Contacts of the strand formed by residues 110 - 115 (chain E) in PDB entry 2OV2
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 ILE 110 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78E PHE* 3.4 16.8 - - + +
80E ILE* 3.9 33.7 - - + -
98E TYR* 4.7 4.5 - - + -
101E VAL* 4.3 10.1 - - + -
102E ARG* 3.2 45.1 - - + +
108E THR 3.3 3.7 + - - +
109E PRO* 1.3 76.2 - - - +
111E LEU* 1.3 77.9 + - - +
112E LEU 4.3 0.4 - - - +
149E ILE* 4.1 24.5 - - + +
150E GLY 5.2 1.0 + - - -
151E SER* 3.1 9.3 + - - +
152E VAL* 2.8 31.5 + - - +
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Residues in contact with LEU 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E VAL* 3.5 26.0 - - + -
78E PHE 2.8 7.5 + - - -
79E LEU* 3.4 17.6 - - + -
80E ILE 3.0 25.1 + - - -
110E ILE* 1.3 82.0 - - - +
112E LEU* 1.3 61.7 + - - +
113E VAL* 3.7 5.2 + - + +
152E VAL* 4.2 9.6 - - + -
153E LYS* 3.7 18.4 - - + +
155E LEU* 4.0 10.3 - - + -
168E VAL 3.9 6.5 - - - +
171E GLU* 3.7 18.2 - - + +
172E ALA* 3.4 32.8 - - + +
175E ALA* 4.1 13.9 - - + -
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Residues in contact with LEU 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E ILE* 3.4 18.8 - - + +
82E PHE* 3.9 27.6 - - + -
93E VAL* 3.8 26.2 - - + -
110E ILE* 4.9 0.7 - - - -
111E LEU* 1.3 71.0 - - - +
113E VAL* 1.3 59.3 + - - +
114E GLY 4.2 0.2 - - - -
142E GLY 3.6 11.9 - - - +
145E MET* 3.7 16.2 - - + +
146E ALA* 3.6 29.2 - - + +
149E ILE* 4.2 9.6 - - + -
151E SER* 3.2 13.4 + - - +
153E LYS 3.1 9.0 + - - +
154E TYR* 3.4 12.5 - - + -
155E LEU* 2.9 25.8 + - - +
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Residues in contact with VAL 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E LEU* 3.9 16.6 - - + -
79E LEU* 4.2 18.4 - - + -
80E ILE 2.9 11.1 + - - +
81E CYS* 3.2 10.7 - - - +
82E PHE* 3.1 31.8 + - - +
111E LEU* 4.1 12.6 - - + +
112E LEU* 1.3 76.5 - - - +
114E GLY* 1.3 61.2 + - - +
115E THR* 3.8 4.2 + - + -
155E LEU* 3.2 11.0 - - + +
157E CYS* 3.9 27.6 - - - -
168E VAL* 3.9 28.3 - - + -
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Residues in contact with GLY 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E PHE* 3.5 25.8 - - - -
84E LEU* 3.8 14.4 - - - +
112E LEU 4.1 0.4 + - - -
113E VAL* 1.3 71.6 - - - +
115E THR* 1.3 58.4 + - - -
154E TYR* 4.2 2.6 - - - -
155E LEU 2.7 13.0 + - - -
156E GLU* 3.2 4.3 - - - -
157E CYS* 2.7 33.8 + - - +
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Residues in contact with THR 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E VAL 2.7 29.1 + - - +
15E GLY* 5.0 4.9 - - - +
19E LEU* 3.8 29.2 - - + -
81E CYS* 4.2 12.3 - - + -
82E PHE 3.0 18.2 + - - +
83E SER* 3.4 5.5 - - - -
84E LEU* 2.9 26.3 + - - +
113E VAL* 4.1 9.4 - - + +
114E GLY* 1.3 74.6 - - - -
116E LYS* 1.3 68.9 + - - +
117E LEU 3.3 2.5 - - - -
157E CYS* 3.3 7.2 - - - -
159E ALA 6.2 0.4 - - - -
200E GCP 5.7 1.3 - - - -
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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