Contacts of the strand formed by residues 43 - 51 (chain E) in PDB entry 5IC4
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 GLU 43 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210B LYS* 6.0 2.8 - - - -
39E MET 6.0 0.2 - - - -
41E TYR* 3.6 3.5 - - - +
42E PRO* 1.3 81.3 - - + +
44E MET* 1.3 60.8 + - - +
45E GLY* 4.0 4.4 + - - +
82E LYS 5.5 0.4 - - - +
84E GLU* 3.8 17.0 - - - +
110E LYS* 2.8 32.8 + - - +
111E ARG* 3.5 35.5 + - + +
112E SER* 2.9 28.9 + - - -
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Residues in contact with MET 44 (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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39E MET* 3.7 37.2 - - + +
43E GLU* 1.3 74.1 - - - +
45E GLY* 1.3 58.3 + - - +
81E LEU* 3.4 25.1 - - + +
82E LYS* 3.3 30.6 + - + +
83E TYR* 3.8 14.1 - - + -
112E SER* 3.6 3.5 - - - -
113E SER* 2.8 35.2 + - - -
274F TYR 5.2 0.2 - - - +
275F PHE* 3.8 48.5 - - + +
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Residues in contact with GLY 45 (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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43E GLU* 3.3 7.3 - - - +
44E MET* 1.3 80.9 - - - +
46E LEU* 1.3 64.0 + - - -
83E TYR* 3.3 8.1 - - - -
84E GLU* 3.0 25.1 + - - +
111E ARG* 3.7 19.3 - - - -
113E SER 3.2 14.4 - - - -
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Residues in contact with LEU 46 (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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45E GLY* 1.3 75.4 - - - -
47E CYS* 1.3 59.7 + - - +
48E ILE* 4.0 9.9 - - + -
83E TYR* 3.6 5.8 - - - -
84E GLU* 3.3 36.6 - - + +
86E ARG* 3.4 31.2 - - - +
103E VAL* 3.9 22.0 - - + -
106E GLU* 3.4 11.9 - - - +
108E HIS* 3.9 4.0 - - + -
111E ARG* 3.4 35.2 - - - +
113E SER 4.0 4.2 + - - -
114E PHE* 4.2 12.2 - - + +
115E VAL 3.0 25.4 + - - -
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Residues in contact with CYS 47 (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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46E LEU* 1.3 74.4 - - - +
48E ILE* 1.3 62.8 + - - +
49E ILE* 3.6 21.2 + - - -
78E PHE* 3.6 35.0 - - + -
83E TYR* 3.9 20.0 - - + -
84E GLU 3.0 9.3 + - - -
85E VAL* 3.4 11.3 - - + +
86E ARG 2.8 26.7 + - - -
115E VAL* 3.2 20.4 - - + -
117E VAL* 4.5 2.5 - - - -
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Residues in contact with ILE 48 (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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46E LEU* 4.3 11.9 - - + -
47E CYS* 1.3 72.3 - - - +
49E ILE* 1.3 56.3 + - - +
50E ILE* 3.9 13.0 + - + -
86E ARG* 3.8 37.9 - - + +
88E LYS* 5.3 2.9 - - + +
99E LEU* 4.1 26.0 - - + -
100E MET* 4.3 9.9 - - - -
103E VAL* 4.3 19.1 - - + -
114E PHE* 3.9 25.4 - - + -
115E VAL 2.8 11.6 + - - +
116E CYS* 3.4 8.8 - - + -
117E VAL 2.7 34.1 + - - +
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Residues in contact with ILE 49 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47E CYS* 4.0 18.2 - - - +
48E ILE* 1.3 75.0 - - - +
50E ILE* 1.3 64.3 + - - +
51E ASN 4.7 0.9 - - - +
71E ALA* 4.4 5.6 - - + -
74E LEU* 3.8 26.9 - - + -
75E ARG* 3.8 9.4 - - - +
85E VAL* 3.7 24.9 - - + -
86E ARG 3.0 9.0 + - - +
87E ASN* 3.6 23.2 + - - +
88E LYS* 2.8 29.8 + - - +
117E VAL* 3.6 15.7 - - + -
119E LEU* 4.1 25.6 - - + -
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Residues in contact with ILE 50 (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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48E ILE* 4.2 13.0 - - + -
49E ILE* 1.3 76.3 - - - +
51E ASN* 1.3 60.4 + - - +
52E ASN* 3.9 20.4 - - - +
88E LYS* 3.6 4.0 - - + -
91E LEU* 4.3 16.4 - - + -
96E ILE* 3.9 34.3 - - + -
99E LEU* 4.3 20.9 - - + -
100E MET* 4.3 13.0 - - - -
116E CYS* 5.0 0.4 - - - -
117E VAL 2.9 12.5 + - - +
118E LEU* 3.7 26.2 - - + -
119E LEU* 2.9 29.8 + - - +
120E SER* 6.4 0.4 - - - -
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Residues in contact with ASN 51 (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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49E ILE* 3.8 2.7 + - + +
50E ILE* 1.3 72.2 - - - +
52E ASN* 1.3 60.8 + - - +
53E LYS* 3.6 4.5 + - - +
67E THR* 2.5 38.9 + - - +
68E ASP* 2.9 27.9 + - - -
71E ALA* 3.9 26.8 - - + +
87E ASN* 5.5 1.1 - - - +
88E LYS 2.8 14.8 + - - +
89E ASN* 3.4 20.8 + - - +
90E ASP* 2.9 20.4 + - - +
119E LEU* 3.8 8.7 - - + +
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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