Contacts of the strand formed by residues 89 - 99 (chain E) in PDB entry 1IB1
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 89 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A HIS* 5.7 5.4 - - - -
165A PRO* 3.7 29.6 - - + +
211A TYR* 4.4 15.6 - - - -
213A ASP* 2.9 36.8 + - + +
85E PHE* 3.1 4.4 - - - -
86E VAL* 2.7 43.2 + - + +
87E GLU 3.3 0.8 + - - -
88E GLY* 1.3 79.1 - - - +
90E LEU* 1.3 63.0 + - - +
91E VAL* 3.4 16.0 + - + +
127E HIS* 3.2 31.7 + - - -
129E SER* 5.8 0.4 - - - -
130E PHE* 3.5 25.2 - - - -
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Residues in contact with LEU 90 (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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212A LYS 5.5 0.9 - - - +
213A ASP* 2.9 39.4 + - - +
40E LEU* 3.8 23.8 - - + -
44E ASP* 4.1 20.4 - - + +
47E GLY* 5.0 4.0 - - - -
48E VAL* 4.1 26.7 - - + +
51E ILE* 4.1 9.0 - - + +
83E GLY* 3.9 0.9 - - - -
84E TRP 3.8 8.1 - - - +
85E PHE* 3.7 32.1 - - + -
89E ARG* 1.3 71.3 - - - +
91E VAL* 1.3 60.5 + - - +
92E ALA 3.6 27.4 - - - +
93E PHE* 4.9 2.9 - - + -
127E HIS* 5.1 0.5 - - - -
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Residues in contact with VAL 91 (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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51E ILE* 4.1 5.2 - - - -
84E TRP* 3.1 15.0 + - + +
86E VAL* 3.6 13.9 - - + -
89E ARG* 3.8 21.8 - - + +
90E LEU* 1.3 79.5 - - - +
92E ALA* 1.3 61.2 + - + +
126E VAL* 3.7 1.7 - - - +
127E HIS* 2.8 34.7 + - + +
130E PHE* 3.5 40.4 - - + -
135E LYS* 3.6 34.3 - - - +
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Residues in contact with ALA 92 (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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51E ILE* 4.5 1.0 - - - +
83E GLY* 3.1 4.2 - - - -
84E TRP* 2.9 39.4 + - + -
90E LEU* 3.6 5.0 - - - +
91E VAL* 1.3 84.0 - - + +
93E PHE* 1.3 64.5 + - - +
125E ALA 3.3 13.2 - - - +
126E VAL* 4.1 17.7 - - + -
135E LYS* 5.2 5.4 - - - +
139E LEU* 3.9 17.7 - - + +
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Residues in contact with PHE 93 (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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40E LEU* 3.9 21.5 - - + -
48E VAL* 3.8 35.4 - - + -
51E ILE* 3.9 22.9 - - + -
52E GLU* 3.8 22.7 - - + -
56E PHE* 4.8 0.2 - + - -
82E LEU 3.4 6.5 - - - -
83E GLY* 4.7 0.7 - - - -
90E LEU* 4.9 4.9 - - + -
92E ALA* 1.3 77.7 - - - +
94E ILE* 1.3 74.7 + - - +
95E ILE* 3.7 16.4 - - + -
123E ALA* 3.8 29.2 - - + -
124E LEU* 3.4 3.6 - - - +
125E ALA* 3.0 55.2 + - + -
139E LEU* 3.7 2.4 - - - +
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Residues in contact with ILE 94 (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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40E LEU* 4.6 0.3 - - - +
81E SER* 3.3 6.8 - - - -
82E LEU 3.0 29.6 + - - +
93E PHE* 1.3 81.2 - - - +
95E ILE* 1.3 66.1 + - - +
121E LEU* 4.0 13.7 - - + -
123E ALA 3.2 10.1 - - - +
124E LEU* 3.5 21.5 - - + -
139E LEU* 3.7 11.0 - - + +
140E LEU* 3.9 29.2 - - + -
143E TYR* 3.6 57.2 - - + +
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Residues in contact with ILE 95 (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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40E LEU* 3.6 30.3 - - + -
48E VAL* 4.4 7.6 - - + -
65E LEU* 3.6 31.4 - - + -
70E VAL* 4.4 15.9 - - + +
73E PHE* 3.8 27.1 - - + -
74E LEU* 4.0 18.2 - - + -
81E SER* 4.4 2.0 - - - -
93E PHE* 3.7 22.0 - - + -
94E ILE* 1.3 74.8 - - - +
96E GLY* 1.3 60.7 + - - +
121E LEU* 3.7 2.6 - - - -
122E HIS* 2.9 25.3 + - - +
123E ALA* 3.0 9.5 + - + +
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Residues in contact with GLY 96 (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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73E PHE* 4.1 10.6 - - - +
77E CYS* 3.6 13.2 - - - +
80E LEU* 3.0 28.5 + - - +
81E SER* 4.4 1.1 - - - +
95E ILE* 1.3 76.6 - - - +
97E SER* 1.3 65.0 + - - -
120E HIS 3.1 13.2 - - - -
121E LEU* 4.5 0.2 - - - -
122E HIS* 3.6 4.9 - - - -
143E TYR* 3.6 7.2 - - - -
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Residues in contact with SER 97 (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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73E PHE* 3.6 19.3 - - - -
77E CYS* 3.8 7.9 - - - -
80E LEU* 3.6 18.4 - - - +
96E GLY* 1.3 76.3 - - - -
98E LEU* 1.3 59.2 + - - +
111E LEU 2.9 17.2 + - - -
112E HIS* 3.9 4.0 - - - -
118E SER 3.7 0.3 - - - +
119E ALA* 3.8 2.6 - - - -
120E HIS* 2.8 31.7 + - - +
122E HIS* 2.5 25.3 + - - -
143E TYR* 4.7 0.6 + - - -
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Residues in contact with LEU 98 (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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80E LEU* 3.5 31.6 - - + -
97E SER* 1.3 76.5 - - - +
99E TRP* 1.3 59.5 + - - +
111E LEU 3.9 4.2 - - - +
112E HIS* 3.2 21.3 + - + +
113E ARG* 2.7 42.7 + - - +
114E PRO 3.5 24.7 - - - +
116E GLY* 4.2 12.6 - - - +
118E SER 3.4 20.0 - - - +
119E ALA* 4.2 1.6 - - - -
150E GLN* 5.9 0.9 - - - +
152E ALA* 6.0 2.0 - - + -
153E VAL* 3.9 23.1 - - + -
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Residues in contact with TRP 99 (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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98E LEU* 1.3 76.1 - - - +
100E ASP* 1.3 66.4 + - - +
101E GLU* 3.4 56.4 - - + +
103E ARG 2.8 23.0 + - - -
104E LEU* 3.7 20.7 - - + +
105E THR* 3.4 27.8 - - + -
107E GLU* 3.9 12.3 - - - -
108E SER* 3.5 28.3 - - - -
111E LEU* 4.2 8.5 - - + -
113E ARG* 3.5 33.2 - - + -
116E GLY* 4.0 1.6 - - - -
117E HIS* 3.1 23.1 + - - -
118E SER* 3.0 22.7 + - - +
120E HIS* 4.2 16.4 - - + +
155E ARG* 5.1 0.9 - - - -
157E VAL* 4.9 4.7 - - + -
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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