Contacts of the strand formed by residues 194 - 200 (chain A) in PDB entry 2BP1
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 PRO 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A LEU* 3.1 33.6 - - + +
170A GLY* 4.3 1.6 - - - -
171A LEU* 3.9 37.9 - - + -
182A ILE* 4.0 17.5 - - + -
183A CYS* 3.9 17.7 - - - -
186A CYS* 4.5 3.1 - - - -
192A ILE 4.3 1.1 - - - +
193A LEU* 1.3 93.6 - - + +
195A THR* 1.3 62.2 + - - +
196A VAL 3.7 0.2 - - - -
219A PHE 5.0 2.6 - - - +
220A GLY 5.1 0.2 - - - +
221A LEU* 3.5 23.1 - - + +
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Residues in contact with THR 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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168A GLU* 2.6 38.7 + - + +
169A LEU 2.8 9.9 + - - -
193A LEU* 4.2 10.5 + - + +
194A PRO* 1.3 78.3 - - - +
196A VAL* 1.3 64.8 + - - +
220A GLY 4.6 2.0 - - - +
221A LEU* 3.3 10.7 - - - +
222A ARG* 2.9 22.9 + - - +
121C ARG* 5.3 4.9 - - - +
159C ARG* 3.4 31.4 + - - +
163C GLU* 4.9 3.8 - - - +
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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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138A LEU* 3.7 28.0 - - + -
140A TYR* 3.6 22.7 - - + +
168A GLU* 4.3 2.2 - - - +
169A LEU 3.6 1.8 + - - -
170A GLY* 3.2 2.3 - - - -
171A LEU 3.0 24.6 + - - +
194A PRO 3.7 0.2 - - - -
195A THR* 1.3 80.8 - - - +
197A TYR* 1.3 66.2 + - - +
198A GLN 4.2 0.2 - - - -
221A LEU* 3.8 8.4 - - - +
222A ARG* 3.3 47.6 - - - +
224A TYR* 3.9 25.6 - - + -
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Residues in contact with TYR 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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171A LEU* 3.3 15.3 - - + -
173A ASN* 3.3 12.9 + - - -
174A TYR* 2.5 46.3 + - + -
179A VAL* 3.5 26.2 - - + -
196A VAL* 1.3 77.1 - - - +
198A GLN* 1.3 78.4 + - - +
199A GLY* 3.8 7.9 - - - -
212A LEU* 3.6 19.3 - - + -
216A LEU* 3.7 35.4 - - + -
221A LEU* 4.1 2.4 - - + +
222A ARG 2.7 10.2 + - - +
223A PHE* 3.2 17.4 - + - -
224A TYR 2.8 26.2 + - - +
358A TYR* 3.6 10.5 - + - -
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Residues in contact with GLN 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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73A ASP* 2.8 28.6 + - - +
106A LYS* 3.2 10.3 - - - +
140A TYR* 3.2 36.9 + - + +
171A LEU 2.9 8.5 + - - -
172A SER* 2.8 33.1 + - - +
173A ASN 3.8 1.4 + - - -
197A TYR* 1.3 77.2 - - - +
199A GLY* 1.3 59.7 + - - +
224A TYR* 3.2 6.1 - - + +
226A TYR* 3.8 9.7 - - + -
315A ILE* 3.4 25.7 - - + +
1361A NDP 2.9 38.1 + - - +
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Residues in contact with GLY 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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173A ASN* 5.2 1.6 - - - -
197A TYR* 3.8 8.7 - - - -
198A GLN* 1.3 76.0 - - - +
200A MET* 1.3 64.3 + - - -
208A VAL* 5.3 1.3 - - - -
223A PHE* 3.4 22.0 - - - -
224A TYR 2.9 7.9 + - - -
225A ALA* 3.3 7.1 - - - -
226A TYR* 2.8 30.2 + - - -
358A TYR* 5.7 1.6 - - - -
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Residues in contact with MET 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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173A ASN* 5.1 0.6 + - - -
199A GLY* 1.3 66.7 - - - -
201A TYR* 1.3 67.4 + - - +
202A ASN* 5.1 0.2 - - - +
205A THR* 3.7 30.1 - - + +
207A GLN 5.8 0.2 + - - -
208A VAL* 3.5 20.8 + - - +
226A TYR* 3.3 30.5 + - + +
227A ASN* 3.6 20.6 - - + +
264A ARG* 3.6 36.3 - - + +
265A PHE* 4.2 3.1 - - + -
356A PRO* 3.9 19.3 - - + +
357A ASN 3.8 20.9 - - - +
358A TYR* 4.6 16.3 - - + +
360A ARG* 4.9 3.6 - - - +
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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