Contacts of the helix formed by residues 62 - 73 (chain A) in PDB entry 1NBP
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 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A LYS 4.5 1.2 - - - +
44A PHE* 3.4 19.5 - - + -
45A TYR* 2.9 59.7 + - + +
58A CYS 3.8 10.3 - - - +
59A LEU 3.0 7.9 + - - +
61A GLU* 1.3 81.5 - - - +
63A LEU* 1.3 60.4 + - - +
64A LYS 3.4 1.8 - - - -
65A PRO* 3.2 19.6 - - - +
66A LEU* 3.1 28.0 + - - +
107A TYR* 4.4 8.7 + - - +
117A PHE* 3.7 22.4 - - + -
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Residues in contact with LEU 63 (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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21A LEU* 6.0 0.2 - - + -
59A LEU* 3.4 30.3 - - + +
60A GLU* 3.3 23.1 + - + +
62A GLU* 1.3 76.4 - - - +
64A LYS* 1.3 63.1 + - + +
66A LEU* 3.5 19.7 + - + +
67A GLU* 2.9 28.8 + - - +
86A ILE* 3.8 18.3 - - + +
89A ILE* 3.7 25.4 - - + +
90A ASN* 3.8 44.9 - - + +
93A VAL* 4.8 4.0 - - + -
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Residues in contact with LYS 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 GLU 4.7 2.4 + - - +
61A GLU 4.5 4.4 + - - +
63A LEU* 1.3 75.9 - - + +
65A PRO* 1.3 67.8 - - + +
67A GLU* 3.2 13.5 + - - +
68A GLU* 3.0 29.0 + - - +
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Residues in contact with PRO 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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43A LYS 5.5 4.0 - - - +
44A PHE* 4.0 12.3 - - + -
61A GLU 3.8 7.4 - - - +
62A GLU* 3.2 36.6 - - - +
64A LYS* 1.3 92.1 - - + +
66A LEU* 1.3 63.6 + - - +
68A GLU* 3.3 6.8 + - + +
69A VAL* 3.0 30.6 + - + +
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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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21A LEU* 5.1 5.2 - - + -
24A ILE* 4.1 25.8 - - + -
44A PHE* 3.6 14.5 - - + -
62A GLU 3.1 18.8 + - - +
63A LEU* 3.6 22.2 - - + +
64A LYS 3.3 0.2 - - - -
65A PRO* 1.3 75.9 - - - +
67A GLU* 1.3 62.4 + - - +
69A VAL* 3.5 1.7 + - - +
70A LEU* 3.1 30.5 + - + +
86A ILE* 3.7 23.3 - - + -
89A ILE* 5.3 0.4 - - + -
114A ILE* 3.6 32.5 - - + -
117A PHE* 4.2 17.7 - - + -
118A LEU* 4.5 7.2 - - + -
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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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63A LEU 2.9 17.3 + - - +
64A LYS* 3.2 13.3 + - - +
66A LEU* 1.3 76.6 - - - +
68A GLU* 1.3 55.9 + - - +
70A LEU* 3.4 4.7 + - - +
71A ASN* 2.9 45.7 + - - +
82A PRO* 4.3 8.7 - - - +
83A ARG* 3.4 29.9 + - - +
86A ILE* 3.8 33.9 - - + +
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Residues in contact with GLU 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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64A LYS 3.0 16.8 + - - +
65A PRO* 3.6 8.3 - - + +
67A GLU* 1.3 75.9 - - - +
69A VAL* 1.3 59.5 + - + +
71A ASN* 3.1 15.5 + - - +
72A LEU* 2.9 61.2 + - + +
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Residues in contact with VAL 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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39A MET* 4.6 18.3 - - + +
42A PHE* 3.7 45.9 - - + -
44A PHE* 3.9 16.8 - - + -
65A PRO* 3.0 18.6 + - + +
66A LEU 4.0 3.4 - - - +
68A GLU* 1.3 75.5 - - + +
70A LEU* 1.3 62.9 + - - +
72A LEU* 3.3 13.0 + - + +
73A ALA* 3.2 20.8 + - - +
114A ILE* 3.9 20.0 - - + -
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Residues in contact with LEU 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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24A ILE* 3.9 26.0 - - + -
28A ILE* 3.9 33.9 - - + -
39A MET* 5.1 3.4 - - + -
66A LEU* 3.1 24.9 + - + +
67A GLU 3.7 4.0 - - - +
69A VAL* 1.3 73.8 - - - +
71A ASN* 1.3 54.3 + - - +
73A ALA* 2.8 32.5 + - - +
82A PRO* 4.1 14.2 - - + +
86A ILE* 4.0 24.9 - - + -
114A ILE* 4.5 3.8 - - + -
201A MHC 3.6 43.1 - - + +
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Residues in contact with ASN 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* 2.9 32.2 + - - +
68A GLU* 3.1 20.7 + - - +
70A LEU* 1.3 76.9 - - - +
72A LEU* 1.3 57.9 + - + +
73A ALA 3.1 12.5 - - - +
74A GLN* 5.0 4.3 - - - +
82A PRO* 3.4 29.2 - - - +
83A ARG* 4.9 3.7 - - - +
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Residues in contact with LEU 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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35A LYS* 4.9 2.9 + - - +
42A PHE* 4.4 24.9 - - + -
68A GLU* 2.9 48.7 + - + +
69A VAL* 3.6 12.3 - - + +
70A LEU 3.3 0.2 - - - -
71A ASN* 1.3 77.7 - - + +
73A ALA* 1.3 57.7 + - - +
74A GLN* 4.3 6.1 + - - +
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Residues in contact with ALA 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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35A LYS* 4.1 9.0 - - + +
39A MET* 3.8 32.5 - - + -
69A VAL 3.2 10.8 + - - +
70A LEU 2.8 16.8 - - - +
71A ASN 3.1 9.8 - - - +
72A LEU* 1.3 77.6 - - - +
74A GLN* 1.3 63.3 + - - +
201A MHC 3.7 27.3 - - - +
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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