Contacts of the helix formed by residues 72 - 84 (chain A) in PDB entry 1I4A
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 SER 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A GLU* 5.4 1.8 + - - -
71A LEU* 1.3 77.0 - - - +
73A GLY* 1.3 69.2 + - - +
75A PHE* 3.8 8.7 + - - +
76A GLU* 3.1 20.4 + - - -
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Residues in contact with GLY 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 SER* 1.3 76.5 + - - +
74A ASN* 1.3 65.8 + - - -
76A GLU* 3.0 9.9 + - - +
77A GLN* 2.9 21.9 + - - +
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Residues in contact with ASN 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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73A GLY* 1.3 72.0 - - - -
75A PHE* 1.3 63.2 + - - +
77A GLN* 3.1 18.4 + - - +
78A VAL* 2.8 28.6 + - - +
264A ASP* 3.7 35.4 + - - +
268A ILE* 4.1 0.8 - - + +
306A TYR* 3.4 41.7 - - + -
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Residues in contact with PHE 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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33A GLU* 3.4 49.1 - - + +
36A ILE* 5.0 3.4 - - + -
37A ILE* 3.5 41.7 - - + -
71A LEU* 3.7 26.5 - - + -
72A SER 3.8 7.2 + - - +
73A GLY 3.2 0.6 - - - -
74A ASN* 1.3 76.5 - - - +
76A GLU* 1.3 61.8 + - - +
78A VAL* 2.8 24.4 - - - +
79A ILE* 3.0 29.7 + - + +
305A ASP* 3.6 23.8 - - + -
306A TYR* 3.7 16.0 - - + +
309A VAL* 4.3 7.2 - - + -
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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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68A LYS* 3.0 37.7 - - - +
71A LEU* 3.3 24.1 - - + +
72A SER* 3.1 29.2 + - - +
73A GLY 3.0 12.5 + - - +
75A PHE* 1.3 80.8 - - - +
77A GLN* 1.3 64.3 + - - +
79A ILE* 3.4 0.9 + - - +
80A LEU* 2.9 43.2 + - + +
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Residues in contact with GLN 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 GLY 2.9 12.3 + - - +
74A ASN* 3.1 18.7 + - - +
76A GLU* 1.3 78.9 - - - +
78A VAL* 1.3 60.3 + - - +
80A LEU* 4.0 5.0 - - - +
81A GLY* 3.0 19.9 + - - -
89A TYR* 5.3 1.6 + - - +
93A GLU* 4.9 1.5 - - - +
96A LYS* 3.4 17.6 + - - +
264A ASP* 5.5 0.8 - - - +
265A ASP* 3.0 32.2 + - - +
268A ILE* 3.5 33.4 - - + +
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Residues in contact with VAL 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 ASN 2.8 18.2 + - - +
75A PHE* 2.8 28.5 - - - +
77A GLN* 1.3 73.4 - - - +
79A ILE* 1.3 66.3 + - + +
81A GLY* 3.2 1.9 + - - -
82A MET* 2.9 36.6 + - - +
268A ILE* 3.4 37.5 - - + -
272A VAL* 4.1 5.0 - - + +
306A TYR* 3.4 13.7 - - + -
309A VAL* 3.5 32.1 - - + -
310A LEU* 3.7 12.6 - - + -
313A LEU* 5.6 0.7 - - + -
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Residues in contact with ILE 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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36A ILE* 4.6 6.1 - - + -
37A ILE* 5.0 5.4 - - + -
40A LEU* 3.8 33.4 - - + -
41A ALA 6.1 0.2 - - - +
67A LEU* 3.9 19.5 - - + -
71A LEU* 4.0 15.3 - - + -
75A PHE* 3.0 50.6 + - + +
76A GLU 3.9 2.7 - - - +
78A VAL* 1.3 82.6 - - + +
80A LEU* 1.3 63.5 + - + +
82A MET* 3.2 23.2 + - + +
83A MET* 3.0 21.5 + - - +
309A VAL* 4.4 9.0 - - + -
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A MET* 4.1 22.6 - - + +
67A LEU* 4.2 17.7 - - + -
68A LYS* 3.5 50.0 - - + +
71A LEU* 6.2 0.4 - - + -
76A GLU* 2.9 39.6 + - + +
77A GLN* 4.1 4.9 - - - +
79A ILE* 1.3 78.0 - - + +
81A GLY* 1.3 56.9 + - - +
83A MET* 3.2 6.0 + - - +
84A THR* 2.7 33.2 + - - +
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Residues in contact with GLY 81 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A GLN 3.0 16.1 + - - -
78A VAL 3.2 3.3 + - - -
80A LEU* 1.3 79.3 - - - +
82A MET* 1.3 61.1 + - - +
84A THR* 3.2 21.3 + - - +
89A TYR* 3.7 31.8 - - - -
272A VAL* 3.6 15.7 - - - +
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Residues in contact with MET 82 (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 LEU* 3.6 22.9 - - + +
41A ALA* 3.7 15.7 - - + +
45A THR* 4.5 5.4 + - - +
48A ARG* 2.9 59.8 + - - +
78A VAL* 2.9 22.4 + - - +
79A ILE* 3.5 13.5 - - + +
81A GLY* 1.3 75.7 - - - +
83A MET* 1.3 59.8 + - + +
84A THR 3.6 3.6 + - - +
272A VAL* 4.0 20.4 - - + -
309A VAL* 3.4 30.3 - - + -
313A LEU* 4.3 16.2 - - + -
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Residues in contact with MET 83 (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 LEU* 3.5 33.0 - - + -
48A ARG* 3.6 24.7 - - + +
49A GLN* 2.9 21.0 + - - +
51A ILE* 5.4 0.4 - - + -
52A ARG* 3.4 47.7 + - + -
63A LEU* 3.6 18.6 - - + -
64A MET* 3.5 17.3 - - - -
67A LEU* 3.8 20.2 - - + -
79A ILE* 3.0 19.9 + - + +
80A LEU* 3.6 7.9 - - - +
81A GLY 3.2 0.6 - - - -
82A MET* 1.3 75.3 - - - +
84A THR* 1.3 58.6 + - - +
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Residues in contact with THR 84 (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 THR* 4.0 9.2 - - - +
49A GLN* 4.0 1.6 - - - -
52A ARG* 4.6 1.6 - - - +
64A MET* 3.9 10.3 - - + +
80A LEU* 2.7 20.6 + - - +
81A GLY* 3.2 16.2 + - - +
82A MET 4.2 1.2 - - - +
83A MET* 1.3 79.3 - - - +
85A PRO* 1.3 77.4 - - + +
86A THR* 3.5 1.6 + - - -
88A LEU* 4.0 9.0 - - + -
89A TYR* 3.6 39.0 - - + +
92A GLN* 3.7 19.2 + - - +
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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