Contacts of the helix formed by residues 68 - 77 (chain A) in PDB entry 1NBI
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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65A CYS* 2.5 39.4 + - - -
66A GLY 3.0 0.6 + - - -
67A THR* 1.3 75.1 - - - +
69A VAL* 1.3 64.0 + - - +
70A ASP 3.3 2.9 - - - -
71A SER* 3.9 7.0 - - - -
72A ILE* 3.0 32.2 + - - +
94A ALA* 4.3 2.9 - - - -
110A TRP* 4.4 2.7 - - - -
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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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34A ILE* 4.3 13.9 - - + -
37A THR* 3.7 30.3 - - + -
40A ARG* 3.7 15.9 - - + +
41A THR* 5.1 8.1 + - - +
65A CYS 4.1 1.2 + - - +
67A THR* 3.6 5.3 + - - +
68A GLY* 1.3 78.6 - - - +
70A ASP* 1.3 91.0 + - - +
72A ILE* 4.1 6.5 - - - +
73A MET* 3.6 14.9 + - - +
293A SAM 3.6 29.1 - - - +
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Residues in contact with ASP 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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40A ARG* 3.0 18.5 + - - -
41A THR* 4.7 1.9 + - - -
44A TYR* 2.6 31.8 + - - -
48A LEU* 5.7 3.1 - - + -
62A ASP* 4.7 3.8 + - - +
65A CYS 5.5 0.4 + - - -
68A GLY 3.3 0.2 - - - -
69A VAL* 1.3 90.7 - - - +
71A SER* 1.3 67.9 + - - +
72A ILE 3.3 0.2 - - - -
73A MET* 3.1 16.7 - - + +
74A LEU* 3.0 26.8 + - + +
134A ILE* 4.4 17.5 - - + -
136A LEU* 4.2 20.9 - - + +
293A SAM 3.8 6.8 + - - +
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Residues in contact with SER 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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62A ASP* 2.7 29.7 + - - +
68A GLY* 3.4 7.0 + - - -
70A ASP* 1.3 77.6 - - - +
72A ILE* 1.3 64.9 + - - +
74A LEU* 2.8 11.0 + - - +
75A VAL* 2.8 25.0 + - - +
81A VAL* 3.4 9.2 - - - +
83A SER* 2.7 31.8 + - - -
110A TRP* 3.6 16.6 - - - -
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Residues in contact with ILE 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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67A THR 4.2 6.3 - - - +
68A GLY 3.0 26.1 + - - +
69A VAL* 4.1 6.5 - - - +
71A SER* 1.3 74.9 - - - +
73A MET* 1.3 54.3 + - - +
75A VAL* 3.1 10.4 + - - +
76A GLU* 2.7 49.1 + - - +
97A GLU* 3.7 27.1 - - + +
101A ARG* 4.1 6.5 - - - +
107A PHE* 3.7 20.6 - - + -
110A TRP* 3.4 30.7 - - + -
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Residues in contact with MET 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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41A THR* 3.3 25.8 - - - +
44A TYR* 4.8 3.8 - - + +
45A LYS* 3.3 41.1 - - + +
48A LEU* 4.5 14.8 - - + -
49A LEU* 3.2 35.4 - - + -
69A VAL 3.6 8.1 + - - +
70A ASP* 3.1 24.8 + - - +
72A ILE* 1.3 81.9 - - - +
74A LEU* 1.3 63.9 + - + +
76A GLU* 3.1 13.8 + - - +
77A GLU* 2.8 34.6 + - + +
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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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48A LEU* 5.0 4.3 - - + -
49A LEU* 3.7 28.9 - - + -
52A LEU* 3.8 21.8 - - + -
60A VAL* 3.9 24.0 - - + -
62A ASP* 6.1 0.2 - - + -
70A ASP* 3.4 11.9 - - + +
71A SER* 2.8 11.8 + - - +
73A MET* 1.3 77.9 - - + +
75A VAL* 1.3 63.1 + - - +
77A GLU* 3.2 1.1 + - - -
78A GLY 3.0 6.1 + - - -
79A PHE* 2.9 40.2 + - + -
81A VAL* 4.1 13.2 - - + -
134A ILE* 3.7 29.2 - - + -
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Residues in contact with VAL 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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71A SER 2.8 16.6 + - - +
72A ILE* 3.1 10.3 + - - +
74A LEU* 1.3 72.0 - - - +
76A GLU* 1.3 55.9 + - - +
78A GLY* 2.8 24.9 + - - -
79A PHE 4.1 4.5 + - - +
81A VAL* 3.2 26.2 - - + +
106A ALA* 3.6 16.7 - - + +
107A PHE* 3.5 49.6 - - + +
110A TRP* 3.6 33.2 - - + -
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Residues in contact with GLU 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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72A ILE* 2.7 24.3 + - - +
73A MET* 3.3 14.9 - - - +
75A VAL* 1.3 71.7 - - - +
77A GLU* 1.3 59.1 + - + +
78A GLY* 2.8 10.1 + - - -
101A ARG* 2.9 43.8 + - - +
104A GLU* 5.3 0.9 - - - +
106A ALA* 5.2 3.5 - - - +
107A PHE* 3.7 9.0 - - + -
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Residues in contact with GLU 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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45A LYS* 2.9 28.0 + - - +
49A LEU* 3.1 30.6 - - + +
53A ARG* 2.8 26.3 + - - -
73A MET* 2.8 20.7 + - + +
74A LEU* 3.2 2.4 + - - -
76A GLU* 1.3 74.8 - - + +
78A GLY* 1.3 62.3 + - - +
79A PHE* 3.2 28.5 - - + -
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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