Contacts of the strand formed by residues 56 - 65 (chain j) in PDB entry 5MQF
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 LEU 56 (chain j).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7i PRO* 4.7 3.8 - - - +
47j ILE* 5.8 6.7 - - + -
49j GLY 3.7 5.6 - - - +
50j PHE* 4.3 4.3 - - + -
54j MET 3.5 6.0 + - - +
55j ASN* 1.3 73.2 - - - +
57j VAL* 1.3 63.3 + - - +
58j LEU* 3.9 5.3 + - + +
78j MET* 3.2 6.3 - - - +
79j LEU* 2.9 42.2 + - + +
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Residues in contact with VAL 57 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5i LEU* 3.7 19.5 - - + +
6i ASN 4.7 9.9 - - - +
7i PRO* 4.7 4.2 - - + +
10i PHE* 5.0 9.4 - - + -
47j ILE* 3.4 3.9 - - - -
48j ILE* 2.8 34.3 + - + -
49j GLY 2.8 18.3 + - - +
56j LEU* 1.3 73.6 - - - +
58j LEU* 1.3 59.2 + - - +
77j ILE 3.4 7.9 - - - +
78j MET* 4.4 2.5 - - + +
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Residues in contact with LEU 58 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44j GLU 4.8 1.3 - - - +
45j GLY* 4.1 21.1 - - - +
46j CYS 3.6 5.2 - - - +
47j ILE* 4.6 1.6 - - - +
48j ILE* 5.7 0.7 - - - -
56j LEU* 3.8 7.7 + - + +
57j VAL* 1.3 73.8 - - - +
59j ASP* 1.3 60.1 - - - +
61j ALA* 4.2 11.2 - - + -
75j GLY 3.6 3.1 - - - +
76j ARG* 3.8 2.1 - - - -
77j ILE* 2.8 41.8 + - + +
79j LEU* 6.0 3.6 - - + +
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Residues in contact with ASP 59 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45j GLY* 3.5 1.6 - - - -
46j CYS* 2.9 43.5 + - + +
48j ILE* 5.3 7.4 - - + +
58j LEU* 1.3 72.6 - - - +
60j ASP* 1.3 74.0 + - + +
61j ALA 3.2 3.2 + - - -
75j GLY 4.4 1.3 - - - -
76j ARG* 5.1 2.0 - - - +
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Residues in contact with ASP 60 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44j GLU 5.1 0.5 - - - -
45j GLY* 4.4 3.6 - - - -
59j ASP* 1.3 76.5 - - + +
61j ALA* 1.3 62.9 + - - +
62j GLU* 4.1 1.9 + - - +
75j GLY* 3.6 18.7 + - - +
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Residues in contact with ALA 61 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43j ILE* 6.3 0.9 - - + -
44j GLU 3.0 18.4 - - - +
58j LEU* 4.2 11.9 - - + -
59j ASP 3.9 1.1 - - - -
60j ASP* 1.3 78.0 - - - +
62j GLU* 1.3 60.7 + - - +
73j GLN* 3.9 2.4 - - - -
74j LEU* 2.9 31.9 + - + +
75j GLY 3.2 18.9 + - - +
77j ILE* 3.9 21.1 - - + -
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Residues in contact with GLU 62 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42j ARG 3.8 0.2 - - - +
43j ILE* 3.3 7.4 - - - +
44j GLU* 2.9 43.5 + - + +
60j ASP 5.1 2.2 - - - +
61j ALA* 1.3 76.0 - - - +
63j GLU* 1.3 64.7 + - - +
64j ILE* 3.9 1.5 + - + -
71j ARG* 5.0 9.9 - - + -
72j LYS 3.2 11.2 - - - +
73j GLN* 5.2 1.6 - - - -
74j LEU* 4.7 2.2 - - - +
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Residues in contact with GLU 63 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41j MET* 5.6 7.2 - - + -
42j ARG 3.6 4.9 - - - +
43j ILE* 4.8 1.6 - - - +
62j GLU* 1.3 73.1 - - - +
64j ILE* 1.3 59.8 + - - +
65j HIS 4.0 0.2 - - - -
70j SER 3.7 1.2 - - - +
71j ARG* 3.2 8.8 - - - +
72j LYS* 2.9 48.6 + - + -
74j LEU* 5.4 1.0 - - - +
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Residues in contact with ILE 64 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41j MET* 3.3 7.6 - - - +
42j ARG* 2.7 45.9 + - + +
43j ILE* 5.5 1.6 - - - -
44j GLU* 5.8 4.3 - - + -
62j GLU* 5.1 3.1 - - + +
63j GLU* 1.3 74.2 - - - +
65j HIS* 1.3 61.7 + - - +
66j SER* 3.5 3.2 + - - -
70j SER 3.9 2.7 - - - -
71j ARG* 4.9 3.1 - - + +
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Residues in contact with HIS 65 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40j ASN 3.4 8.3 - - - +
41j MET* 4.8 2.9 - - + +
63j GLU 4.0 0.6 + - - -
64j ILE* 1.3 69.8 - - - +
66j SER* 1.3 57.2 + - - +
67j LYS* 3.1 1.8 - - + +
68j THR* 4.0 22.7 - - - +
69j LYS* 2.7 35.7 + - - -
70j SER* 2.9 21.5 + - - +
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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