Contacts of the strand formed by residues 179 - 187 (chain A) in PDB entry 2BS3
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 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A LEU* 3.9 16.6 - - + +
35A SER 3.0 21.1 + - - +
36A LEU* 3.6 2.3 + - - +
176A GLN* 3.6 33.6 + - - +
177A ASP 3.0 13.6 + - - -
178A ARG* 1.3 77.9 - - - +
180A GLU* 1.3 60.1 + - - +
196A VAL* 3.1 27.4 - - + -
197A ARG 3.7 1.8 - - - -
198A ASP* 3.0 39.7 + - + +
199A LEU* 4.3 0.2 - - - +
205A ILE* 4.8 6.2 - - + +
207A TYR* 4.0 16.0 + - - +
1656A FAD 3.6 7.8 - - - -
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Residues in contact with GLU 180 (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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36A LEU* 3.5 20.2 - - + +
178A ARG 4.3 0.2 - - - -
179A LYS* 1.3 73.3 - - - +
181A ALA* 1.3 72.4 + - - +
182A ILE* 3.3 9.9 + - + +
196A VAL* 3.4 4.3 - - - +
197A ARG* 2.8 38.3 + - + +
199A LEU* 3.4 11.2 - - + +
235A THR* 4.2 12.6 + - - +
521A TYR* 2.7 33.6 + - - +
522A ARG* 2.9 48.1 + - - +
525A MET* 5.7 1.0 - - - +
1656A FAD 3.7 6.5 + - - +
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Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 3.8 41.3 - - + -
34A LEU* 5.0 1.9 - - + +
179A LYS 4.3 0.2 + - - -
180A GLU* 1.3 73.9 - - - +
182A ILE* 1.3 59.7 + - - +
183A ALA 3.6 0.2 - - - -
194A ALA* 4.3 9.4 - - + -
195A VAL 3.6 6.7 - - - -
196A VAL* 4.2 8.4 - - + +
235A THR* 5.2 1.2 - - - -
239A ILE* 3.9 19.9 - - + +
525A MET* 5.5 0.5 - - - +
1656A FAD 3.1 26.5 + - + +
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Residues in contact with ILE 182 (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 GLU* 3.7 16.4 - - + +
181A ALA* 1.3 77.5 - - - +
183A ALA* 1.3 64.4 + - - +
195A VAL* 3.0 21.5 + - + +
197A ARG* 4.1 19.7 - - + +
204A ILE* 4.2 9.9 - - + -
239A ILE* 3.5 15.0 - - - +
242A GLU* 4.7 5.5 - - - +
447A GLN* 3.5 40.1 + - + +
451A MET* 4.3 11.7 - - + -
521A TYR* 3.7 33.9 - - + -
525A MET* 3.9 16.5 - - + +
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Residues in contact with ALA 183 (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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181A ALA 3.6 1.2 - - - -
182A ILE* 1.3 84.4 - - - +
184A LEU* 1.3 67.1 + - - +
194A ALA* 3.2 7.8 - - - +
195A VAL* 2.8 39.9 + - + -
239A ILE* 3.8 10.4 - - - +
242A GLU* 6.0 0.4 - - - +
443A PHE* 5.1 6.1 - - + -
447A GLN* 4.0 24.5 - - + +
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Residues in contact with LEU 184 (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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11A ILE* 4.2 9.6 - - + -
183A ALA* 1.3 76.0 - - - +
185A ILE* 1.3 63.4 + - - +
186A HIS* 3.6 7.9 - - + -
191A CYS* 4.5 7.2 - - - -
193A GLY 3.5 13.5 - - - +
194A ALA* 4.1 10.8 - - + -
212A THR* 4.5 8.1 - - + -
214A ILE* 4.0 10.5 - - + -
239A ILE* 4.0 28.5 + - + +
240A ALA* 3.8 18.6 - - - -
243A THR* 3.7 29.4 - - + +
385A LEU* 4.5 3.1 - - + -
388A LEU* 4.0 22.7 - - + -
443A PHE* 3.3 20.8 - - - -
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Residues in contact with ILE 185 (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 LEU* 1.3 70.3 - - - +
186A HIS* 1.3 63.5 + - - +
191A CYS* 3.5 3.6 - - - -
192A TYR* 2.8 37.2 + - + -
193A GLY 2.8 18.2 + - - +
194A ALA 3.8 27.8 - - - +
195A VAL* 3.8 21.8 - - + -
206A ALA* 4.0 21.3 - - + -
207A TYR 4.4 4.5 - - - +
208A VAL* 4.4 3.1 - - + -
439A THR* 4.3 8.7 - - + -
440A LEU* 4.1 28.3 - - + +
443A PHE* 4.1 24.5 - - + -
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Residues in contact with HIS 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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184A LEU 3.6 16.4 - - - -
185A ILE* 1.3 77.4 - - - +
187A GLN* 1.3 65.2 + - - +
189A GLY 5.4 0.4 + - - -
190A LYS 3.0 17.3 - - - +
192A TYR* 4.5 4.3 - - - +
242A GLU 5.1 0.4 + - - -
243A THR* 3.5 47.2 + - + -
245A ILE* 4.0 19.7 - - + +
385A LEU* 4.0 18.6 - - + -
439A THR* 4.3 1.0 - - - +
442A LYS* 5.4 1.9 + - - -
443A PHE* 3.5 31.9 - + - -
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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
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186A HIS* 1.3 79.5 - - - +
188A ASP* 1.3 95.6 + - - +
189A GLY 3.1 1.8 - - - -
190A LYS* 2.9 22.8 + - - +
192A TYR* 3.6 24.3 + - + -
434A ASP 5.1 0.9 - - - +
436A GLU* 2.7 33.6 + - - +
438A LYS* 6.4 0.2 - - - -
439A THR* 2.6 34.2 + - + +
442A LYS* 6.2 2.5 - - - +
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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