Contacts of the helix formed by residues 75 - 80 (chain A) in PDB entry 1I2M
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 LEU 75 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A THR* 2.9 46.0 - - + +
43A LEU* 4.6 11.4 - - + +
74A GLY* 1.3 77.0 - - - +
76A ARG* 1.3 66.0 + - - +
77A ASP 3.2 0.2 + - - -
78A GLY* 2.8 33.1 + - - -
79A TYR* 3.1 36.1 + - + +
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Residues in contact with ARG 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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73A GLY 5.2 0.4 + - - -
74A GLY* 3.1 16.1 + - - +
75A LEU* 1.3 79.8 - - - +
77A ASP* 1.3 67.0 + - + +
78A GLY 3.0 4.7 + - - -
79A TYR* 3.2 24.2 + - - +
80A TYR* 5.0 2.6 + - - -
268B ASN 3.3 22.0 + - - -
269B TYR* 3.2 44.1 - - - +
270B HIS* 4.3 7.3 - - - -
334B GLU* 2.7 42.8 + - - -
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Residues in contact with ASP 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU 3.2 0.2 + - - -
76A ARG* 1.3 82.5 - - - +
78A GLY* 1.3 58.4 + - - +
79A TYR 3.2 0.9 - - - -
80A TYR* 3.1 9.0 + - - +
81A ILE* 2.9 33.3 + - + +
110A ARG* 3.1 36.4 + - - -
111A VAL* 3.5 23.4 - - + +
320B ARG* 5.4 0.3 + - - -
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Residues in contact with GLY 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LYS* 4.0 5.4 + - - -
64A TRP* 4.4 7.1 - - - -
75A LEU* 2.8 28.9 + - - +
77A ASP* 1.3 78.5 - - - +
79A TYR* 1.3 61.2 + - - +
80A TYR 3.5 0.2 + - - -
81A ILE* 3.6 21.9 - - - +
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Residues in contact with TYR 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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12A LYS* 3.3 16.8 + - - -
14A VAL* 3.7 12.8 - - - +
42A THR* 5.0 1.1 - - + -
43A LEU* 4.5 3.6 + - - +
45A VAL* 3.9 21.5 - - + -
64A TRP* 4.1 10.8 - + - -
66A THR* 4.4 12.3 - - + +
69A GLN* 3.4 38.7 + - + +
70A GLU* 3.9 17.9 - - + -
73A GLY* 3.3 10.3 - - - -
74A GLY 3.2 11.6 + - - -
75A LEU* 3.1 54.4 + - + +
76A ARG* 3.2 23.3 - - - +
77A ASP 3.1 0.8 + - - -
78A GLY* 1.3 76.7 - - - +
80A TYR* 1.3 75.0 + + + +
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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
----------------------------------------------------------
14A VAL* 3.8 28.9 - - + -
16A VAL* 3.9 9.5 - - + +
66A THR* 4.6 0.7 - - + -
70A GLU* 3.4 21.1 - - + +
76A ARG 5.7 1.6 - - - -
77A ASP* 3.1 7.6 + - - +
79A TYR* 1.3 94.9 - + + +
81A ILE* 1.3 68.1 + - - +
83A ALA* 3.0 22.5 + - - +
104A TRP* 3.4 29.3 - - - -
107A ASP* 3.5 42.7 + - + +
108A LEU* 4.0 18.2 - - + -
110A ARG* 5.7 0.4 - - - -
111A VAL* 3.8 22.4 - - + -
112A CYS* 3.1 12.2 - - - -
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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