Contacts of the helix formed by residues 62 - 84 (chain B) in PDB entry 2M8L
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B VAL* 3.6 33.8 + - + +
28B GLU* 5.4 6.5 + - - -
31B ALA* 6.2 2.2 - - - -
32B PHE* 4.3 22.6 - + + -
59B VAL* 3.4 25.1 + - + +
60B GLY 3.0 3.7 - - - +
61B GLY* 1.3 73.1 - - - +
63B GLN* 1.3 61.2 + - - +
64B ALA 3.4 2.5 - - - -
65B ALA* 3.3 17.2 + - + +
66B MET* 2.9 27.5 + - - +
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Residues in contact with GLN 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLY 4.1 8.3 - - - +
61B GLY 2.8 12.0 + - - +
62B HIS* 1.3 72.6 - - - +
64B ALA* 1.3 95.7 + - - +
66B MET* 3.4 15.2 + - + +
67B GLN* 2.9 29.3 + - - +
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Residues in contact with ALA 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLN* 1.3 100.7 + - - +
65B ALA* 1.3 61.8 + - - +
67B GLN* 3.2 13.0 + - + +
68B MET* 3.1 21.0 + - - +
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B PHE* 4.2 11.9 - - + -
62B HIS* 3.3 21.6 + - + +
63B GLN 3.3 0.2 - - - -
64B ALA* 1.3 76.3 - - - +
66B MET* 1.3 65.5 + - - +
68B MET* 3.0 7.4 + - - +
69B LEU* 2.9 20.0 + - - +
141B ILE* 3.4 38.2 - - + +
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Residues in contact with MET 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B VAL 5.8 0.4 - - - +
60B GLY* 4.3 20.0 - - - +
62B HIS 2.9 20.0 + - - +
63B GLN* 3.8 16.2 - - + +
65B ALA* 1.3 72.5 - - - +
67B GLN* 1.3 68.4 + - + +
69B LEU* 3.3 13.7 + - + +
70B LYS* 2.9 41.8 + - - -
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Residues in contact with GLN 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLN 2.9 16.9 + - - +
64B ALA* 3.2 16.8 + - + +
65B ALA 3.2 0.2 - - - -
66B MET* 1.3 87.1 - - + +
68B MET* 1.3 83.0 + - - +
70B LYS* 3.3 22.4 + - - +
71B GLU* 3.2 27.8 + - - +
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Residues in contact with MET 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ALA 3.1 8.5 + - - +
65B ALA 3.0 8.4 + - - +
67B GLN* 1.3 96.0 - - - +
69B LEU* 1.3 61.6 + - - +
71B GLU* 3.5 17.9 + - + +
72B THR* 3.1 35.8 + - - +
137B GLY 3.8 9.0 - - - +
140B LYS* 3.6 44.2 - - + +
141B ILE* 3.7 19.3 - - + +
144B MET* 5.5 7.2 - - + -
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 3.4 43.7 - - + -
65B ALA 2.9 12.0 + - - +
66B MET* 3.6 15.5 - - + +
68B MET* 1.3 73.5 - - - +
70B LYS* 1.3 61.9 + - - +
72B THR* 3.3 5.7 + - - -
73B ILE* 2.8 51.7 + - + +
134B ILE* 3.6 37.5 - - + +
137B GLY* 4.3 9.2 - - - -
138B LEU* 4.3 14.1 - - + +
141B ILE* 4.5 4.7 - - + +
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Residues in contact with LYS 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B MET* 2.9 26.0 + - - +
67B GLN* 3.3 29.4 + - - +
69B LEU* 1.3 76.4 - - - +
71B GLU* 1.3 62.2 + - - +
73B ILE* 3.3 8.6 + - - +
74B ASN* 2.8 32.1 + - + +
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Residues in contact with GLU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLN* 3.2 22.8 + - - +
68B MET* 3.6 22.2 - - + +
69B LEU 3.3 0.2 - - - -
70B LYS* 1.3 81.8 - - - +
72B THR* 1.3 66.9 + - - +
74B ASN* 3.5 7.9 + - - +
75B GLU* 3.0 39.2 + - - +
140B LYS* 4.6 5.0 + - - -
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Residues in contact with THR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B MET* 3.1 34.1 + - - +
69B LEU 3.6 7.0 - - - -
71B GLU* 1.3 78.5 + - - +
73B ILE* 1.3 61.6 + - - +
75B GLU* 3.1 1.8 + - - -
76B GLU* 2.4 55.2 + - + +
133B TRP 3.6 24.2 - - - +
136B LEU* 3.9 10.8 - - + -
137B GLY* 3.6 17.0 - - - +
140B LYS* 4.5 7.7 + - + +
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Residues in contact with ILE 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 5.0 0.2 - - + -
69B LEU* 2.8 47.7 + - + +
70B LYS* 3.7 7.0 - - - +
72B THR* 1.3 76.5 - - - +
74B ASN* 1.3 64.4 + - - +
76B GLU* 4.1 4.2 - - - +
77B ALA* 2.9 30.1 + - + +
105B ALA* 4.1 15.3 - - + -
130B TYR* 3.6 43.1 - - + +
133B TRP* 4.4 20.3 - - + -
134B ILE* 4.5 5.4 - - + -
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Residues in contact with ASN 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LYS* 2.8 20.7 + - + +
71B GLU* 3.9 7.8 + - - +
73B ILE* 1.3 77.2 - - - +
75B GLU* 1.3 62.1 + - - +
77B ALA* 3.8 6.4 - - - +
78B ALA* 3.0 30.4 + - - +
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Residues in contact with GLU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B GLU* 3.0 31.9 + - - +
72B THR* 3.1 1.1 + - - -
74B ASN* 1.3 81.7 + - - +
76B GLU* 1.3 71.8 + - - +
78B ALA* 3.2 5.9 + - - +
79B GLU* 2.3 68.3 + - - +
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Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B THR* 2.4 41.8 + - + +
73B ILE 4.1 0.9 - - - +
75B GLU* 1.3 83.8 - - - +
77B ALA* 1.3 60.8 + - - +
79B GLU* 2.7 28.9 + - - +
80B TRP* 2.8 28.9 + - - +
133B TRP* 3.6 37.8 - - + +
136B LEU* 3.5 30.3 - - + +
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Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ILE* 2.9 23.0 + - + +
74B ASN* 3.8 6.7 - - - +
76B GLU* 1.3 75.4 - - - +
78B ALA* 1.3 61.9 + - - +
80B TRP* 3.4 3.1 + - - +
81B ASP* 3.1 23.7 + - - +
101B GLY* 3.9 24.8 - - - +
102B SER* 4.7 0.7 - - - +
105B ALA* 5.8 0.9 - - + -
133B TRP* 3.8 19.8 - - + -
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Residues in contact with ALA 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ASN* 3.0 22.6 + - - +
75B GLU* 3.5 10.1 - - - +
76B GLU 3.2 0.2 - - - -
77B ALA* 1.3 77.4 - - - +
79B GLU* 1.3 65.7 + - - +
81B ASP* 3.4 7.3 + - - +
82B ARG* 3.2 26.6 + - - +
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Residues in contact with GLU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B GLU* 2.3 62.4 + - - +
76B GLU* 2.7 27.8 + - - +
78B ALA* 1.3 78.4 - - - +
80B TRP* 1.3 67.2 + - - +
82B ARG* 3.0 11.1 + - + +
83B LEU* 2.9 33.9 + - + +
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Residues in contact with TRP 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B GLU 2.8 13.7 + - - +
77B ALA 3.5 7.9 - - - +
79B GLU* 1.3 75.2 - - - +
81B ASP* 1.3 53.4 + - - +
83B LEU* 3.0 7.4 + - + +
84B HIS* 2.6 95.9 + + + +
98B GLU* 5.3 1.8 - - - -
99B PRO* 2.8 40.7 + - + -
100B ARG* 3.6 2.0 - - - -
101B GLY* 3.3 26.2 - - - -
104B ILE* 3.5 22.5 - - + +
124B ILE* 5.8 2.2 - - + -
129B ILE* 4.2 26.7 - - + -
133B TRP* 4.0 16.2 - + + -
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Residues in contact with ASP 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ALA 3.1 15.9 + - - +
78B ALA* 3.7 7.9 - - - +
79B GLU 3.2 0.2 - - - -
80B TRP* 1.3 81.9 - - + +
82B ARG* 1.3 62.6 + - + +
84B HIS 3.2 25.7 - - - +
85B PRO* 3.4 9.2 - - - +
86B VAL* 4.5 1.9 + - - +
100B ARG* 2.9 42.1 + - + +
101B GLY 5.1 4.9 - - - +
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Residues in contact with ARG 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ALA* 3.2 17.4 + - + +
79B GLU* 3.0 13.1 + - + +
81B ASP* 1.3 78.6 - - - +
83B LEU* 1.3 66.9 + - + +
85B PRO* 3.9 12.1 - - - +
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLU* 2.9 22.0 + - + +
80B TRP* 3.5 5.4 - - + +
82B ARG* 1.3 81.8 - - + +
84B HIS* 1.3 81.4 + - + +
85B PRO* 3.3 9.2 - - - +
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Residues in contact with HIS 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B TRP* 2.6 91.2 + + + +
81B ASP* 3.2 14.6 - - - +
83B LEU* 1.3 92.3 - - + +
85B PRO* 1.3 68.0 - - - +
86B VAL* 3.6 2.4 + - - +
98B GLU* 5.2 16.8 - - + -
99B PRO 4.9 2.9 - - - +
100B ARG* 5.5 4.3 - - - +
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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