Contacts of the helix formed by residues 68 - 80 (chain A) in PDB entry 3L2Q
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 GLY 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A HIS 4.1 0.4 + - - -
67A THR* 1.3 72.8 - - - +
69A ARG* 1.3 66.9 + - - -
70A GLU 3.6 1.3 - - - -
71A ALA* 4.3 6.2 - - - +
72A THR* 2.5 29.9 + - - -
93A LEU* 3.9 11.4 - - - -
103A ASN* 5.9 5.6 - - - +
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Residues in contact with ARG 69 (chain A).
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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68A GLY* 1.3 71.1 - - - +
70A GLU* 1.3 95.2 + - - +
72A THR* 3.7 1.6 - - - -
73A LEU* 2.9 29.5 + - - +
86A ARG* 4.1 25.0 - - + +
89A VAL* 4.0 8.0 - - + +
90A VAL* 4.5 19.3 - - + +
93A LEU* 3.7 20.5 - - + +
374A HIS* 5.9 3.4 - - + -
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Residues in contact with GLU 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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68A GLY 3.6 0.2 - - - -
69A ARG* 1.3 106.5 + - - +
71A ALA* 1.3 67.5 + - - +
73A LEU* 3.3 4.5 + - - +
74A LEU* 3.1 38.1 + - + +
86A ARG* 2.7 46.6 + - - -
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Residues in contact with ALA 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 THR* 3.5 29.6 - - + -
68A GLY 3.8 5.9 + - - +
69A ARG 3.4 0.6 - - - -
70A GLU* 1.3 79.5 - - - +
72A THR* 1.3 63.1 + - - +
73A LEU 3.3 0.2 + - - -
74A LEU* 3.3 15.4 + - - +
75A LYS* 3.4 15.3 + - - +
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Residues in contact with THR 72 (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* 4.2 6.5 - - + +
61A ALA* 4.2 3.6 - - + -
62A HIS* 3.6 37.4 + - + +
67A THR* 2.6 30.4 + - - -
68A GLY 2.5 24.6 + - - -
69A ARG 3.7 2.2 - - - -
71A ALA* 1.3 78.0 - - - +
73A LEU* 1.3 63.2 - - - +
75A LYS* 3.5 6.8 + - - +
76A ILE* 3.4 23.0 + - + +
89A VAL* 3.9 19.1 - - + -
93A LEU* 5.6 0.2 - - + -
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Residues in contact with LEU 73 (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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69A ARG 2.9 16.7 + - - +
70A GLU* 3.8 7.2 - - - +
71A ALA 3.3 0.2 - - - -
72A THR* 1.3 74.1 - - - +
74A LEU* 1.3 74.6 + - + +
76A ILE* 2.8 12.6 + - + +
77A ALA* 2.8 41.8 + - + +
85A MET* 3.9 29.6 - - + -
86A ARG* 3.5 60.3 - - + +
89A VAL* 4.7 8.4 - - + +
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Residues in contact with LEU 74 (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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70A GLU* 3.1 32.1 + - + +
71A ALA* 3.3 8.0 + - - +
73A LEU* 1.3 86.8 - - + +
75A LYS* 1.3 66.0 + - - +
77A ALA* 3.7 5.9 + - + +
78A ASN* 3.1 23.2 + - - +
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Residues in contact with LYS 75 (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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61A ALA* 4.4 15.7 - - + +
64A LEU* 4.3 25.8 - - + -
67A THR* 5.9 1.3 - - - +
71A ALA 3.4 8.9 + - - +
72A THR* 3.7 9.6 - - - +
73A LEU 3.1 0.6 - - - -
74A LEU* 1.3 78.1 - - - +
76A ILE* 1.3 64.9 + - - +
78A ASN* 3.0 36.2 + - - +
79A LEU* 4.3 1.9 + - - +
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Residues in contact with ILE 76 (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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57A ILE* 4.2 10.5 - - + -
58A VAL* 3.8 33.0 - - + -
61A ALA* 3.3 24.2 - - + -
72A THR* 3.4 13.5 - - + +
73A LEU* 2.8 11.8 + - + +
75A LYS* 1.3 72.3 - - - +
77A ALA* 1.3 55.6 + - - +
78A ASN 3.0 3.3 + - - -
79A LEU* 3.2 3.5 + - - +
80A TYR* 2.9 32.4 + - + -
82A TRP* 3.9 17.0 - - + -
85A MET* 3.7 26.2 - - + -
89A VAL* 4.1 22.9 - - + -
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Residues in contact with ALA 77 (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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46A LYS* 2.7 35.9 + - - +
73A LEU* 2.8 36.3 + - + +
74A LEU* 4.1 7.6 - - + +
76A ILE* 1.3 69.5 - - - +
78A ASN* 1.3 53.1 + - - +
79A LEU 3.4 0.4 - - - -
80A TYR 3.6 12.7 - - - +
85A MET* 5.2 6.5 - - - +
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Residues in contact with ASN 78 (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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46A LYS* 3.1 21.5 - - - +
74A LEU 3.1 12.6 + - - +
75A LYS* 3.0 33.7 + - - +
77A ALA* 1.3 77.5 - - - +
79A LEU* 1.3 70.7 + - + +
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Residues in contact with LEU 79 (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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45A VAL 4.8 0.3 - - - +
46A LYS* 3.5 9.0 - - - +
47A ILE* 3.0 35.5 + - + +
75A LYS 5.4 1.3 - - - +
76A ILE 3.2 3.4 + - - +
78A ASN* 1.3 86.6 - - + +
80A TYR* 1.3 97.5 + - + +
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Residues in contact with TYR 80 (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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46A LYS* 3.8 4.4 - - - +
47A ILE* 3.2 39.5 - - + +
49A PRO* 3.7 15.5 - - + -
57A ILE* 3.7 40.3 - - + +
76A ILE* 2.9 18.1 + - + +
77A ALA* 3.6 23.7 - - - +
79A LEU* 1.3 108.8 - - + +
81A TRP* 1.3 64.2 + - - +
82A TRP* 3.7 20.0 - + + -
85A MET* 4.2 5.1 - - - +
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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