Contacts of the strand formed by residues 61 - 69 (chain B) in PDB entry 3LQM
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 ILE 61 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B LEU* 4.0 4.3 - - - -
58B SER* 2.8 46.9 + - - +
59B TYR 3.6 0.2 - - - -
60B ARG* 1.3 89.3 - - + +
62B PHE* 1.3 63.6 + - - +
63B GLN* 5.1 10.5 - - + +
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Residues in contact with PHE 62 (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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55B GLN* 3.3 24.0 + - + +
56B TYR* 3.4 17.5 - - - -
57B LEU* 3.6 33.4 - - + -
60B ARG 5.7 0.7 - - - -
61B ILE* 1.3 79.6 - - - +
63B GLN* 1.3 61.2 + - - +
64B ASP 4.4 0.2 + - - -
86B THR* 3.9 19.7 - - + -
88B ARG* 3.4 54.3 - - + +
102B GLN* 3.5 25.8 - - - -
611B SO4 4.9 6.5 - - - +
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Residues in contact with GLN 63 (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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55B GLN* 3.0 20.7 - - - +
56B TYR* 2.8 52.7 + - + +
58B SER* 3.9 21.5 + - - -
61B ILE* 3.8 11.4 + - + +
62B PHE* 1.3 76.5 - - - +
64B ASP* 1.3 67.0 + - - +
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Residues in contact with ASP 64 (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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53B THR* 3.7 9.2 - - - +
54B ALA 4.0 2.2 - - - -
55B GLN* 2.9 26.4 + - - +
56B TYR* 4.0 8.9 - - - -
62B PHE 4.4 0.6 + - - -
63B GLN* 1.3 79.0 + - - +
65B LYS* 1.3 59.2 + - - +
67B MET* 3.5 49.9 - - + +
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Residues in contact with LYS 65 (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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54B ALA 3.0 14.5 + - - +
56B TYR* 4.4 15.2 - - + -
64B ASP* 1.3 75.9 - - - +
66B CYS* 1.3 64.6 + - - +
67B MET* 4.5 2.0 + - - +
74B CYS* 3.4 20.2 - - - -
75B ASP 3.4 20.6 - - - +
76B PHE* 3.6 31.4 - - + +
78B SER* 3.1 27.8 + - - +
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Residues in contact with CYS 66 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B PHE 4.5 0.7 - - - -
53B THR* 3.3 3.7 - - - -
54B ALA* 2.9 32.9 + - + +
65B LYS* 1.3 82.5 - - - +
67B MET* 1.3 64.0 + - - +
69B THR* 4.4 18.8 - - + -
73B GLU 4.6 2.0 - - - -
74B CYS* 2.0 54.1 - - + -
75B ASP 4.3 2.7 - - - -
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Residues in contact with MET 67 (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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53B THR* 3.7 9.4 - - + +
64B ASP* 3.5 47.6 - - + +
65B LYS 5.6 1.8 - - - +
66B CYS* 1.3 78.9 - - - +
68B GLN* 1.3 78.0 - - + +
69B THR* 3.2 4.1 + - - +
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Residues in contact with GLN 68 (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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51B THR* 3.7 26.8 + - + +
52B PHE 2.9 11.2 + - - -
53B THR* 3.2 6.8 + - - +
67B MET* 1.3 76.8 - - + +
69B THR* 1.3 62.7 + - - +
70B THR* 4.0 1.9 + - - +
92B GLU* 3.5 20.5 + - - +
94B ALA 5.4 5.9 + - - -
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Residues in contact with THR 69 (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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40B TRP* 4.5 7.9 - - + -
51B THR* 3.1 4.7 - - - -
52B PHE* 2.8 51.5 + - + +
54B ALA* 6.5 0.2 - - + -
66B CYS* 4.4 22.0 - - + -
67B MET 3.2 3.7 - - - -
68B GLN* 1.3 78.4 - - - +
70B THR* 1.3 62.6 + - - +
71B LEU* 3.1 41.8 + - + +
73B GLU 4.8 2.8 + - - +
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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