Contacts of the strand formed by residues 75 - 80 (chain B) in PDB entry 3IFP
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 ASP 75 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B SER* 4.6 7.8 + - - -
23B CYS 4.9 0.2 - - - -
24B ARG* 2.9 32.5 - - + +
71B GLY* 3.1 21.3 - - - -
72B SER 3.1 10.9 + - - +
74B THR* 1.3 82.6 - - - +
76B PHE* 1.3 69.8 + - - +
77B THR* 4.9 3.6 + - - -
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Residues in contact with PHE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B SER* 3.4 4.7 + - - -
23B CYS* 2.8 54.7 + - + +
25B SER* 4.3 6.5 - - - -
29B ILE* 3.6 33.7 - - + -
36B THR* 4.3 4.0 - - + -
38B LEU* 3.4 38.8 - - + -
40B TRP* 4.5 2.9 - - + -
56B VAL* 4.1 16.4 - - + -
70B SER 3.4 4.7 - - - +
71B GLY* 3.7 12.1 - - - -
72B SER* 3.7 18.6 - - - -
73B GLY 3.7 19.3 - - - -
74B THR* 3.7 16.2 - - - -
75B ASP* 1.3 81.4 + - - +
77B THR* 1.3 67.0 + - - +
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Residues in contact with THR 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B SER* 4.0 8.3 - - - +
21B ILE 3.3 15.5 - - - +
22B SER* 4.7 5.6 + - - +
40B TRP* 3.9 8.1 + - - -
68B SER 4.1 0.2 - - - +
69B GLY* 3.2 4.9 - - - -
70B SER* 2.9 47.8 + - - +
75B ASP* 4.9 4.9 + - - -
76B PHE* 1.3 77.9 + - - +
78B LEU* 1.3 71.6 + - - +
79B LYS* 3.8 24.7 - - - +
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ALA 3.8 0.3 - - - +
20B SER* 3.3 4.7 - - - -
21B ILE* 2.9 40.6 + - + +
40B TRP* 3.7 49.3 - - + -
52B LEU* 4.6 3.8 - - + -
53B ILE* 4.2 19.3 - - + -
67B PHE* 4.8 4.5 - - + -
68B SER 3.7 17.3 - - - +
69B GLY* 4.5 0.7 - - - -
77B THR* 1.3 76.1 - - - +
79B LYS* 1.3 62.4 + - - +
80B ILE* 3.7 21.9 - - + +
91B TYR* 3.6 32.8 - - + -
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Residues in contact with LYS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLN* 5.8 6.1 - - - +
19B ALA 3.4 6.3 - - - +
20B SER* 3.3 19.6 + - - +
66B ARG 3.5 2.8 - - - +
67B PHE* 3.5 1.7 - - - -
68B SER* 2.8 50.2 + - - +
70B SER* 4.9 8.1 - - - +
77B THR* 3.8 20.2 - - + -
78B LEU* 1.3 79.5 - - - +
80B ILE* 1.3 65.3 + - - +
81B SER 4.0 1.1 - - - +
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Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ASP 3.9 0.7 - - - +
18B GLN* 3.2 4.8 - - - +
19B ALA* 2.9 48.2 + - + +
21B ILE* 5.0 7.0 - - + -
66B ARG* 3.3 10.1 - - - +
67B PHE* 3.3 29.4 - - + -
78B LEU* 3.7 30.1 - - + +
79B LYS* 1.3 78.1 - - - +
81B SER* 1.3 68.9 + - - +
83B VAL* 3.7 25.8 - - + -
87B ASP* 3.8 20.0 - - + +
91B TYR* 4.5 11.0 - - + +
109B LEU* 5.4 3.8 - - + -
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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