Contacts of the strand formed by residues 200 - 210 (chain A) in PDB entry 3BWC
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 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A ASN* 3.2 10.6 - - - +
170A TYR 3.3 14.4 - - - +
171A ASP 3.6 21.3 - - - +
172A VAL 3.9 0.2 - - - +
173A VAL* 3.4 29.4 - - + +
196A VAL* 3.3 20.9 + - + +
197A LEU 3.6 6.1 - - - +
198A ARG 3.2 1.3 - - - +
199A ILE* 1.3 78.5 - - - +
201A LYS* 1.3 65.3 + - - +
204A GLY* 3.9 8.5 - - - +
205A ILE 3.9 3.6 - - - +
206A CYS* 4.0 21.3 - - + +
232A PHE* 3.7 27.6 - - + -
257A LYS* 2.8 26.8 + - + -
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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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93A HIS* 6.0 0.4 - - - +
97A GLU* 5.4 5.3 + - - +
98A ARG* 4.8 7.3 - - - +
168A ASN* 3.3 36.6 - - + +
169A THR 3.5 17.0 + - - +
170A TYR 2.8 16.8 + - - +
171A ASP* 3.5 31.3 + - - +
200A LEU* 1.3 76.8 - - - +
202A PRO* 1.4 69.5 - - + +
203A ASP* 3.2 3.6 - - + +
204A GLY* 2.7 25.9 + - - +
257A LYS* 3.6 5.9 - - - +
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Residues in contact with PRO 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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168A ASN* 4.3 11.6 - - + +
201A LYS* 1.4 91.6 - - + +
203A ASP* 1.3 63.9 + - - +
204A GLY 3.5 1.9 + - - -
257A LYS* 3.8 14.9 - - + +
258A LYS* 3.5 31.2 + - + +
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Residues in contact with ASP 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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93A HIS* 3.0 29.5 - - + +
94A PRO* 4.4 22.8 - - + +
201A LYS* 3.1 2.4 + - - +
202A PRO* 1.3 80.6 - - - +
204A GLY* 1.3 61.6 + - - +
205A ILE* 4.2 4.6 - - - +
256A SER* 5.9 0.2 - - - -
258A LYS* 3.6 32.9 - - + +
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Residues in contact with GLY 204 (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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93A HIS* 4.1 0.7 - - - -
171A ASP* 3.2 15.3 - - - -
200A LEU* 3.9 15.9 - - - +
201A LYS 2.7 24.2 + - - -
202A PRO 3.2 2.2 + - - -
203A ASP* 1.3 75.4 - - - +
205A ILE* 1.3 63.9 + - - +
206A CYS 4.3 0.2 + - - -
256A SER* 4.4 0.3 + - - -
257A LYS* 3.1 27.2 + - - +
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Residues in contact with ILE 205 (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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89A SER* 3.8 26.5 - - - +
92A SER* 3.9 26.2 - - - +
93A HIS* 4.0 15.7 - - + -
171A ASP 3.0 8.6 + - - +
172A VAL* 3.2 9.9 - - + +
173A VAL 3.0 23.6 + - - -
200A LEU* 3.9 4.1 - - - +
203A ASP 4.2 2.9 - - - +
204A GLY* 1.3 75.5 - - - +
206A CYS* 1.3 70.3 + - - +
254A VAL* 4.0 14.1 - - + -
255A CYS 3.5 11.2 - - - +
256A SER* 3.6 26.7 - - - +
261A VAL* 5.6 1.1 - - + -
263A VAL* 4.1 12.6 - - + -
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Residues in contact with CYS 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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173A VAL 3.4 7.0 - - - +
175A ILE* 6.1 2.2 - - + -
193A TYR* 6.5 0.7 - - + -
196A VAL* 4.2 10.3 - - + -
200A LEU* 4.0 8.3 - - + +
205A ILE* 1.3 77.3 - - - +
207A CYS* 1.3 61.1 + - - +
232A PHE* 3.1 35.9 - - + -
254A VAL* 3.5 3.5 - - - -
255A CYS* 2.0 90.2 + - - +
256A SER* 4.8 0.2 - - - -
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Residues in contact with CYS 207 (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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85A LEU* 3.8 36.3 - - - -
88A THR* 6.3 0.2 - - - -
89A SER* 3.9 21.1 - - - -
172A VAL* 5.3 0.2 - - + -
173A VAL 2.7 13.8 + - - +
174A ILE* 3.4 11.1 - - + -
175A ILE* 2.6 37.4 + - - +
206A CYS* 1.3 77.5 - - - +
208A ASN* 1.3 54.7 + - - +
252A THR* 3.3 23.8 - - - -
253A LEU 3.4 4.5 - - - -
254A VAL* 4.9 7.6 - - + -
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Residues in contact with ASN 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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85A LEU* 5.1 0.7 - - - -
175A ILE* 3.2 32.5 - - + +
177A THR 4.0 7.7 + - - +
178A THR* 5.2 1.7 - - - -
188A PHE* 5.6 0.6 - - - -
193A TYR* 2.6 37.1 + - + -
207A CYS* 1.3 77.1 - - - +
209A GLN* 1.3 80.5 + - - +
223A MSE 4.2 15.7 - - - +
227A ILE* 5.1 3.6 - - + +
252A THR* 2.6 24.8 + - - -
253A LEU* 2.8 33.2 + - + +
255A CYS* 5.9 2.7 - - - -
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Residues in contact with GLN 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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81A TYR* 3.2 33.8 + - + +
85A LEU* 4.8 1.9 - - + +
175A ILE 3.3 4.2 + - - +
176A ASP* 3.5 2.8 - - - +
177A THR* 3.1 21.2 + - - +
178A THR* 2.6 55.0 + - - +
208A ASN* 1.3 87.4 + - - +
210A GLY* 1.3 62.6 + - - +
223A MSE 4.5 6.4 - - - +
250A ILE* 3.8 16.7 - - + +
251A GLY 3.7 6.3 - - - +
252A THR* 4.3 2.9 - - - -
501A SAM 3.4 25.2 + - - +
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Residues in contact with GLY 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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178A THR* 5.5 0.6 + - - -
208A ASN 3.5 4.0 + - - -
209A GLN* 1.3 76.9 + - - +
211A GLU* 1.3 69.4 + - - -
220A ILE* 5.5 0.4 - - - -
223A MSE 4.7 11.4 - - - -
237A TYR* 4.4 8.1 - - - -
250A ILE* 3.4 24.1 - - - +
251A GLY 2.8 17.6 + - - +
252A THR* 4.4 1.8 - - - -
253A LEU* 4.7 7.4 - - - -
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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