Contacts of the strand formed by residues 67 - 72 (chain E) in PDB entry 1I5L
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 VAL 67 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19E VAL* 4.0 16.8 - - + -
20E ARG 3.7 5.4 - - - +
21E LEU* 4.6 0.9 - - + -
22E LYS* 3.9 10.4 + - - -
38E MET* 4.3 13.5 - - + +
40E LEU* 4.2 10.8 - - + -
62E ILE* 4.1 18.6 - - + -
63E ARG 4.2 2.0 - - - +
64E GLY* 2.9 14.1 + - - +
66E THR* 1.3 80.1 - - - +
68E VAL* 1.3 66.6 + - - +
69E PHE* 3.6 15.7 - - - +
70E VAL* 3.9 23.6 - - + -
63F ARG* 3.3 31.5 + - + +
66F THR* 4.1 1.0 + - - -
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Residues in contact with VAL 68 (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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20E ARG* 3.0 17.3 + - + +
21E LEU 4.0 5.6 - - - +
22E LYS* 3.9 32.5 - - + +
67E VAL* 1.3 76.9 - - - +
69E PHE* 1.3 84.5 + - + +
21F LEU* 4.2 10.3 - - + -
25F ARG* 5.4 3.8 - - - -
62F ILE* 3.6 4.9 - - + +
63F ARG* 3.1 24.3 + - - +
66F THR* 3.7 30.8 + - + +
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Residues in contact with PHE 69 (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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18E ILE* 4.9 8.7 - - + -
20E ARG* 3.0 63.9 + - + -
67E VAL* 3.6 4.1 - - - +
68E VAL* 1.3 97.9 - - + +
70E VAL* 1.3 73.2 + - - +
71E SER* 4.6 11.2 - - - -
21F LEU* 4.9 0.9 - - + -
25F ARG* 4.6 9.2 - - - -
27F PHE* 3.8 33.2 - + - -
47F GLU* 4.3 10.1 - - - -
57F VAL* 6.0 2.9 - - + -
60F VAL* 4.1 18.8 - - + -
61F VAL 3.0 14.6 - - - +
62F ILE* 4.1 13.9 - - + -
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Residues in contact with VAL 70 (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 LEU* 4.3 24.9 - - + -
12E SER* 6.5 0.2 - - - -
17E VAL* 4.3 17.9 - - + -
18E ILE 3.4 7.6 - - - +
19E VAL* 4.2 12.8 - - + -
31E LEU* 5.6 3.1 - - + -
38E MET* 5.6 5.8 - - - -
40E LEU* 3.8 29.6 - - + -
67E VAL* 3.9 12.6 - - + -
69E PHE* 1.3 82.7 - - - +
71E SER* 1.3 68.4 + - - +
72E PRO* 4.6 0.7 - - - +
60F VAL* 3.5 1.9 - - - -
61F VAL* 2.9 35.8 + - + +
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Residues in contact with SER 71 (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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17E VAL* 3.2 6.6 - - - -
18E ILE* 2.7 56.5 + - - +
69E PHE* 4.6 7.3 - - - -
70E VAL* 1.3 77.7 - - - +
72E PRO* 1.3 68.7 + - - +
57F VAL* 3.9 16.4 - - - +
59F SER 3.4 19.1 - - - -
60F VAL* 3.5 12.6 - - - -
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Residues in contact with PRO 72 (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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8E VAL* 6.2 3.4 - - + -
12E SER* 4.7 16.2 - - - +
15E SER* 5.7 2.0 - - - +
16E PRO 3.8 10.8 - - - +
17E VAL* 4.4 2.9 - - + -
18E ILE* 5.0 2.1 - - - +
70E VAL 4.6 0.9 - - - +
71E SER* 1.3 96.5 + - - +
73E ALA* 1.3 60.9 + - - +
57F VAL* 5.1 5.4 - - - +
58F GLY* 5.4 6.1 + - - +
59F SER* 3.5 33.4 - - - +
60F VAL* 5.3 0.2 - - - -
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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