Contacts of the strand formed by residues 213 - 218 (chain A) in PDB entry 3CQU
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 213 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A ASN* 4.1 2.9 - - - +
202A LEU* 4.1 39.2 + - + +
203A GLN* 4.1 10.8 - - + -
206A ARG* 5.1 3.6 + - - +
211A THR 3.8 1.2 + - - -
212A ALA* 1.3 75.6 - - - +
214A LYS* 1.3 63.2 + - - +
215A TYR 3.4 24.9 - - - +
216A SER* 3.2 23.3 - - - +
225A PHE* 3.9 14.8 - - + -
226A VAL 3.5 8.7 - - - +
227A MET* 4.0 12.1 - - + -
474A TYR* 3.6 30.0 + - + -
476A ALA* 3.7 15.9 - - - +
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Residues in contact with LYS 214 (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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176A TYR* 3.4 44.2 - - + +
212A ALA* 3.4 24.2 - - - +
213A LEU* 1.3 77.7 + - - +
215A TYR* 1.3 83.4 + - + +
226A VAL* 3.0 10.0 + - + +
228A GLU* 4.2 23.4 + - - +
474A TYR* 4.7 1.1 - - - -
475A SER* 3.5 0.2 - - - -
476A ALA* 3.1 33.5 + - + +
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Residues in contact with TYR 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A VAL* 3.4 30.7 - - + -
150A PHE* 3.8 27.1 - + - -
169A GLU* 2.6 37.7 + - - -
176A TYR* 4.8 2.8 + + - -
213A LEU* 3.4 9.5 - - - +
214A LYS* 1.3 92.8 - - + +
216A SER* 1.3 63.6 + - - +
217A PHE* 4.5 7.2 - - + -
224A CYS 4.0 0.3 - - - +
226A VAL* 2.8 51.4 + - + +
474A TYR 3.2 8.3 - - - +
475A SER* 3.5 20.6 - - - -
476A ALA 5.6 0.2 - - - -
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Residues in contact with SER 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ASN* 3.0 18.1 + - - -
213A LEU* 3.2 15.9 - - - +
215A TYR* 1.3 72.5 - - - +
217A PHE* 1.3 63.8 + - - +
224A CYS 3.4 6.7 - - - -
225A PHE* 3.3 10.4 - - - -
472A PHE* 3.5 35.0 - - - -
473A ASP* 3.0 4.9 - - - +
474A TYR* 2.7 39.3 + - - +
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Residues in contact with PHE 217 (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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145A VAL* 3.7 39.0 - - + +
146A THR* 3.6 27.8 - - - -
147A MET* 3.7 19.7 - - + -
150A PHE* 4.1 9.9 - + - -
178A MET* 4.2 4.7 - - - -
215A TYR* 4.5 3.4 - - + -
216A SER* 1.3 76.8 - - - +
218A GLN* 1.3 72.0 + - - +
219A THR* 4.2 3.1 - - + -
224A CYS* 3.0 64.4 + - + +
226A VAL* 3.8 25.8 - - + -
472A PHE* 3.5 4.9 - - - -
473A ASP* 3.4 14.1 - - + +
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Residues in contact with GLN 218 (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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145A VAL 5.4 0.3 - - - +
183A LYS* 2.7 26.6 + - - -
217A PHE* 1.3 80.5 - - - +
219A THR* 1.3 73.1 + - - +
222A ARG 3.3 12.1 - - - +
223A LEU* 3.9 13.9 - - + +
468A HIS* 3.4 23.3 + - + -
469A PHE* 2.7 38.1 + - - +
471A GLN 5.1 0.2 - - - +
472A PHE* 3.5 6.6 - - + +
473A ASP* 2.7 31.7 + - - +
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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