Contacts of the strand formed by residues 220 - 226 (chain F) in PDB entry 4CEV
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 220 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113F TYR* 3.5 14.4 - - - -
116F LEU* 3.5 6.6 - - - -
117F GLY 2.8 24.1 + - - -
218F THR* 3.6 3.0 + - - -
219F ASP* 1.3 80.7 + - - +
221F VAL* 1.3 66.8 + - - +
263F ILE 4.6 1.3 - - - -
265F THR* 3.4 17.9 - - - -
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Residues in contact with VAL 221 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F LEU* 4.2 0.4 - - - -
117F GLY* 3.4 7.2 - - - +
119F ILE* 4.0 7.2 - - + -
214F LEU* 3.9 35.2 - - + -
215F LYS* 5.5 0.4 - - - +
218F THR* 3.5 18.6 - - - +
220F GLY* 1.3 80.2 - - - +
222F HIS* 1.3 69.3 + - - +
263F ILE* 3.4 29.1 + - + +
264F ILE* 3.4 25.1 - - + -
265F THR* 2.7 38.0 + - - -
266F SER 3.5 1.4 + - - +
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Residues in contact with HIS 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F THR* 3.4 30.2 - - + +
106F LEU* 3.8 31.0 - - + +
109F VAL* 5.1 1.8 - - + +
116F LEU* 4.0 8.7 - - + +
117F GLY 2.9 12.8 + - - +
118F VAL* 3.4 7.8 - - + -
119F ILE 3.0 24.3 + - - +
221F VAL* 1.3 75.9 - - - +
223F LEU* 1.3 77.7 + - - +
224F SER* 3.8 8.7 - - - -
266F SER* 2.7 30.0 + - - +
267F ALA* 4.0 8.3 - - - -
268F GLU* 2.7 30.8 + - + +
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Residues in contact with LEU 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119F ILE* 3.8 31.0 - - + +
121F TYR* 4.7 4.7 - - + -
221F VAL 4.0 0.6 + - - -
222F HIS* 1.3 74.2 + - - +
224F SER* 1.3 59.7 + - - +
225F LEU* 4.2 15.7 - - + -
255F MET* 3.7 35.0 - - + -
258F LEU* 4.2 12.6 - - + -
264F ILE* 4.1 12.8 - - + +
266F SER 2.9 10.6 + - - +
267F ALA* 3.2 11.9 - - + -
268F GLU 3.0 27.4 + - - +
269F PHE* 4.3 10.5 - - + -
293F LEU* 4.0 23.6 - - + -
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Residues in contact with SER 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F HIS* 2.8 29.4 + - - -
118F VAL* 4.7 0.2 - - - -
119F ILE 2.9 11.0 + - - -
120F TRP* 3.6 29.6 - - - -
121F TYR 3.1 24.5 + - - +
222F HIS* 3.8 8.6 + - - -
223F LEU* 1.3 73.7 - - - +
225F LEU* 1.3 58.6 + - - +
226F ASP 3.7 0.7 + - - -
268F GLU* 2.8 28.0 + - - +
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Residues in contact with LEU 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121F TYR* 3.7 33.9 - - + -
223F LEU* 3.6 9.8 - - + -
224F SER* 1.3 72.0 - - - +
226F ASP* 1.3 67.8 + - - +
227F LEU* 3.7 21.4 + - + +
230F LEU* 4.9 1.3 - - + -
251F SER* 6.1 0.2 - - - -
255F MET* 3.7 37.9 - - + -
268F GLU 2.9 14.2 + - - +
269F PHE* 3.3 33.2 - - + -
270F VAL* 2.9 27.6 + - - -
289F LEU* 4.4 11.2 - - + -
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Residues in contact with ASP 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F HIS* 3.4 8.5 + - + -
121F TYR* 2.8 19.3 + - - +
122F ASP* 3.3 16.8 - - - +
224F SER 3.7 1.4 + - - -
225F LEU* 1.3 75.5 - - - +
227F LEU* 1.3 59.5 + - - +
228F ASP* 2.9 29.4 + - - +
229F GLY* 2.8 21.3 + - - -
230F LEU* 4.6 0.3 + - - +
270F VAL* 3.5 6.5 - - - +
271F GLU* 3.3 22.1 - - - +
300F MN 2.5 13.7 + - - -
301F MN 2.2 26.5 + - - -
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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