Contacts of the helix formed by residues 60 - 70 (chain D) in PDB entry 3NBT
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 LYS 60 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D PHE* 4.0 17.0 - - + -
37D GLY* 5.3 0.9 - - - +
58D THR* 3.7 24.6 - - + +
59D TRP* 1.3 76.2 - - - +
61D GLU* 1.3 69.0 + - - +
62D GLU* 3.1 22.6 + - - +
63D THR* 3.0 22.2 + - - +
64D LEU* 2.9 23.8 + - - +
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Residues in contact with GLU 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ILE* 3.9 20.5 - - + +
96B ALA* 6.1 0.7 - - - -
99B LYS* 3.2 35.0 + - + +
36D PHE* 3.9 15.2 - - + -
60D LYS* 1.3 73.8 - - + +
62D GLU* 1.3 75.7 + - - +
64D LEU* 3.4 1.6 + - - +
65D MET* 2.9 38.0 + - + +
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Residues in contact with GLU 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D LYS* 3.7 27.4 - - + +
61D GLU* 1.3 94.3 + - - +
63D THR* 1.3 63.9 + - + +
65D MET* 3.4 15.1 + - - +
66D GLU* 3.4 13.7 + - - +
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Residues in contact with THR 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D ILE* 4.0 16.2 - - + -
58D THR 2.8 29.2 + - - +
59D TRP* 3.5 5.4 - - - -
60D LYS* 3.0 28.6 + - + +
62D GLU* 1.3 77.8 - - + +
64D LEU* 1.3 58.9 + - - +
66D GLU* 3.2 5.4 + - - +
67D TYR* 2.9 30.1 + - - +
74D TYR* 3.1 27.8 - - - +
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Residues in contact with LEU 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ILE* 3.8 23.3 - - + -
98B LEU* 4.6 5.8 - - + -
35D LEU* 4.0 14.6 - - + -
36D PHE* 3.3 44.2 - - + -
59D TRP* 3.6 26.5 - - + -
60D LYS 2.9 17.7 + - - +
63D THR* 1.3 77.0 - - - +
65D MET* 1.3 57.7 + - - +
67D TYR* 4.4 0.9 - - + -
68D LEU* 2.9 48.4 + - + +
105D HEC 3.8 24.0 - - + -
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Residues in contact with MET 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B LYS* 3.8 29.4 - - + +
91B ARG* 3.0 66.6 + - - +
92B GLU* 4.0 21.8 - - + -
95B ILE* 3.3 24.5 - - + -
61D GLU* 2.9 28.0 + - + +
62D GLU* 3.5 8.5 - - - +
64D LEU* 1.3 78.7 - - - +
66D GLU* 1.3 61.8 + - - +
69D GLU* 3.6 2.9 + - - +
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Residues in contact with GLU 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D GLU 3.4 8.6 + - - +
63D THR* 3.2 8.2 + - - +
64D LEU 3.2 0.2 - - - -
65D MET* 1.3 77.1 - - - +
67D TYR* 1.3 66.1 + - - +
69D GLU* 3.2 25.7 + - - +
70D ASN* 3.6 5.7 + - - +
73D LYS* 5.8 3.6 - - - -
74D TYR* 3.5 34.3 + - + +
1006D PG4 3.7 18.2 - - - +
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Residues in contact with TYR 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B PHE* 5.3 1.4 - + - -
52D ASN* 4.9 0.9 + - - -
59D TRP* 3.4 21.5 - + + -
63D THR 2.9 16.6 + - - +
64D LEU* 3.9 1.8 - - + +
66D GLU* 1.3 76.8 - - - +
68D LEU* 1.3 75.2 + - + +
70D ASN 2.9 19.6 + - - -
71D PRO* 2.9 54.3 - - + +
74D TYR* 3.5 32.0 - + + -
75D ILE* 3.7 20.9 - - + -
78D THR* 4.8 8.0 + - + -
80D MET* 4.8 4.3 - - - -
105D HEC 3.3 60.3 + + + +
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Residues in contact with LEU 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B PHE* 4.0 13.8 - - + -
84B GLY* 3.2 6.7 - - - -
85B ILE* 2.7 27.8 + - + +
91B ARG* 3.8 19.1 - - + +
94B LEU* 3.9 20.6 - - + -
95B ILE* 3.8 27.1 - - + -
98B LEU* 4.5 7.0 - - + -
64D LEU* 2.9 34.3 + - + +
67D TYR* 1.3 95.4 - - + +
69D GLU* 1.3 59.1 + - - +
71D PRO* 4.4 0.2 - - - -
105D HEC 3.9 27.4 - - + -
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Residues in contact with GLU 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ALA 4.2 0.7 - - - +
84B GLY* 3.6 10.8 - - - -
85B ILE 3.5 15.7 + - - +
86B LYS* 4.7 6.7 - - - +
91B ARG* 3.5 36.6 + - - +
65D MET 3.6 5.2 + - - +
66D GLU* 3.2 17.6 + - - +
67D TYR 3.0 1.0 + - - -
68D LEU* 1.3 80.3 - - - +
70D ASN* 1.3 64.8 + - + +
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Residues in contact with ASN 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ALA 4.0 9.5 - - - +
66D GLU 3.6 3.5 + - - +
67D TYR 2.9 5.6 + - - +
68D LEU 3.2 0.2 - - - -
69D GLU* 1.3 88.8 - - + +
71D PRO* 1.3 67.4 - - - +
72D LYS* 3.5 8.3 + - - +
73D LYS* 3.1 42.0 + - + +
74D TYR* 3.0 20.3 + - - +
73E LYS* 6.2 0.2 - - - +
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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