Contacts of the strand formed by residues 111 - 119 (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 ARG 111 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41E TYR* 3.9 4.9 - - - -
43E GLU* 3.5 28.0 + - + +
45E GLY* 3.7 25.4 - - - -
46E LEU* 3.4 24.7 - - - +
84E GLU* 4.1 5.1 + - - -
86E ARG* 4.0 4.8 - - - +
106E GLU* 3.0 32.1 + - - +
107E ASP 4.0 11.0 + - - +
108E HIS* 3.0 53.0 + - + +
110E LYS* 1.3 84.4 - - - +
112E SER* 1.3 63.8 + - - +
113E SER 4.1 5.4 - - - +
151E LEU* 5.4 0.2 - - + -
154E LYS* 3.1 26.9 + - - +
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Residues in contact with SER 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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38E LYS 3.9 5.7 - - - +
39E MET* 3.3 39.5 + - - +
41E TYR* 3.2 32.2 + - - +
43E GLU 2.9 18.3 + - - -
44E MET* 3.4 10.6 + - - -
111E ARG* 1.3 74.4 - - - +
113E SER* 1.3 61.6 + - - +
154E LYS* 3.4 20.8 - - - +
155E PRO* 3.6 7.6 - - - +
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Residues in contact with SER 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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39E MET* 3.9 7.0 - - - +
44E MET 2.8 13.7 + - - -
45E GLY* 3.2 20.9 - - - -
46E LEU 4.0 0.5 + - - -
83E TYR* 2.6 31.5 + - - -
108E HIS* 5.1 0.3 + - - -
111E ARG* 3.4 7.2 - - - +
112E SER* 1.3 79.6 - - - +
114E PHE* 1.3 64.3 + - - +
115E VAL* 5.4 1.1 - - - -
151E LEU* 4.3 6.7 - - - +
154E LYS* 4.6 4.0 - - - -
155E PRO* 3.4 28.5 - - - -
157E LEU* 5.5 3.4 - - - -
273F LEU* 5.7 0.4 - - - -
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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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46E LEU* 3.9 17.7 - - + -
48E ILE* 3.9 15.0 - - + -
100E MET* 3.9 12.3 - - + -
103E VAL* 3.6 22.7 - - + -
108E HIS* 4.3 11.2 - + - +
113E SER* 1.3 78.8 - - - +
115E VAL* 1.3 69.5 + - - +
116E CYS* 3.9 17.0 - - + -
143E PHE* 3.4 37.7 - + - -
151E LEU* 3.7 22.2 - - + -
155E PRO 3.2 7.1 + - - +
156E LYS* 4.6 8.3 - - + -
157E LEU* 2.8 29.0 + - - +
158E PHE* 3.8 23.3 - + - -
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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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46E LEU 3.0 13.6 + - - +
47E CYS* 3.2 17.6 - - + -
48E ILE* 2.8 31.5 + - - +
78E PHE* 3.9 30.5 - - + -
83E TYR* 3.6 29.4 - - + +
113E SER* 4.8 0.7 - - - +
114E PHE* 1.3 84.9 - - - +
116E CYS* 1.3 58.9 + - - +
117E VAL* 4.1 10.8 - - + -
157E LEU* 3.4 25.4 - - + +
159E ILE* 4.4 7.4 - - + -
275F PHE* 5.9 0.2 - - + -
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Residues in contact with CYS 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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48E ILE* 3.4 11.0 - - + +
50E ILE* 5.0 0.2 - - - -
100E MET* 3.5 25.4 - - - -
114E PHE* 3.9 11.6 - - + -
115E VAL* 1.3 74.1 - - - +
117E VAL* 1.3 60.8 + - - +
118E LEU* 3.7 30.1 - - - +
139E ILE* 5.3 0.2 - - - -
157E LEU 2.9 9.7 + - - -
158E PHE* 3.4 29.9 - - + +
159E ILE* 2.7 33.1 + - - +
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Residues in contact with VAL 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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47E CYS* 4.5 4.7 - - - -
48E ILE 2.7 13.3 + - - +
49E ILE* 4.2 19.3 - - + -
50E ILE 2.9 28.1 + - - +
74E LEU* 3.6 37.7 - - + -
78E PHE* 4.5 1.3 - - + -
115E VAL* 4.1 17.3 - - + -
116E CYS* 1.3 78.5 - - - +
118E LEU* 1.3 67.9 + - - +
119E LEU* 4.0 16.6 - - + -
159E ILE* 3.3 27.1 - - + +
216F ILE* 4.6 0.4 - - + -
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Residues in contact with LEU 118 (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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50E ILE* 3.7 35.2 - - + -
96E ILE* 5.3 1.8 - - + -
116E CYS* 3.7 21.8 - - - +
117E VAL* 1.3 73.3 - - - +
119E LEU* 1.3 61.4 + - - +
120E SER 4.0 0.9 - - - -
127E ILE* 4.0 24.5 - - + -
136E LEU* 3.6 31.4 - - + -
139E ILE* 4.5 18.6 - - + -
158E PHE* 5.3 5.8 - - + -
159E ILE 2.7 14.0 + - - +
160E ILE* 4.2 12.7 - - + +
161E GLN* 2.7 35.2 + - - +
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Residues in contact with LEU 119 (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* 4.1 16.8 - - + -
50E ILE 2.9 14.1 + - - +
51E ASN* 3.8 16.2 - - + +
52E ASN 2.8 29.8 + - - -
64E ARG* 3.2 8.1 + - - +
67E THR* 3.8 13.7 - - - +
70E ASP* 4.3 6.5 - - + +
71E ALA* 4.1 13.0 - - + +
74E LEU* 3.6 19.7 - - + -
117E VAL* 4.0 9.6 - - + -
118E LEU* 1.3 73.9 - - - +
120E SER* 1.3 61.1 + - - +
161E GLN* 3.6 28.5 - - + -
216F ILE* 3.8 25.4 - - + -
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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