Contacts of the strand formed by residues 19 - 26 (chain E) in PDB entry 1I3R
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 19 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12E PHE* 4.0 8.0 - - + -
13E TYR* 3.2 5.4 - - - -
14E LEU* 2.6 45.1 + - + +
17E ASP* 3.8 24.7 + - + +
18E LYS* 1.3 81.6 - - - +
20E GLY* 1.3 60.2 + - - +
21E GLU* 6.1 1.6 - - + -
36E ILE* 4.6 4.7 - - - -
115E PRO 5.6 2.0 - - - +
116E VAL* 3.8 24.2 - - + +
137E PHE* 5.8 4.6 - - - -
2K NAG 4.2 23.4 - - - +
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Residues in contact with GLY 20 (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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12E PHE* 3.2 13.2 - - - -
13E TYR* 4.1 7.9 - - - -
19E ARG* 1.3 78.5 - - - +
21E GLU* 1.3 72.5 + - - +
34E VAL 5.0 0.2 - - - +
36E ILE* 2.9 40.9 + - - +
63E ILE* 4.5 3.4 - - - -
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Residues in contact with GLU 21 (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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10E ALA 4.4 0.9 - - - -
11E GLN* 3.1 23.7 - - - -
12E PHE* 3.1 34.3 + - + -
19E ARG* 6.1 0.7 - - + -
20E GLY* 1.3 85.5 - - - +
22E PHE* 1.3 61.2 + - - +
23E MET* 5.8 2.6 - - + +
33E HIS* 6.3 2.5 - - + -
34E VAL 4.8 4.9 - - - +
36E ILE* 4.2 3.4 - - - -
63E ILE* 3.1 10.2 - - - +
136E VAL* 3.4 26.8 - - + +
137E PHE* 3.2 52.3 + - - +
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Residues in contact with PHE 22 (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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9E GLN* 3.4 41.7 - - + -
10E ALA 3.5 2.2 - - - -
11E GLN* 3.5 19.3 - - + -
21E GLU* 1.3 77.0 - - - +
23E MET* 1.3 68.6 + - - +
24E PHE* 3.8 18.6 - + - -
32E PHE* 4.3 2.5 - + - -
33E HIS* 3.2 2.4 - - - +
34E VAL* 2.9 43.8 + - + +
36E ILE* 5.9 0.4 - - + -
54E PHE* 3.8 21.1 - + - -
59E ALA* 3.6 27.1 - - + -
62E ASN* 4.0 20.4 - - + -
63E ILE* 4.0 10.1 - - + -
7F ALA* 3.9 13.9 - - + -
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Residues in contact with MET 23 (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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9E GLN* 3.3 4.5 - - - +
10E ALA* 2.8 54.7 + - + +
21E GLU* 5.8 3.4 - - + +
22E PHE* 1.3 82.3 - - - +
24E PHE* 1.3 89.2 + - - +
25E ASP* 4.0 11.2 - - + +
30E GLU* 3.7 23.1 - - + -
32E PHE* 3.3 14.4 - - - +
33E HIS* 3.7 11.4 - - + +
136E VAL* 4.7 4.7 - - + -
137E PHE 4.6 12.8 - - - +
138E LEU* 4.2 9.0 - - + -
139E PRO* 3.8 29.8 - - + -
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Residues in contact with PHE 24 (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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7E ILE* 4.0 26.2 - - + -
8E ILE 3.1 4.7 - - - -
9E GLN* 3.4 39.7 - - + -
22E PHE* 3.8 12.8 - + - -
23E MET* 1.3 93.7 - - - +
25E ASP* 1.3 59.3 + - - +
30E GLU* 3.6 0.2 - - - -
31E ILE* 3.0 37.2 + - + -
32E PHE* 3.1 42.8 + + + +
54E PHE* 4.8 2.7 - + - -
5F ILE* 3.9 10.8 - - + -
6F THR 3.8 16.6 - - - -
7F ALA* 4.6 0.7 - - - -
8F PHE* 5.1 5.4 - + - -
108F ASN* 3.8 18.8 - - - -
112F PHE* 4.3 4.9 - + - -
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Residues in contact with ASP 25 (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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6E THR* 4.4 0.9 - - - +
7E ILE* 3.1 8.5 - - - +
8E ILE* 2.7 61.8 + - + +
23E MET* 4.0 12.5 - - + +
24E PHE* 1.3 75.2 - - - +
26E PHE* 1.3 63.1 + - - +
27E ASP 3.5 1.2 + - - -
28E GLY* 2.8 46.4 + - - +
29E ASP 3.2 7.8 + - - +
31E ILE* 4.0 2.9 - - - -
138E LEU* 5.9 0.2 - - - +
139E PRO* 4.0 20.4 - - + +
146E ARG* 4.5 2.9 + - - -
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Residues in contact with PHE 26 (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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5E HIS* 3.5 26.9 - + + -
6E THR 3.5 6.7 - - - -
7E ILE* 4.1 18.2 - - + -
25E ASP* 1.3 73.0 - - - +
27E ASP* 1.3 92.9 + - - +
28E GLY 3.1 0.4 - - - -
29E ASP* 2.7 27.2 + - - +
31E ILE* 3.8 21.4 - - + +
109F TYR* 5.5 1.8 - + - -
112F PHE* 4.9 5.2 - + + -
116F LEU* 3.8 27.4 - - + -
117F VAL* 3.8 30.1 - - + -
149F TYR* 3.9 12.9 + + - -
179F TRP* 3.7 21.0 - + + -
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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