Contacts of the strand formed by residues 46 - 52 (chain B) in PDB entry 5JDS
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 GLU 46 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B PHE* 3.3 5.3 - - - -
38B ARG* 2.9 79.7 + - + +
43B LYS* 5.9 2.8 - - - +
44B GLU 3.4 5.3 + - - +
45B ARG* 1.3 74.7 - - - +
47B ARG* 1.3 67.0 + - - +
48B VAL* 3.6 3.8 + - + +
63B SER* 4.6 4.0 + - - -
110B THR 5.4 1.1 - - - -
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Residues in contact with ARG 47 (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 ALA* 4.1 11.2 - - + -
36B TRP 3.6 10.8 - - - +
37B PHE* 3.4 35.6 - - + -
46B GLU* 1.3 77.6 - - - +
48B VAL* 1.3 66.3 + - - +
49B ALA 3.9 6.1 - - - +
50B LYS* 3.8 16.9 - - - +
59B TYR* 3.6 15.6 - - - -
61B ALA* 3.8 6.9 - - - +
106B CYS 2.8 27.5 + - - -
107B THR 2.7 23.5 + - - -
109B VAL 2.9 24.8 + - - -
110B THR* 3.7 23.3 + - - +
115B PHE* 4.6 4.4 - - - -
203B CL 3.0 33.2 - - + +
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Residues in contact with VAL 48 (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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36B TRP* 2.8 34.5 + - + +
37B PHE* 4.7 2.2 - - - +
38B ARG* 3.5 41.3 - - + +
46B GLU* 3.6 4.9 + - - +
47B ARG* 1.3 79.9 - - - +
49B ALA* 1.3 60.1 + - + +
60B LEU* 3.6 0.7 - - - -
61B ALA* 3.0 24.9 + - - -
63B SER* 4.6 4.5 - - - +
64B VAL* 3.5 24.2 - - + +
68B PHE* 4.6 5.4 - - + -
81B LEU* 4.4 13.9 - - + -
94B TYR* 4.6 10.5 - - + -
203B CL 3.7 5.8 - - - -
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Residues in contact with ALA 49 (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 ALA* 3.2 8.7 - - - +
36B TRP* 3.0 30.7 + - + +
47B ARG* 3.9 4.9 - - - +
48B VAL* 1.3 80.1 - - - +
50B LYS* 1.3 61.2 + - - +
59B TYR 3.3 7.4 - - - -
60B LEU* 3.9 17.9 - - + -
70B ILE* 3.9 18.8 - - + -
81B LEU* 4.0 20.4 - - + -
203B CL 3.9 2.3 - - - +
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Residues in contact with LYS 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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33B CYS* 4.9 0.4 - - - -
34B MET 3.4 8.1 - - - +
35B ALA* 4.9 0.9 - - + -
47B ARG* 3.8 23.3 - - - +
49B ALA* 1.3 76.1 - - - +
51B LEU* 1.3 61.0 + - - +
52B LEU 3.6 10.0 - - - +
57B SER* 2.9 28.0 + - - +
58B THR* 3.2 9.8 - - - +
59B TYR* 2.9 42.0 + - + +
70B ILE* 3.5 6.7 - - - +
103B ASP* 2.8 27.5 + - - -
106B CYS* 3.5 43.3 - - - +
107B THR* 3.0 23.7 + - - +
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Residues in contact with LEU 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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32B ARG 3.5 1.4 - - - +
33B CYS* 3.8 0.9 - - - -
34B MET* 2.9 35.6 + - + +
50B LYS* 1.3 79.4 - - - +
52B LEU* 1.3 77.6 + - - +
53B THR* 4.1 8.3 - - + +
56B GLY* 3.7 15.7 - - - +
57B SER 3.4 3.6 - - - -
58B THR* 3.7 20.4 - - + -
70B ILE* 3.8 15.0 - - + -
71B SER* 4.4 13.9 - - - +
72B GLN* 3.7 42.4 - - + +
79B VAL* 4.4 11.7 - - + -
106B CYS* 4.3 0.2 - - - -
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Residues in contact with LEU 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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32B ARG* 3.3 24.7 - - + +
50B LYS* 3.6 6.3 - - - +
51B LEU* 1.3 72.0 - - - +
53B THR* 1.3 60.5 + - - +
54B THR* 3.2 19.2 + - - +
55B SER* 3.6 20.6 - - - +
56B GLY* 2.8 31.2 + - - -
57B SER 3.0 8.1 + - - -
101B PHE 3.4 25.1 - - - +
102B GLU* 4.3 6.3 - - - +
103B ASP* 3.7 38.8 - - + +
106B CYS* 4.2 10.3 - - + -
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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