Contacts of the helix formed by residues 62 - 84 (chain A) in PDB entry 2M8N
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 HIS 62 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 3.7 33.4 + - + +
28A GLU* 5.6 3.3 - - - -
31A ALA* 5.9 3.0 + - - -
32A PHE* 4.0 26.9 - + + -
59A VAL* 3.5 20.3 + - + +
60A GLY 3.0 3.8 - - - +
61A GLY* 1.3 73.0 + - - +
63A GLN* 1.3 59.0 + - - +
64A ALA 3.4 2.2 - - - -
65A ALA* 3.3 16.1 + - + -
66A MET* 2.9 27.9 + - - +
181A VAL* 5.8 5.5 - - - +
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Residues in contact with GLN 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLY 4.1 7.0 - - - +
61A GLY 2.8 12.4 + - - +
62A HIS* 1.3 69.6 - - - +
64A ALA* 1.3 66.6 + - - +
66A MET* 3.8 18.8 - - + +
67A GLN* 2.9 46.3 + - - +
176A GLN* 5.6 10.0 - - + +
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Residues in contact with ALA 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A HIS 3.4 0.4 - - - -
63A GLN* 1.3 86.9 - - - +
65A ALA* 1.3 57.2 + - - +
67A GLN* 3.5 5.9 + - - +
68A MET* 2.7 45.1 + - + +
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Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PHE* 4.2 21.3 - - + -
62A HIS* 3.3 20.9 + - + +
64A ALA* 1.3 76.7 - - - +
66A MET* 1.3 64.6 + - - +
68A MET* 3.0 8.3 + - - +
69A LEU* 2.9 22.6 + - + +
141A ILE* 3.4 29.0 - - + +
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Residues in contact with MET 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A VAL 5.8 0.4 - - - +
60A GLY* 4.3 20.0 - - - +
62A HIS 2.9 20.7 + - - +
63A GLN* 3.8 24.7 - - + +
65A ALA* 1.3 72.7 - - - +
67A GLN* 1.3 64.9 + - + +
69A LEU* 3.3 16.1 + - + +
70A LYS* 2.9 38.7 + - + +
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Residues in contact with GLN 67 (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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63A GLN* 2.9 35.8 + - - +
64A ALA* 3.6 8.6 - - - +
65A ALA 3.2 0.2 - - - -
66A MET* 1.3 84.5 - - + +
68A MET* 1.3 72.7 + - - +
70A LYS* 3.3 10.5 + - + +
71A GLU* 3.2 41.8 + - + +
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Residues in contact with MET 68 (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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64A ALA* 2.7 34.8 - - + +
65A ALA* 3.0 9.1 + - - +
67A GLN* 1.3 90.4 - - - +
69A LEU* 1.3 60.9 + - - +
71A GLU* 3.5 13.4 + - - +
72A THR* 3.1 27.0 + - - -
137A GLY* 5.3 0.9 - - - +
140A LYS* 4.0 26.0 + - + +
141A ILE* 3.7 24.9 - - + -
144A MET* 4.3 27.1 - - + -
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Residues in contact with LEU 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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56A LEU* 3.9 31.4 - - + -
59A VAL* 6.2 2.0 - - + -
65A ALA* 2.9 17.7 + - + +
66A MET* 3.3 17.5 + - + +
68A MET* 1.3 73.2 - - - +
70A LYS* 1.3 60.4 + - - +
72A THR* 3.3 4.8 + - - -
73A ILE* 2.8 44.6 + - + +
134A ILE* 3.8 31.0 - - + +
137A GLY* 3.9 9.9 - - - -
138A LEU* 3.9 12.1 - - + +
141A ILE* 3.8 20.2 - - + -
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Residues in contact with LYS 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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66A MET* 2.9 27.0 + - - +
67A GLN* 3.3 16.1 + - + +
69A LEU* 1.3 75.2 - - - +
71A GLU* 1.3 60.2 + - + +
73A ILE* 3.3 9.2 + - - +
74A ASN* 2.8 33.2 + - + +
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Residues in contact with GLU 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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67A GLN* 3.2 37.5 + - + +
68A MET* 3.9 13.7 - - - +
69A LEU 3.3 0.2 - - - -
70A LYS* 1.3 78.8 - - + +
72A THR* 1.3 60.5 + - - +
74A ASN* 3.5 6.0 + - - +
75A GLU* 3.0 28.6 + - - +
140A LYS* 4.9 11.6 + - - -
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Residues in contact with THR 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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68A MET 3.1 15.6 + - - -
69A LEU 3.6 7.0 - - - -
71A GLU* 1.3 73.5 - - - +
73A ILE* 1.3 60.1 - - - +
75A GLU* 3.1 3.5 + - - -
76A GLU* 2.3 49.7 + - + +
133A TRP 3.6 24.7 - - - +
136A LEU* 3.9 11.6 - - + -
137A GLY* 3.6 24.1 - - - +
140A LYS* 4.1 15.8 - - - +
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Residues in contact with ILE 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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56A LEU* 5.0 5.2 - - + -
69A LEU* 2.8 34.0 + - + +
70A LYS* 3.7 6.7 - - - +
72A THR* 1.3 75.0 - - - +
74A ASN* 1.3 64.6 + - - +
76A GLU* 4.0 4.3 - - - +
77A ALA* 2.9 30.0 + - + +
105A ALA* 4.1 15.5 - - + -
130A TYR* 3.6 42.6 - - + +
133A TRP* 4.4 21.1 - - + -
134A ILE* 4.5 13.0 - - + -
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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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70A LYS* 2.8 20.7 + - + +
71A GLU* 3.9 6.7 - - - +
73A ILE* 1.3 78.3 - - - +
75A GLU* 1.3 60.2 + - - +
77A ALA* 3.8 5.3 - - - +
78A ALA* 3.0 30.1 + - - +
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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
----------------------------------------------------------
71A GLU 3.0 17.7 + - - +
72A THR* 3.1 2.2 + - - +
74A ASN* 1.3 79.8 + - - +
76A GLU* 1.3 83.0 + - - +
78A ALA* 3.2 8.9 + - - +
79A GLU* 3.1 42.7 + - - +
82A ARG* 5.6 0.5 + - - -
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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
----------------------------------------------------------
72A THR* 2.3 41.4 + - + +
73A ILE 4.1 0.7 - - - +
75A GLU* 1.3 88.2 - - - +
77A ALA* 1.3 61.4 + - - +
79A GLU* 3.2 23.2 + - - +
80A TRP* 2.8 29.3 + - - +
133A TRP* 3.6 45.1 + - + +
136A LEU* 3.8 28.8 - - + +
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Residues in contact with ALA 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 ILE* 2.9 21.7 + - + +
74A ASN* 3.8 7.0 - - - +
76A GLU* 1.3 76.5 - - - +
78A ALA* 1.3 61.5 + - - +
80A TRP* 3.4 2.6 + - - +
81A ASP* 3.1 30.2 + - - +
101A GLY* 3.9 21.4 - - - +
102A SER* 4.7 2.9 - - - +
105A ALA* 5.8 1.1 - - + -
133A TRP* 3.8 20.3 - - + -
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Residues in contact with ALA 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* 3.0 22.3 + - - +
75A GLU* 3.5 12.3 - - - +
76A GLU 3.2 0.4 - - - -
77A ALA* 1.3 76.4 - - - +
79A GLU* 1.3 60.7 + - + +
81A ASP* 3.4 9.1 + - - +
82A ARG* 3.2 27.4 + - + +
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Residues in contact with GLU 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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75A GLU* 3.1 37.8 + - - +
76A GLU* 3.5 24.8 - - - +
78A ALA* 1.3 74.8 - - + +
80A TRP* 1.3 67.9 + - - +
82A ARG* 3.0 33.8 + - - +
83A LEU* 2.9 34.4 + - + +
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Residues in contact with TRP 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 GLU 2.8 13.4 + - - +
77A ALA 3.4 8.0 + - - +
79A GLU* 1.3 75.2 - - - +
81A ASP* 1.3 54.6 + - - +
83A LEU* 3.0 7.8 + - + +
84A HIS* 2.6 95.2 + + + +
98A GLU* 5.1 2.0 - - - -
99A PRO* 2.9 38.0 + - + -
100A ARG 3.7 1.1 - - - -
101A GLY* 3.4 25.6 - - - -
104A ILE* 3.5 22.0 - - + +
124A ILE* 5.9 3.6 - - + -
129A ILE* 4.2 26.9 - - + -
133A TRP* 4.0 15.5 - + + -
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Residues in contact with ASP 81 (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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77A ALA* 3.1 16.0 + - - +
78A ALA* 3.7 7.7 - - - +
79A GLU 3.2 0.2 - - - -
80A TRP* 1.3 79.8 - - - +
82A ARG* 1.3 62.9 + - + +
84A HIS 3.2 25.0 - - - +
85A PRO* 3.4 7.1 - - - +
100A ARG* 3.1 42.5 + - - +
101A GLY* 2.8 25.4 + - - -
102A SER 5.1 0.5 + - - -
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Residues in contact with ARG 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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75A GLU* 5.6 0.8 + - - -
78A ALA 3.2 13.2 + - - +
79A GLU* 3.0 38.3 + - - +
81A ASP* 1.3 77.7 - - + +
83A LEU* 1.3 67.7 + - + +
85A PRO* 3.9 12.3 - - - +
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU* 2.9 21.1 + - + +
80A TRP* 3.5 6.1 - - + +
82A ARG* 1.3 81.5 - - + +
84A HIS* 1.3 81.0 + - + +
85A PRO* 3.3 8.4 - - - +
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Residues in contact with HIS 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TRP* 2.6 91.2 + + - +
81A ASP* 3.2 14.7 - - - +
83A LEU* 1.3 91.6 - - + +
85A PRO* 1.3 66.5 - - - +
86A VAL* 3.6 1.7 + - - -
98A GLU* 5.1 18.4 - - + -
99A PRO 4.9 3.6 - - - +
100A ARG* 5.9 3.3 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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