Contacts of the strand formed by residues 220 - 226 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113C TYR* 3.6 13.0 - - - -
116C LEU* 3.3 10.1 - - - +
117C GLY 2.8 24.1 + - - -
218C THR* 3.5 3.2 + - - -
219C ASP* 1.3 79.8 + - - +
221C VAL* 1.3 65.3 + - - +
263C ILE 4.6 1.3 - - - -
265C THR* 3.5 17.3 - - - -
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Residues in contact with VAL 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C LEU* 4.2 0.7 - - - -
117C GLY* 3.4 10.3 - - - +
119C ILE* 4.0 22.9 - - + -
214C LEU* 4.0 22.2 - - + -
215C LYS* 5.5 0.7 - - - +
218C THR* 3.6 17.9 - - - +
220C GLY* 1.3 77.9 - - - +
222C HIS* 1.3 65.5 + - - +
263C ILE* 3.3 31.0 + - + +
264C ILE* 3.4 24.9 - - + -
265C THR* 2.8 35.7 + - - -
266C SER 3.6 1.6 + - - +
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Residues in contact with HIS 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C THR* 3.4 29.6 - - + +
106C LEU* 3.6 33.5 - - + +
109C VAL* 5.0 1.9 - - + +
116C LEU* 3.9 8.9 - - + +
117C GLY 2.9 14.6 + - - +
118C VAL* 3.4 7.5 - - + -
119C ILE 3.0 24.3 + - - -
221C VAL* 1.3 75.1 - - - +
223C LEU* 1.3 77.6 + - - +
224C SER* 3.7 8.9 + - - -
266C SER* 2.7 30.7 + - - +
267C ALA* 3.9 9.2 - - - -
268C GLU* 2.8 28.1 + - - -
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Residues in contact with LEU 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C ILE* 3.7 33.7 - - + +
121C TYR* 4.6 7.6 - - + -
221C VAL 3.9 1.0 + - - -
222C HIS* 1.3 73.8 + - - +
224C SER* 1.3 58.9 + - - +
225C LEU* 4.2 19.5 - - + -
255C MET* 3.8 31.6 - - + -
258C LEU* 4.3 10.5 - - + -
264C ILE* 4.0 15.7 - - + +
266C SER 2.9 9.3 + - - -
267C ALA* 3.1 10.9 - - + -
268C GLU 3.0 27.1 + - - +
269C PHE* 4.3 7.0 - - + -
293C LEU* 4.0 24.0 - - + -
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Residues in contact with SER 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C HIS* 2.7 29.8 + - - -
118C VAL* 4.7 0.4 - - - -
119C ILE 3.0 9.7 + - - +
120C TRP* 3.5 28.9 - - - -
121C TYR 3.1 24.3 + - - +
222C HIS* 3.7 7.9 + - - -
223C LEU* 1.3 72.5 - - - +
225C LEU* 1.3 60.9 + - - +
226C ASP 3.8 0.6 + - - -
268C GLU* 2.9 27.5 + - - +
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Residues in contact with LEU 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C TYR* 3.7 31.9 - - + -
223C LEU* 3.6 10.7 - - + -
224C SER* 1.3 71.5 - - - +
226C ASP* 1.3 72.4 + - - +
227C LEU* 3.8 16.6 + - + -
230C LEU* 4.8 2.0 - - + -
255C MET* 3.6 38.1 - - + -
268C GLU 2.9 15.5 + - - +
269C PHE* 3.3 33.8 - - + -
270C VAL* 2.9 27.1 + - - -
289C LEU* 4.5 11.9 - - + -
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Residues in contact with ASP 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C HIS* 3.7 7.9 - - + -
121C TYR* 2.9 14.7 + - - +
122C ASP* 3.3 20.2 - - - +
224C SER 3.8 1.4 + - - -
225C LEU* 1.3 76.9 - - - +
227C LEU* 1.3 62.3 + - - +
228C ASP* 3.0 23.8 + - - +
229C GLY* 2.9 20.4 + - - -
230C LEU* 4.6 0.3 + - - +
270C VAL* 3.7 6.3 - - - -
271C GLU* 3.2 23.9 - - - +
300C MN 2.5 13.9 + - - -
301C MN 2.2 26.7 + - - -
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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