Contacts of the strand formed by residues 220 - 226 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113D TYR* 3.6 11.9 - - - -
116D LEU* 3.3 9.1 - - - +
117D GLY 2.7 30.8 + - - -
218D THR* 3.5 3.0 + - - -
219D ASP* 1.3 79.3 + - - +
221D VAL* 1.3 60.0 + - - +
263D ILE 4.6 0.9 - - - -
265D THR* 3.4 17.7 - - - -
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Residues in contact with VAL 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D LEU* 4.2 0.2 - - - -
117D GLY* 3.4 11.2 - - - +
119D ILE* 4.0 19.3 - - + -
214D LEU* 4.0 22.7 - - + -
215D LYS* 5.9 0.2 - - - -
218D THR* 3.6 17.7 - - - +
220D GLY* 1.3 79.3 - - - +
222D HIS* 1.3 69.5 + - - +
263D ILE* 3.4 29.5 + - + +
264D ILE* 3.4 24.6 - - + -
265D THR* 2.7 36.6 + - - -
266D SER 3.5 1.2 + - - -
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Residues in contact with HIS 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D THR* 3.3 30.4 - - + +
106D LEU* 3.6 31.8 - - + +
109D VAL* 5.1 1.2 - - + +
116D LEU* 3.9 8.8 - - + +
117D GLY 2.9 13.0 + - - +
118D VAL* 3.4 7.1 - - + -
119D ILE 3.0 24.4 + - - -
221D VAL* 1.3 76.3 - - - +
223D LEU* 1.3 76.4 + - - +
224D SER* 3.8 8.2 - - - -
266D SER* 2.7 31.4 + - - +
267D ALA* 3.9 8.1 - - - -
268D GLU* 2.8 29.4 + - + +
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Residues in contact with LEU 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D ILE* 3.7 33.0 - - + +
121D TYR* 4.7 5.2 - - + -
221D VAL 4.0 1.0 + - - -
222D HIS* 1.3 73.1 + - - +
224D SER* 1.3 60.1 + - - +
225D LEU* 4.2 14.4 - - + -
255D MET* 3.8 34.3 - - + -
258D LEU* 4.2 12.6 - - + -
264D ILE* 4.1 13.2 - - + +
266D SER 2.9 10.4 + - - +
267D ALA* 3.2 11.6 - - + -
268D GLU 3.0 27.4 + - - +
269D PHE* 4.3 10.8 - - + -
293D LEU* 3.9 23.8 - - + -
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Residues in contact with SER 224 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99D HIS* 2.9 26.8 + - - -
118D VAL* 4.7 0.2 - - - -
119D ILE 2.9 12.1 + - - -
120D TRP* 3.5 30.3 - - - -
121D TYR 3.1 22.7 + - - +
222D HIS* 3.7 8.0 + - - -
223D LEU* 1.3 71.3 - - - +
225D LEU* 1.3 61.0 + - - +
226D ASP 3.7 1.7 + - - -
268D GLU* 2.8 28.9 + - - -
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Residues in contact with LEU 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D TYR* 3.6 32.3 - - + -
223D LEU* 3.6 12.3 - - + -
224D SER* 1.3 72.0 - - - +
226D ASP* 1.3 72.4 - - - +
227D LEU* 3.7 17.4 + - + +
230D LEU* 4.8 1.6 - - + -
255D MET* 3.7 32.1 - - + -
268D GLU 2.9 14.9 + - - +
269D PHE* 3.3 36.6 - - + -
270D VAL* 3.0 26.0 + - - -
289D LEU* 4.5 11.0 - - + -
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Residues in contact with ASP 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D HIS* 3.4 8.5 + - + -
121D TYR* 2.9 22.3 + - - +
122D ASP* 3.4 12.8 - - - +
224D SER 3.7 1.6 + - - -
225D LEU* 1.3 76.9 - - - +
227D LEU* 1.3 65.5 + - - +
228D ASP* 2.8 21.2 + - - +
229D GLY* 3.0 12.5 + - - -
230D LEU* 4.6 0.3 + - - +
270D VAL* 3.7 6.9 - - - +
271D GLU* 3.2 23.3 - - - +
300D MN 2.5 13.0 + - - -
301D MN 2.2 34.2 + - - -
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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