Contacts of the helix formed by residues 72 - 80 (chain A) in PDB entry 2IBN
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 THR 72 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A MSE 1.3 77.0 - - - +
73A VAL* 1.3 66.1 + - - +
74A MSE 3.6 7.6 + - - +
75A GLU* 3.0 35.4 + - - +
76A ALA* 3.1 20.7 + - - +
272A GLN* 5.7 3.8 + - - -
275A ILE* 5.8 3.6 - - - -
281A GLY* 3.5 31.0 - - - +
282A ILE* 4.1 15.0 - - + -
283A LEU* 4.9 0.2 - - - -
285A TRP* 4.7 1.8 - - - -
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Residues in contact with VAL 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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72A THR* 1.3 73.1 - - - +
74A MSE 1.3 62.5 + - - +
76A ALA* 3.0 10.1 + - - +
77A VAL* 3.0 25.4 + - + +
121A LEU* 4.5 3.1 - - + -
122A LEU* 3.7 22.9 - - + -
125A LEU* 3.9 10.5 - - + -
207A PHE* 4.2 6.5 - - + -
275A ILE* 3.6 30.9 - - + +
279A CYS* 3.8 24.7 - - - +
281A GLY 4.6 0.8 + - - -
283A LEU* 3.5 27.1 - - + +
285A TRP* 4.5 5.2 - - + -
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Residues in contact with MSE 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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72A THR* 3.3 6.9 + - - +
73A VAL* 1.3 78.6 - - - +
75A GLU* 1.3 62.3 + - - +
77A VAL* 3.4 14.0 + - - +
78A ASP* 3.1 24.3 + - - +
100A PHE* 4.1 22.2 - - + -
121A LEU* 5.2 1.1 - - + -
268A ARG* 3.5 65.1 - - + +
271A TYR* 4.2 9.0 - - + -
272A GLN* 3.8 36.8 - - + +
275A ILE* 4.0 14.7 - - + +
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Residues in contact with GLU 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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69A LYS* 5.9 1.7 + - - -
70A LYS 4.6 0.9 - - - +
71A MSE 3.4 24.9 - - + -
72A THR* 3.0 46.0 + - - +
74A MSE 1.3 74.8 - - - +
76A ALA* 1.3 52.8 + - - +
78A ASP* 3.3 7.5 + - - +
79A LEU* 2.8 39.5 + - + +
282A ILE* 5.0 2.8 - - - +
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Residues in contact with ALA 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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71A MSE 3.9 19.6 - - + -
72A THR 3.1 5.4 + - - +
73A VAL* 3.0 10.0 + - - +
75A GLU* 1.3 73.1 - - - +
77A VAL* 1.3 66.2 + - - +
79A LEU* 3.3 13.4 + - - +
80A LEU* 3.4 17.2 + - - +
125A LEU* 4.4 10.1 - - + -
128A VAL* 4.1 5.6 - - + +
285A TRP* 3.6 38.1 - - + -
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Residues in contact with VAL 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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73A VAL 3.0 19.1 + - - +
74A MSE 3.6 13.5 - - - +
76A ALA* 1.3 74.2 - - - +
78A ASP* 1.3 67.9 + - - +
80A LEU* 3.3 8.7 + - - +
96A SER* 3.3 33.9 - - - +
99A ALA* 4.6 5.2 - - + -
100A PHE* 3.5 35.9 - - + -
121A LEU* 4.0 27.8 - - + -
125A LEU* 3.8 27.1 - - + +
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Residues in contact with ASP 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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74A MSE 3.1 18.7 + - - +
75A GLU* 3.7 6.1 - - - +
77A VAL* 1.3 77.6 - - - +
79A LEU* 1.3 65.3 + - - +
81A ASP* 3.0 38.3 - - - +
96A SER* 5.8 0.2 - - - -
100A PHE* 5.3 1.0 - - - -
268A ARG* 2.8 46.0 + - - -
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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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69A LYS* 3.9 19.7 - - + -
71A MSE 3.7 31.9 - - + -
75A GLU* 2.8 21.4 + - + +
76A ALA* 3.3 10.5 + - - +
78A ASP* 1.3 72.7 - - - +
80A LEU* 1.3 55.8 + - - +
81A ASP 3.1 0.2 - - - -
82A GLY* 3.3 15.2 + - - -
128A VAL* 4.5 2.9 - - + -
131A LEU* 3.5 43.7 - - + +
132A PHE* 5.0 3.4 - - + -
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Residues in contact with LEU 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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76A ALA 3.5 8.7 - - - +
77A VAL 3.3 8.6 + - - +
78A ASP 3.2 1.2 - - - -
79A LEU* 1.3 73.3 - - - +
81A ASP* 1.3 63.3 + - - +
82A GLY 3.1 1.3 - - - +
83A LEU* 3.4 26.8 + - + +
95A ASN* 3.6 21.3 + - + +
96A SER* 3.4 25.2 + - - +
124A ASP 3.8 9.2 - - - +
125A LEU* 3.7 47.6 - - + +
127A LYS* 3.6 22.4 - - + +
128A VAL* 3.6 3.4 - - + +
131A LEU* 3.4 24.2 - - + -
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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