Contacts of the helix formed by residues 63 - 71 (chain A) in PDB entry 3LRA
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 ASN 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A TYR 5.0 0.8 + - - -
57A GLU 3.7 2.6 + - - +
58A VAL* 3.0 23.0 - - + +
59A THR 2.5 40.3 + - - +
60A LEU* 3.7 2.9 - - - +
62A ASP* 1.3 83.4 + - - +
64A PRO* 1.3 59.2 - - - +
65A LYS 3.2 3.1 - - - -
66A LEU* 3.2 26.3 - - + +
251A THR 3.0 29.3 + - - +
252A VAL* 3.6 25.8 - - + +
253A ASP 4.8 1.2 - - - +
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Residues in contact with PRO 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU* 3.2 15.9 - - - +
61A LEU 3.6 10.1 - - - +
62A ASP 3.4 9.6 - - - +
63A ASN* 1.3 83.0 - - - +
65A LYS* 1.3 65.4 + - + +
66A LEU 3.0 6.5 + - - -
67A GLU* 3.3 24.4 + - - +
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Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ASN 3.2 2.0 - - - -
64A PRO* 1.3 81.6 - - + +
66A LEU* 1.3 60.3 + - - +
67A GLU 3.2 0.4 - - - -
68A VAL* 3.4 27.1 - - - +
250A GLU* 3.9 44.4 - - + +
251A THR* 3.6 24.9 - - + +
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A VAL* 3.6 29.2 - - + -
59A THR 4.5 2.0 - - - +
60A LEU* 3.8 25.6 - - + -
63A ASN* 3.2 20.2 - - + +
64A PRO 3.0 0.6 - - - -
65A LYS* 1.3 74.4 - - - +
67A GLU* 1.3 51.3 + - - +
68A VAL 3.0 5.8 - - - -
69A LEU* 2.7 52.4 + - + +
70A PHE* 4.3 3.8 - - - -
118A ILE* 4.0 21.1 - - + -
251A THR* 3.7 29.4 - - + +
252A VAL* 5.2 1.8 - - + -
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Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU* 4.0 30.7 - - - +
64A PRO* 3.3 16.9 + - - +
65A LYS 3.2 0.2 - - - -
66A LEU* 1.3 76.3 - - - +
68A VAL* 1.3 62.9 + - + +
69A LEU 3.1 1.6 + - - -
70A PHE* 3.2 45.7 + - + +
71A GLN* 3.8 14.3 - - - +
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Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LYS* 3.4 22.9 - - - +
66A LEU 2.7 4.7 + - - +
67A GLU* 1.3 74.1 - - + +
69A LEU* 1.3 73.2 + - + +
70A PHE 3.3 1.1 + - - -
71A GLN* 3.6 30.6 + - - +
121A LYS* 4.6 1.2 + - - -
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A LEU* 2.7 35.8 + - + +
68A VAL* 1.3 79.0 - - + +
70A PHE* 1.3 59.0 + - + +
71A GLN 3.1 8.3 + - - -
74A GLY 4.8 1.6 - - - +
75A SER* 4.8 1.0 - - - -
117A LYS 5.1 1.4 - - - +
118A ILE* 3.9 42.2 - - + -
121A LYS* 3.0 49.7 - - + +
122A LEU* 4.3 21.1 - - + -
125A TYR* 4.6 9.0 - - + +
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Residues in contact with PHE 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU* 3.6 36.6 - - + -
66A LEU 4.3 4.0 - - - -
67A GLU* 3.2 48.6 + - + +
69A LEU* 1.3 79.8 - - - +
71A GLN* 1.3 66.8 + - + +
75A SER* 3.6 17.0 - - - +
114A SER* 4.0 14.1 - - - -
117A LYS* 3.9 38.6 - - + -
118A ILE* 4.1 18.8 - - + -
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Residues in contact with GLN 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A GLU* 3.8 19.1 - - - +
68A VAL* 3.6 19.2 + - - +
69A LEU 3.1 1.2 + - - -
70A PHE* 1.3 87.4 - - + +
72A GLY* 1.3 57.1 + - - +
75A SER* 3.7 6.2 - - - -
121A LYS* 2.4 30.5 + - - -
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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