Contacts of the strand formed by residues 112 - 117 (chain E) in PDB entry 4XH9
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 112 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80E ILE* 3.4 18.2 - - + +
82E MET* 3.8 40.2 - - + -
100E THR* 5.2 0.9 - - + -
103E VAL* 3.8 22.0 - - + -
104E LYS* 4.0 30.7 - - + +
110E VAL 3.5 10.7 + - - +
111E PRO* 1.3 78.0 - - - +
113E ILE* 1.3 67.5 + - - +
114E LEU 4.5 0.2 - - - +
151E ILE* 4.4 16.8 - - + +
152E GLY 5.2 3.1 + - - +
153E ALA* 3.2 9.4 - - + +
154E PHE* 2.6 36.8 + - - +
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Residues in contact with ILE 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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79E VAL* 4.6 1.8 - - + +
80E ILE 2.9 15.4 + - - +
81E LEU* 3.9 20.2 - - + -
82E MET* 2.8 28.4 + - - +
112E ILE* 1.3 80.4 - - - +
114E LEU* 1.3 59.8 + - - +
115E VAL* 4.0 12.7 - - + +
154E PHE* 4.2 5.8 - - + -
155E GLY 3.6 7.2 - - - +
170E VAL* 3.5 25.8 - - + +
173E MET* 3.9 30.7 - - + +
174E ALA* 3.6 18.4 - - + +
177E ALA* 4.1 22.7 - - + -
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Residues in contact with LEU 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 MET* 3.4 32.8 - - + +
84E PHE* 3.8 26.5 - - + -
95E ILE* 4.3 12.1 - - + -
112E ILE 4.2 0.4 - - - -
113E ILE* 1.3 73.2 - - - +
115E VAL* 1.3 62.9 + - - +
144E GLY 3.4 25.1 - - - +
147E MET* 3.9 14.8 - - + -
148E ALA* 3.6 22.2 - - + +
151E ILE* 4.4 10.1 - - + -
153E ALA* 4.2 2.0 - - + +
155E GLY 3.0 10.5 + - - +
156E TYR* 3.3 16.8 - - + -
157E MET* 3.2 23.7 + - - +
173E MET* 5.6 0.2 - - - +
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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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21E LEU* 4.2 11.0 - - + -
81E LEU* 3.5 29.6 - - + -
82E MET 2.7 10.0 + - - +
83E CYS* 3.5 5.7 - - - +
84E PHE* 3.0 32.2 + - - +
113E ILE* 4.0 11.2 - - + -
114E LEU* 1.3 81.7 - - - +
116E GLY* 1.3 63.8 + - - +
117E ASN* 4.3 1.8 - - + +
157E MET* 3.3 11.4 - - + +
159E CYS* 3.8 28.9 - - - -
170E VAL* 3.7 24.0 - - + -
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Residues in contact with GLY 116 (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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84E PHE* 3.4 31.4 - - - -
86E ILE* 3.6 9.9 - - - +
115E VAL* 1.3 71.2 - - - +
117E ASN* 1.3 65.4 + - - -
156E TYR* 4.0 4.4 - - - -
157E MET 3.2 9.5 + - - -
158E GLU* 3.2 8.4 - - - +
159E CYS 3.0 23.0 + - - +
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Residues in contact with ASN 117 (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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16E CYS 3.6 18.9 + - - +
17E GLY* 3.3 28.4 + - - +
20E CYS* 5.0 1.0 - - - +
21E LEU* 4.9 7.5 - - + +
83E CYS* 5.7 3.8 - - - -
84E PHE 2.8 11.9 + - - +
85E SER* 3.6 0.6 - - - -
86E ILE* 2.9 26.3 + - - +
115E VAL* 3.7 5.0 + - + +
116E GLY* 1.3 73.4 - - - +
118E LYS* 1.3 86.0 + - + +
119E LYS 3.3 2.2 + - - -
159E CYS* 3.2 27.3 - - - +
161E ALA* 3.5 26.3 + - - +
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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