Contacts of the strand formed by residues 197 - 206 (chain B) in PDB entry 2O05
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 LEU 197 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165B ASP* 3.5 12.8 - - - +
167B PHE 3.4 14.6 - - - +
168B ASP 3.9 5.2 - - - +
169B VAL 4.1 0.2 - - - +
170B ILE* 3.8 22.9 - - + -
193B MET 2.9 16.5 + - - +
194B LYS* 3.5 11.5 - - - +
195B THR 3.2 2.2 - - - +
196B ALA* 1.3 77.4 - - - +
198B LYS* 1.3 60.1 + - - +
201B GLY* 3.8 19.7 - - - +
202B VAL* 3.6 33.2 - - - +
203B LEU* 4.0 19.5 - - + +
228B PHE* 4.5 2.7 - - + -
251B CYS 5.1 0.2 - - - +
253B LYS* 2.8 39.1 + - + -
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Residues in contact with LYS 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B LYS* 4.1 18.1 - - - +
165B ASP* 3.4 31.8 + - - +
166B ALA* 3.5 20.6 + - - +
167B PHE 2.7 21.3 + - - +
168B ASP* 3.8 23.8 - - - +
196B ALA 3.9 0.4 + - - -
197B LEU* 1.3 78.8 - - - +
199B GLU* 1.3 67.0 + - + +
200B ASP* 3.2 13.2 - - - +
201B GLY* 3.2 11.4 + - - +
253B LYS* 3.1 10.9 + - - +
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Residues in contact with GLU 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ASP* 3.7 8.7 + - - +
198B LYS* 1.3 76.1 - - - +
200B ASP* 1.3 66.8 + - + +
201B GLY 3.5 0.2 - - - -
253B LYS* 3.2 33.5 - - - +
254B ASN* 4.8 0.2 - - - -
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Residues in contact with ASP 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B HIS* 3.5 28.8 + - - -
92B PRO* 5.2 8.2 - - + +
168B ASP* 4.9 2.3 - - - +
198B LYS* 3.9 10.9 - - - +
199B GLU* 1.3 87.2 + - + +
201B GLY* 1.3 63.2 + - - +
202B VAL* 4.2 2.9 - - - +
254B ASN* 4.0 36.0 + - + +
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Residues in contact with GLY 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B HIS* 4.3 1.6 - - - -
167B PHE 4.4 3.4 - - - -
168B ASP* 3.3 14.6 - - - -
197B LEU* 3.8 17.3 - - - +
198B LYS* 3.2 16.6 + - - -
199B GLU 3.5 1.0 + - - -
200B ASP* 1.3 81.1 + - - +
202B VAL* 1.3 60.1 + - - +
252B SER* 3.5 1.6 - - - -
253B LYS* 3.0 28.4 + - - +
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Residues in contact with VAL 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B PRO* 3.6 33.0 - - + +
90B SER 4.3 13.0 - - - +
91B HIS* 4.1 14.4 - - + -
92B PRO* 6.3 0.2 - - + -
168B ASP 2.8 6.6 + - - +
169B VAL* 3.1 43.4 - - + +
170B ILE 3.2 2.1 + - - -
197B LEU* 3.6 6.7 - - - +
200B ASP 4.2 2.2 - - - +
201B GLY* 1.3 74.4 - - - -
203B LEU* 1.3 62.6 + - - +
251B CYS 3.3 8.1 - - - +
252B SER* 3.4 27.6 - - - +
257B THR* 4.4 2.2 - - - +
259B PHE* 4.2 13.5 - - + -
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Residues in contact with LEU 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B PRO* 4.5 4.2 - - - +
170B ILE* 3.2 19.1 - - + +
190B TYR* 3.7 14.4 - - + -
193B MET* 3.8 29.2 - - + -
197B LEU* 4.0 13.0 - - + -
202B VAL* 1.3 76.3 - - - +
204B CYS* 1.3 62.5 + - - +
205B CYS* 3.6 31.0 - - - +
228B PHE* 3.5 32.8 - - + -
249B MET 4.4 2.0 - - - +
250B LEU* 3.4 10.2 - - - +
251B CYS* 2.8 44.3 + - + +
259B PHE* 4.7 0.7 - - - -
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Residues in contact with CYS 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ILE* 3.8 29.2 - - + +
86B LEU* 4.9 1.3 - - - -
87B PRO* 3.5 26.4 - - + +
170B ILE 2.9 10.1 + - - +
171B ILE* 3.3 7.3 - - + +
172B THR 3.1 22.9 + - - +
203B LEU* 1.3 73.9 - - - +
205B CYS* 1.3 66.4 + - - +
248B PHE* 3.8 25.8 - - - -
249B MET 3.3 4.0 - - - -
250B LEU* 3.7 18.4 - - + -
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Residues in contact with CYS 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ILE* 4.7 1.6 - - - -
172B THR* 3.9 23.1 - - - -
189B TYR* 4.7 2.2 - - - -
190B TYR* 2.9 32.8 - - + +
193B MET* 3.3 31.9 - - - -
203B LEU* 3.6 9.4 - - - -
204B CYS* 1.3 79.3 - - - +
206B GLN* 1.3 69.3 + - - +
207B GLY 3.2 0.5 + - - -
248B PHE* 3.3 5.4 - - - +
249B MET 2.9 27.4 + - - +
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Residues in contact with GLN 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B TYR* 3.6 27.6 + - + +
83B ILE* 4.3 1.0 - - - +
172B THR 3.6 11.1 + - - +
174B SER* 3.9 22.1 + - - +
175B SER 5.3 0.7 - - - +
185B PHE* 5.7 8.6 - - + -
190B TYR* 4.6 2.9 + - - -
205B CYS* 1.3 78.7 - - - +
207B GLY* 1.3 62.2 + - - +
208B GLU 3.9 2.4 + - - +
241B TYR* 3.5 31.1 + - - -
246B ILE* 3.5 26.1 - - + +
247B GLY 3.8 3.1 - - - +
248B PHE* 4.4 4.9 - - - -
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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