Contacts of the strand formed by residues 49 - 56 (chain B) in PDB entry 3A7H
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 49 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B LYS* 3.7 28.9 - - + -
41B GLY 3.1 12.6 - - - +
42B ILE* 3.9 16.8 - - + -
47B GLN 5.0 2.2 - - - +
48B LYS* 1.3 79.2 - - - +
50B VAL* 1.3 69.2 + - - +
86B TYR* 5.8 0.3 - - - -
100B GLU* 5.7 0.2 - - - -
101B TYR* 3.6 40.6 + - + +
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Residues in contact with VAL 50 (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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24B PHE* 4.0 14.1 - - + -
40B LYS* 3.7 3.3 - - - -
41B GLY 2.6 45.8 + - - +
42B ILE 4.3 0.4 - - - +
43B ASP* 4.5 11.7 - - + +
48B LYS* 4.2 10.5 - - + +
49B VAL* 1.3 82.9 - - - +
51B ALA* 1.3 59.8 + - - +
52B ILE* 3.8 22.9 - - + -
86B TYR* 4.4 13.9 - - + -
98B ILE* 3.9 22.9 - - + -
99B MET 3.6 11.7 - - - +
101B TYR* 3.6 9.8 - - - +
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Residues in contact with ALA 51 (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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30B ILE* 4.6 0.4 - - + -
38B VAL* 4.4 7.9 - - + -
39B PHE 3.4 7.6 - - - +
50B VAL* 1.3 73.2 - - - +
52B ILE* 1.3 61.2 + - - +
53B LYS 4.1 0.4 - - - -
97B ILE 3.6 1.4 - - - +
98B ILE* 3.7 1.7 - - - -
99B MET* 2.8 43.7 + - + +
100B GLU 3.9 1.3 - - - +
101B TYR* 3.8 8.5 - - + +
400B ATP 3.6 43.5 - - + +
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Residues in contact with ILE 52 (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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24B PHE* 4.0 25.6 - - + -
25B THR 4.4 3.1 - - - +
26B LYS* 4.6 7.9 - - + -
37B GLU 3.7 1.6 - - - +
38B VAL* 3.4 2.9 - - - +
39B PHE* 2.7 47.0 + - + +
40B LYS 4.8 1.1 - - - +
41B GLY* 3.7 26.0 - - - +
50B VAL* 3.8 14.4 - - + -
51B ALA* 1.3 76.9 - - - +
53B LYS* 1.3 62.2 + - - +
54B ILE* 3.6 17.3 - - + -
96B TRP* 3.5 33.4 - - + -
97B ILE 3.4 6.7 - - - +
98B ILE* 4.0 12.6 - - + -
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Residues in contact with LYS 53 (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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35B PHE* 5.2 9.2 - - - +
36B GLY* 5.0 6.5 - - - +
37B GLU 3.3 12.1 - - - +
38B VAL* 4.2 13.9 - - + +
51B ALA 4.1 0.8 - - - -
52B ILE* 1.3 71.8 - - - +
54B ILE* 1.3 61.1 + - - +
55B ILE* 4.1 29.6 - - + -
70B GLU* 4.6 16.4 + - - -
95B LEU 3.4 2.8 - - - +
96B TRP* 3.5 0.7 - - - -
97B ILE* 2.7 55.4 + - + +
99B MET* 4.7 24.2 - - + +
400B ATP 3.2 41.0 + - + +
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Residues in contact with ILE 54 (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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26B LYS* 3.6 27.1 - - + -
36B GLY* 3.2 2.8 - - - -
37B GLU* 2.8 38.9 + - + +
39B PHE* 4.2 11.7 - - + -
52B ILE* 3.6 16.8 - - + +
53B LYS* 1.3 76.0 - - - +
55B ILE* 1.3 63.1 + - - +
56B ASP 4.5 0.2 + - - -
94B LYS* 3.8 34.8 - - + -
95B LEU 3.2 7.4 - - - +
96B TRP* 3.4 42.0 - - + +
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Residues in contact with ILE 55 (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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35B PHE* 4.4 18.8 - - + +
36B GLY* 4.0 14.6 - - - +
53B LYS* 4.1 22.4 - - + -
54B ILE* 1.3 79.7 - - - +
56B ASP* 1.3 70.0 + - - +
57B LEU* 3.3 9.9 + - + -
60B ALA* 5.1 7.4 - - + -
67B ILE* 3.8 35.7 - - + -
94B LYS* 3.3 4.6 - - - -
95B LEU* 2.8 46.8 + - + +
97B ILE* 3.8 27.4 - - + -
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Residues in contact with ASP 56 (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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35B PHE 5.1 2.2 + - - -
36B GLY* 5.4 0.4 - - - -
54B ILE 4.5 0.4 + - - -
55B ILE* 1.3 75.6 - - - +
57B LEU* 1.3 56.5 + - - +
58B GLU* 3.1 17.7 + - - +
59B GLU* 3.0 62.7 + - + +
60B ALA* 3.6 5.0 + - - +
93B THR* 3.0 26.5 + - - -
94B LYS* 3.5 28.3 + - + +
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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