Contacts of the strand formed by residues 106 - 114 (chain D) in PDB entry 2OVI
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 HIS 106 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30D LEU* 3.8 30.8 - - + +
34D ARG* 3.2 30.5 + - - -
41D VAL* 4.1 19.3 - - + -
42D VAL 3.4 10.8 - - - +
43D PRO* 4.9 4.1 - - + +
44D GLY 4.0 0.9 - - - +
104D CYS* 3.3 7.9 - - - -
105D THR* 1.3 105.4 + - - +
107D ILE* 1.3 61.5 + - - +
125D PHE* 2.7 37.4 + - + -
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Residues in contact with ILE 107 (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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40D THR 3.7 1.2 - - - +
41D VAL* 3.4 2.8 - - - -
42D VAL* 2.8 47.6 + - + +
43D PRO 4.7 2.7 - - - +
44D GLY 4.1 7.4 - - - +
45D ASP 4.2 4.0 - - - +
46D LYS* 4.3 2.5 - - + -
47D PHE* 3.6 20.6 - - - +
50D VAL* 3.3 33.7 - - + -
104D CYS* 3.6 13.0 - - - -
106D HIS* 1.3 79.0 - - - +
108D ALA* 1.3 61.4 + - - +
109D LEU* 4.4 12.2 - - + +
122D ILE* 3.9 20.6 - - + -
123D LEU 3.0 12.6 - - - +
124D PHE* 3.9 13.0 - - + -
125D PHE* 4.8 0.7 - - - -
160D LEU* 6.0 0.4 - - + -
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Residues in contact with ALA 108 (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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33D VAL* 3.4 33.4 - - + -
39D SER* 5.3 0.7 - - - -
40D THR 3.3 7.2 - - - +
41D VAL* 4.1 11.0 - - + -
107D ILE* 1.3 75.0 - - - +
109D LEU* 1.3 66.9 + - - +
110D ILE* 3.9 1.9 + - + +
121D SER 3.6 1.4 - - - +
122D ILE* 3.3 4.7 - - - +
123D LEU* 2.9 34.5 + - + +
125D PHE* 3.8 13.0 - - + -
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Residues in contact with LEU 109 (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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38D SER 4.8 0.5 - - - +
39D SER* 3.8 2.3 - - - -
40D THR* 3.0 41.6 + - - +
50D VAL* 5.1 1.8 - - + -
107D ILE* 4.4 14.4 - - + -
108D ALA* 1.3 76.9 - - - +
110D ILE* 1.3 59.2 + - - +
121D SER 3.5 4.7 - - - -
122D ILE* 4.1 16.2 - - + -
153D PHE* 3.5 34.0 - - + +
156D LEU* 3.8 20.6 - - + -
157D ALA* 3.5 38.8 - - + +
160D LEU* 3.9 18.6 - - + -
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Residues in contact with ILE 110 (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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18D LEU* 5.2 6.7 - - + -
33D VAL* 5.1 7.2 - - + -
36D LEU* 3.4 36.3 - - + -
38D SER* 4.3 6.3 - - - +
39D SER* 3.9 25.1 - - - +
108D ALA 5.1 2.0 - - - +
109D LEU* 1.3 74.6 - - - +
111D GLU* 1.3 82.5 + - - +
112D ARG* 4.2 15.9 - - + +
119D THR* 4.6 0.7 + - - -
120D ALA* 3.3 2.3 - - - -
121D SER* 2.8 56.4 + - - +
123D LEU* 4.7 14.1 - - + -
153D PHE* 3.5 2.7 - - - -
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Residues in contact with GLU 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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38D SER* 4.3 9.3 + - - +
109D LEU 4.5 0.2 + - - -
110D ILE* 1.3 86.8 - - - +
112D ARG* 1.3 65.5 + - - +
118D ASP* 5.5 10.1 - - - +
119D THR 3.3 12.7 - - - +
120D ALA* 4.3 7.0 - - + +
145D LEU* 5.5 1.6 - - - +
150D VAL* 4.5 7.8 - - - +
153D PHE* 4.0 15.1 - - + -
154D HIS* 2.9 37.1 + - - +
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Residues in contact with ARG 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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14D PRO* 3.6 19.6 + - - +
16D GLY 3.2 30.9 + - - +
17D THR* 4.3 1.8 - - - +
18D LEU* 3.3 46.4 - - - +
36D LEU* 5.1 6.1 - - + -
110D ILE* 4.5 18.4 - - + +
111D GLU* 1.3 78.5 - - - +
113D LYS* 1.3 75.6 + - - +
114D PHE* 6.3 1.0 - - - -
118D ASP* 3.4 5.0 - - - +
119D THR* 2.8 42.2 + - - +
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Residues in contact with LYS 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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13D GLU* 5.7 3.8 - - - +
14D PRO 5.3 1.0 - - - +
15D ASP* 3.8 9.0 - - - +
112D ARG* 1.3 92.4 + - - +
114D PHE* 1.3 61.4 + - - +
115D MET 3.9 1.3 - - - +
116D GLY* 3.0 42.8 + - - +
117D MET 3.5 2.7 - - - -
118D ASP* 2.5 38.9 + - - +
119D THR* 5.1 1.1 - - - -
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Residues in contact with PHE 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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15D ASP* 3.5 8.1 - - + +
16D GLY* 4.9 21.5 - - - -
112D ARG* 6.3 1.1 - - - -
113D LYS* 1.3 73.1 - - - +
115D MET* 1.3 97.8 + - + +
116D GLY 3.2 0.2 - - - -
117D MET* 3.0 38.2 + - + +
119D THR* 4.4 13.9 - - + -
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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