Contacts of the helix formed by residues 75 - 97 (chain A) in PDB entry 2MI2
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 75 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A LEU* 3.3 41.0 + - + +
73A ASN* 3.5 3.6 + - - -
74A LEU* 1.3 87.1 + - - +
76A PRO* 1.3 76.9 - - + +
77A GLU* 3.5 9.4 + - + +
78A LEU* 3.7 14.9 + - - +
79A LYS* 3.7 17.9 + - - +
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Residues in contact with PRO 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A THR* 1.3 90.1 - - + +
77A GLU* 1.3 68.6 + - + +
79A LYS* 3.3 19.3 + - + +
80A ALA* 3.0 23.1 + - - +
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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
----------------------------------------------------------
75A THR* 3.3 7.4 - - + -
76A PRO* 1.3 82.7 - - + +
78A LEU* 1.3 74.3 + - + +
80A ALA* 3.0 14.5 + - - +
81A SER* 3.0 26.1 + - - -
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LYS* 5.1 15.3 - - + -
71A LEU* 3.4 62.1 - - + +
72A THR* 5.1 5.6 - - - +
75A THR* 3.7 11.1 + - - +
76A PRO 3.3 0.4 - - - -
77A GLU* 1.3 83.8 - - + +
79A LYS* 1.3 66.2 + - - +
81A SER* 2.8 21.7 + - - +
82A MET* 2.8 34.7 + - + +
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Residues in contact with LYS 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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72A THR 5.1 9.4 + - - +
73A ASN* 5.6 10.5 - - + +
75A THR 3.7 15.5 + - - +
76A PRO* 3.3 18.3 + - + +
78A LEU* 1.3 78.3 - - + +
80A ALA* 1.3 54.8 + - - +
82A MET* 4.1 5.5 - - - +
83A ASP* 2.8 47.1 + - - +
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Residues in contact with ALA 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 PRO 3.0 11.3 + - - +
77A GLU* 3.2 17.5 - - - +
79A LYS* 1.3 76.4 - - - +
81A SER* 1.3 66.0 + - - +
83A ASP* 3.4 6.2 + - - +
84A GLU* 3.0 29.7 + - + +
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Residues in contact with SER 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLU* 3.0 17.1 + - - -
78A LEU* 2.8 20.4 + - - -
80A ALA* 1.3 73.5 - - - +
82A MET* 1.3 58.7 + - - -
84A GLU* 3.3 4.8 + - - +
85A LEU* 2.9 44.6 + - - +
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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
----------------------------------------------------------
68A LYS* 4.5 27.8 - - + +
72A THR* 5.5 14.8 - - - +
78A LEU* 2.8 41.3 + - + +
79A LYS* 4.1 5.2 - - - +
81A SER* 1.3 74.1 - - - +
83A ASP* 1.3 54.2 + - - +
85A LEU* 3.6 11.8 - - + +
86A ARG* 2.7 43.4 + - - +
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Residues in contact with ASP 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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79A LYS* 2.8 37.2 + - - +
80A ALA* 3.6 7.2 + - - +
82A MET* 1.3 78.2 - - - +
84A GLU* 1.3 58.9 + - + +
86A ARG* 3.8 5.5 - - - +
87A GLN* 3.0 39.9 + - + +
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Residues in contact with GLU 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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80A ALA* 3.0 19.3 + - + +
81A SER* 3.7 5.4 - - - +
83A ASP* 1.3 77.8 - - + +
85A LEU* 1.3 61.0 + - + +
87A GLN* 4.3 3.3 - - - +
88A ALA* 2.9 33.3 + - - +
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A SER* 2.9 37.9 + - - +
82A MET* 3.7 12.8 - - + +
84A GLU* 1.3 78.5 - - + +
86A ARG* 1.3 61.6 + - - +
88A ALA* 4.2 3.1 - - - +
89A ALA* 2.9 33.3 + - - +
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Residues in contact with ARG 86 (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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82A MET* 2.7 22.2 + - - +
83A ASP* 3.8 6.7 - - - +
85A LEU* 1.3 75.4 - - - +
87A GLN* 1.3 57.8 + - + +
89A ALA* 4.6 2.0 - - - -
90A GLU* 2.7 72.3 + - + +
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Residues in contact with GLN 87 (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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83A ASP* 3.0 22.4 + - + +
84A GLU* 4.3 3.1 - - - +
86A ARG* 1.3 76.6 - - + +
88A ALA* 1.3 51.4 + - - +
90A GLU* 4.5 9.9 - - - +
91A SER* 2.7 43.2 + - - -
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Residues in contact with ALA 88 (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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84A GLU 2.9 22.3 + - - +
85A LEU* 4.2 3.1 - - - +
87A GLN* 1.3 79.0 - - - +
89A ALA* 1.3 57.0 + - - +
91A SER* 3.0 17.9 + - - -
92A MET* 3.0 33.8 + - + +
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Residues in contact with ALA 89 (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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85A LEU 2.9 22.4 + - - +
86A ARG* 3.9 2.9 - - - +
88A ALA* 1.3 74.4 - - - +
90A GLU* 1.3 62.3 + - + +
92A MET* 4.0 9.8 - - - +
93A LYS* 2.9 31.5 + - - +
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Residues in contact with GLU 90 (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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86A ARG* 2.7 62.3 + - + +
87A GLN* 4.0 8.2 - - - +
89A ALA* 1.3 72.0 - - + +
91A SER* 1.3 59.1 + - - +
93A LYS* 3.2 13.2 + - + +
94A ARG* 2.8 31.3 + - - +
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Residues in contact with SER 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLN 2.7 27.8 + - - -
88A ALA* 3.0 11.1 + - - -
90A GLU* 1.3 72.9 - - - +
92A MET* 1.3 67.4 + - - +
94A ARG* 3.1 8.7 + - - +
95A SER* 2.6 33.9 + - - -
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Residues in contact with MET 92 (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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88A ALA* 3.0 28.6 + - + +
89A ALA* 4.0 7.0 - - - +
91A SER* 1.3 83.9 + - - +
93A LYS* 1.3 53.6 + - - +
95A SER* 3.2 5.6 + - - -
96A TYR* 2.7 42.8 + - + +
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Residues in contact with LYS 93 (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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89A ALA 2.9 21.5 + - - +
90A GLU* 3.2 12.5 + - + +
92A MET* 1.3 76.7 - - - +
94A ARG* 1.3 82.3 + - - +
96A TYR* 4.4 2.7 - - - -
97A VAL* 2.7 63.9 + - + +
98A ALA* 3.6 6.7 + - - +
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Residues in contact with ARG 94 (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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90A GLU 2.8 13.3 + - - +
91A SER* 3.1 11.9 + - - +
93A LYS* 1.3 100.4 - - - +
95A SER* 1.3 59.0 + - - +
96A TYR 3.3 0.7 - - - -
98A ALA* 3.1 32.6 - - + +
99A ASN* 3.8 5.3 + - - +
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Residues in contact with SER 95 (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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91A SER* 2.6 19.8 + - - -
92A MET* 3.5 5.6 - - - -
94A ARG* 1.3 74.4 - - - +
96A TYR* 1.3 52.6 + - - +
99A ASN* 2.7 45.8 - - - +
100A ASP* 3.6 3.3 - - - +
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Residues in contact with TYR 96 (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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92A MET* 2.7 20.4 + - + +
93A LYS* 4.4 2.0 - - - +
94A ARG 3.3 0.2 - - - -
95A SER* 1.3 80.8 - - - +
97A VAL* 1.3 68.3 + - + +
98A ALA 3.0 6.6 + - - -
99A ASN 3.3 2.4 + - - -
100A ASP* 3.3 25.2 - - + +
101A PRO* 2.8 40.8 - - + +
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Residues in contact with VAL 97 (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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93A LYS* 2.7 53.3 + - + +
96A TYR* 1.3 85.4 - - + +
98A ALA* 1.3 58.8 + - - +
101A PRO* 4.5 6.9 - - + +
102A LEU* 3.8 13.7 - - - +
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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