Contacts of the strand formed by residues 219 - 223 (chain A) in PDB entry 3BSQ
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 GLY 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A CYS* 3.1 26.3 - - - +
177A ALA 3.1 12.3 + - - -
185A ASN* 3.5 15.1 + - - -
186A ALA* 6.2 1.6 - - - -
207A TRP 3.9 7.0 - - - -
208A GLY* 4.8 3.1 - - - -
218A PRO* 1.3 72.9 - - - +
220A VAL* 1.3 65.5 + - - +
221A TYR* 3.5 15.7 - - - -
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Residues in contact with VAL 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A TYR* 4.3 13.2 - - + -
170A LEU* 4.1 7.9 - - + -
174A MET* 3.7 19.5 - - + -
175A LEU 3.1 12.8 - - - +
176A CYS* 4.4 4.7 - - - -
205A VAL* 3.8 3.1 - - - +
206A SER* 2.8 19.8 + - - -
207A TRP* 2.9 70.2 + - + +
218A PRO 4.4 0.4 - - - +
219A GLY* 1.3 79.9 - - - +
221A TYR* 1.3 70.0 + - - +
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Residues in contact with TYR 221 (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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132A VAL* 3.6 27.6 - - + +
154A VAL* 4.9 1.4 - - - +
174A MET* 3.2 5.1 - - - -
175A LEU* 2.5 59.5 + - + +
177A ALA* 3.6 28.9 - - + +
185A ASN* 4.7 5.4 - - - +
186A ALA* 4.4 11.5 + - + +
195A LEU* 3.6 35.6 - - + +
204A LEU 2.9 32.0 + - - +
205A VAL* 3.6 24.0 - - + -
206A SER* 3.2 5.0 - - - +
219A GLY* 3.5 19.7 - - - -
220A VAL* 1.3 79.9 + - - +
222A THR* 1.3 55.9 + - - +
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Residues in contact with THR 222 (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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95A HIS 5.2 0.5 + - - -
97A ASN* 5.5 0.2 - - - -
98A ASP* 3.0 41.4 + - - +
99A LEU* 4.2 17.9 - - + -
173A SER 3.9 4.3 - - - +
174A MET* 4.2 6.9 - - - +
203A GLY* 2.9 27.8 - - - -
204A LEU* 3.2 18.7 + - + -
206A SER* 4.0 7.7 - - - -
221A TYR* 1.3 63.8 + - - +
223A GLN* 1.3 61.9 + - - +
224A VAL* 2.9 5.7 + - - +
227A PHE* 4.0 26.0 - - + -
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Residues in contact with GLN 223 (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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8A SO4 4.1 9.2 + - - -
123A CYS* 3.1 26.9 - - - +
124A GLU 5.5 1.4 - - - +
172A ASN 3.0 27.3 + - - -
173A SER* 3.0 15.9 + - - +
174A MET 3.8 9.7 + - - +
175A LEU* 3.5 36.8 - - + +
202A GLN* 3.4 9.0 + - - +
221A TYR 3.9 1.0 - - - -
222A THR* 1.3 67.2 - - - +
224A VAL* 1.3 67.6 + - - +
225A CYS* 3.0 3.2 - - + +
226A LYS* 2.9 33.9 + - + +
227A PHE* 3.1 15.7 - - - -
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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