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