Contacts of the strand formed by residues 61 - 67 (chain H) in PDB entry 1LNU
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 61 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57H ILE* 3.1 4.7 - - - +
58H TYR* 2.7 37.5 + - + +
59H ASN* 5.8 0.2 - - + -
60H ARG* 1.3 81.0 - - - +
62H GLU* 1.3 74.1 + - - +
63H TYR* 3.1 3.0 + - + +
76H VAL* 5.6 0.4 - - + -
77H THR* 2.8 32.3 + - + +
79H LEU* 5.1 4.0 - - - +
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Residues in contact with GLU 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G TYR* 3.7 19.9 + - + +
55H ARG* 2.6 39.1 + - + +
56H TYR 3.4 2.2 - - - +
57H ILE* 3.4 21.4 - - + +
60H ARG 4.2 0.6 + - - -
61H GLU* 1.3 73.7 - - - +
63H TYR* 1.3 56.7 + - - +
64H VAL 3.9 10.1 - - - +
65H ARG* 2.7 41.9 + - - +
76H VAL* 3.1 33.8 - - + +
77H THR* 3.3 8.8 - - - +
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Residues in contact with TYR 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G ASN* 4.3 8.0 + - - -
74G LEU* 3.4 25.2 - - + +
77G ARG* 3.9 0.9 - - - -
11H ALA* 4.6 0.2 - - - +
35H TYR* 2.6 40.9 + + - -
56H TYR* 3.0 37.6 + - + +
58H TYR* 3.9 15.3 - - + -
61H GLU* 3.1 6.8 + - + +
62H GLU* 1.3 71.5 - - - +
64H VAL* 1.3 81.9 + - + +
76H VAL* 2.8 22.2 + - - +
77H THR* 3.2 19.4 + - + +
79H LEU* 3.1 39.7 - - + -
80H GLY* 3.4 5.9 - - - -
83H ASP* 2.9 29.0 + - - -
87H TRP* 4.3 4.0 - - - -
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Residues in contact with VAL 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56H TYR* 3.2 32.2 + - + +
62H GLU* 3.9 3.1 - - - +
63H TYR* 1.3 118.7 - - + +
65H ARG* 1.3 75.7 + - - +
73H HIS* 4.8 4.5 - - + +
74H ARG 4.0 5.2 - - - +
75H ALA* 4.5 0.7 - - - +
76H VAL* 3.5 6.0 - - - +
80H GLY* 3.4 25.4 - - - +
83H ASP* 3.9 7.2 - - + +
84H ALA* 4.8 6.7 - - + +
87H TRP* 3.7 28.7 - - + -
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Residues in contact with ARG 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H VAL* 3.8 20.9 - - + -
54H THR 3.4 13.0 - - - +
55H ARG* 3.7 7.7 - - + +
56H TYR* 4.7 2.0 - - - -
62H GLU* 2.7 44.5 + - - +
64H VAL* 1.3 83.8 - - - +
66H TYR* 1.3 75.1 + - - +
67H ASP* 4.8 13.4 + - - +
73H HIS* 3.0 9.9 - - - +
74H ARG* 2.8 41.7 + - - +
76H VAL* 3.9 20.3 - - + +
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Residues in contact with TYR 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52H TYR* 4.1 20.4 - + + -
53H VAL* 3.2 6.4 - - - +
54H THR* 3.0 43.1 + - - +
56H TYR* 5.5 0.4 - - + -
65H ARG* 1.3 81.0 - - - +
67H ASP* 1.3 76.3 + - - +
68H SER* 3.9 13.3 + - - -
71H GLY* 3.8 7.2 - - - -
72H GLU* 3.5 38.6 - - - -
73H HIS* 3.4 26.9 - + - +
94H LEU* 5.1 2.9 - - + -
97H THR* 4.0 15.0 - - + -
98H ARG* 3.0 43.0 + - - -
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Residues in contact with ASP 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51H ARG* 2.7 41.4 + - - -
52H TYR 3.9 1.3 - - - -
53H VAL* 3.8 15.2 - - + +
55H ARG* 5.6 1.2 + - - -
65H ARG* 4.3 14.5 + - - +
66H TYR* 1.3 84.2 - - - +
68H SER* 1.3 75.4 + - - +
69H ASP* 3.0 12.4 + - - -
70H VAL* 3.6 24.6 - - + +
71H GLY 3.1 22.7 + - - -
72H GLU 3.9 5.8 + - - -
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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