Contacts of the strand formed by residues 110 - 115 (chain D) in PDB entry 4OV6
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 LYS 110 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B HIS* 3.5 16.4 - - + +
109D THR* 1.3 74.0 - - - +
111D ILE* 1.3 69.9 + - - +
112D LEU* 3.4 25.7 + - + +
124D VAL* 3.4 2.5 - - - -
125D LYS* 2.9 43.9 + - + -
201D PG4 4.0 43.0 + - - +
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Residues in contact with ILE 111 (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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213B GLY* 3.4 22.7 - - - -
216B PHE* 4.2 17.9 - - + -
217B HIS* 2.9 16.3 + - - +
95D ALA* 3.9 32.1 - - + +
98D LEU* 5.3 0.7 - - + -
99D GLN* 3.5 30.3 - - + +
110D LYS* 1.3 71.4 - - - +
112D LEU* 1.3 60.4 + - - +
113D HIS 4.0 14.4 - - - +
114D VAL* 4.1 18.2 - - + -
122D PHE* 3.9 21.1 - - + -
123D LEU 3.6 7.0 - - - +
124D VAL* 3.9 17.5 - - + -
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Residues in contact with LEU 112 (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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211B GLU* 5.7 2.9 - - - +
212B ASP* 4.1 11.8 + - - +
213B GLY 4.3 4.0 + - - -
77D THR* 4.1 17.7 - - + -
110D LYS* 3.7 43.1 - - + +
111D ILE* 1.3 73.6 - - - +
113D HIS* 1.3 59.1 + - - +
123D LEU* 2.8 41.2 + - + +
125D LYS* 4.0 20.0 - - + +
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Residues in contact with HIS 113 (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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212B ASP* 3.2 28.1 + - + -
213B GLY 5.5 0.2 - - - +
111D ILE* 3.5 3.1 - - - +
112D LEU* 1.3 81.0 - - - +
114D VAL* 1.3 86.5 + - - +
115D PHE* 3.6 21.0 - + - -
122D PHE* 3.3 5.9 - - - +
123D LEU* 2.8 41.2 + - + +
266E ILE* 4.0 33.3 - - + +
269E GLU* 3.0 30.2 + - - -
273E LYS* 5.0 5.8 + - - -
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Residues in contact with VAL 114 (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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212B ASP* 3.3 21.6 + - - +
215B ARG* 4.5 4.9 - - - +
216B PHE* 3.5 36.6 - - + -
88D LEU* 3.8 26.7 - - + -
91D SER* 4.0 18.4 - - - -
92D GLU* 5.0 2.2 - - + -
95D ALA* 5.7 1.6 - - + -
111D ILE* 4.1 9.4 - - + -
113D HIS* 1.3 90.4 - - - +
115D PHE* 1.3 65.2 + - - +
116D HIS* 3.5 14.2 + - - +
121D GLY 3.7 11.0 - - - +
122D PHE* 4.3 4.7 - - + -
269E GLU* 4.1 0.3 - - - +
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Residues in contact with PHE 115 (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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79D VAL* 4.0 17.9 - - + -
88D LEU* 5.0 1.0 - - - +
91D SER* 4.3 4.9 + - - -
113D HIS* 3.6 10.8 - + - -
114D VAL* 1.3 75.4 - - - +
116D HIS* 1.3 60.6 + - - +
118D LEU* 6.4 0.4 - - + -
119D LEU* 3.1 32.7 - - + +
120D PRO* 3.9 2.8 - - - +
121D GLY* 2.8 29.6 + - - +
122D PHE* 3.8 32.8 - - - -
123D LEU* 4.0 13.5 - - + -
262E SER 4.7 1.1 - - - -
265E LEU* 4.0 27.8 - - + -
266E ILE* 3.5 38.4 - - + -
269E GLU* 3.1 20.9 - - + +
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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