Contacts of the strand formed by residues 110 - 115 (chain E) in PDB entry 5ITX
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 LEU 110 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E LEU* 4.4 14.8 - - + -
87E LEU* 3.7 31.9 - - + -
88E VAL* 3.2 23.8 - - - +
89E PRO* 4.3 4.9 - - + -
90E ARG* 4.0 4.4 - - - +
102E TYR* 4.1 1.7 - - - -
103E THR* 3.2 41.3 + - + +
108E PRO* 3.9 27.4 - - + -
109E ARG* 1.3 83.3 - - - +
111E ALA* 1.3 61.2 + - - +
112E LEU 4.2 0.2 - - - -
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Residues in contact with ALA 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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86E GLN 3.3 0.7 - - - +
87E LEU* 4.4 2.0 - - - -
88E VAL* 2.9 45.2 + - + +
90E ARG* 3.9 10.0 - - - +
93E LEU* 3.7 20.0 - - + -
100E ARG* 5.6 0.2 - - + -
101E PHE 3.6 5.8 - - - +
102E TYR* 3.6 31.2 - - + -
110E LEU* 1.3 75.7 - - - +
112E LEU* 1.3 62.2 + - - +
113E CYS* 4.7 0.2 - - - -
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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
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13E PHE* 4.9 10.1 - - + -
14E VAL* 4.9 8.5 - - + -
17E ALA* 6.2 0.2 - - + -
18E CYS* 4.2 20.2 - - - -
23E PHE* 3.8 16.8 - - + -
47E ILE* 4.3 20.0 - - + -
58E LEU* 5.2 2.9 - - + -
85E PHE* 4.7 19.5 - - + -
86E GLN 3.4 12.6 - - - +
87E LEU* 4.3 18.2 - - + +
100E ARG* 3.4 3.1 - - - +
101E PHE* 2.8 70.0 + - + +
110E LEU 4.2 0.6 - - - -
111E ALA* 1.3 72.4 - - - +
113E CYS* 1.3 66.5 + - - +
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Residues in contact with CYS 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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85E PHE* 3.3 11.0 - - - -
86E GLN 2.8 37.2 + - - +
88E VAL* 3.7 21.1 - - - -
93E LEU* 3.6 31.2 - - - -
94E PRO* 3.7 11.9 - - + -
97E ALA* 3.8 21.1 - - + -
99E LEU 3.3 6.3 - - - +
100E ARG* 4.0 3.1 - - - -
101E PHE* 5.3 0.4 - - - -
111E ALA 3.9 0.4 - - - -
112E LEU* 1.3 79.4 - - - +
114E PHE* 1.3 61.0 + - - +
115E VAL* 4.1 8.7 - - + +
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Residues in contact with PHE 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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77E PHE* 3.6 40.6 - + + -
78E ARG 4.5 10.1 - - - -
79E PHE* 4.2 12.8 - + - -
83E GLY* 4.3 4.5 - - - -
84E SER 3.2 31.2 - - - -
85E PHE* 3.9 14.6 - + + -
97E ALA* 3.5 2.1 - - - -
98E HIS* 3.1 30.5 + - + -
99E LEU* 2.7 21.0 + - + +
101E PHE* 4.8 2.3 - - + -
113E CYS* 1.3 73.1 - - - +
115E VAL* 1.3 61.9 + - - +
116E ASP* 3.6 36.6 - - + -
121E GLY* 5.3 4.0 - - - -
122E ARG 6.5 0.2 - - - -
123E TRP* 4.2 28.0 - + - -
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Residues in contact with VAL 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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82E SER 2.9 15.5 - - - +
84E SER* 3.0 35.7 + - - +
86E GLN* 3.8 34.1 - - + +
94E PRO* 4.0 15.9 - - + -
95E ARG 3.9 20.2 - - - +
96E HIS* 3.8 9.4 - - + +
97E ALA* 4.3 3.8 - - - -
113E CYS* 4.1 8.3 - - + +
114E PHE* 1.3 84.4 - - - +
116E ASP* 1.3 61.6 + - - +
117E ILE* 4.6 10.1 - - + +
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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