Contacts of the helix formed by residues 57 - 69 (chain B) in PDB entry 1MN8
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 ASN 57 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55B THR* 3.0 16.7 + - - +
56B PHE* 1.3 77.1 - - - +
58B ARG* 1.3 65.2 + - - +
59B ASP* 2.9 18.2 + - - +
60B LEU* 2.9 40.4 + - + +
61B ILE* 3.1 24.3 + - - +
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Residues in contact with ARG 58 (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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56B PHE 3.4 1.7 + - - +
57B ASN* 1.3 77.0 - - - +
59B ASP* 1.3 60.6 + - - +
61B ILE* 3.4 8.2 + - + +
62B THR* 2.9 34.5 + - - +
87B GLU* 6.0 1.1 - - + -
90B ALA* 3.9 32.1 + - + +
91B PHE* 3.6 55.5 + - + +
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Residues in contact with ASP 59 (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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57B ASN* 2.9 14.6 + - - +
58B ARG* 1.3 80.9 - - - +
60B LEU* 1.3 63.0 + - + +
62B THR* 3.3 9.6 + - - -
63B GLN* 3.1 27.3 + - - +
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Residues in contact with LEU 60 (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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48B VAL 4.4 4.9 - - - +
49B GLY* 3.4 35.0 - - - +
50B TRP* 3.9 13.8 - - + -
51B PRO* 4.3 7.4 - - + -
55B THR* 3.8 35.2 - - + +
57B ASN* 2.9 20.4 + - + +
59B ASP* 1.3 73.6 - - + +
61B ILE* 1.3 67.9 + - - +
63B GLN* 3.2 17.6 + - + +
64B VAL* 3.3 8.7 + - - +
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Residues in contact with ILE 61 (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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50B TRP* 3.8 24.2 - - + -
55B THR 3.7 17.7 - - - +
56B PHE* 6.0 0.2 - - + -
57B ASN 3.1 20.1 + - - +
58B ARG* 3.7 6.7 - - + +
60B LEU* 1.3 75.9 - - - +
62B THR* 1.3 58.0 + - - +
64B VAL* 3.2 5.2 + - - +
65B LYS* 2.9 25.7 + - + +
83B ILE* 3.8 16.5 - - + +
86B TRP* 3.7 15.7 - - + +
87B GLU* 3.8 32.8 - - + +
90B ALA* 3.6 31.0 - - + -
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Residues in contact with THR 62 (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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58B ARG* 2.9 19.7 + - - +
59B ASP* 3.6 10.2 + - - -
60B LEU 3.2 0.4 - - - -
61B ILE* 1.3 77.2 - - - +
63B GLN* 1.3 65.9 + - - +
65B LYS* 3.2 13.5 + - + +
66B ILE* 3.0 35.2 + - + +
87B GLU* 4.4 10.9 + - - -
91B PHE* 6.0 1.0 - - - -
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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
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48B VAL* 3.5 52.4 + - + +
59B ASP 3.1 17.5 + - - +
60B LEU* 3.2 15.7 + - + +
62B THR* 1.3 80.5 - - - +
64B VAL* 1.3 64.1 + - - +
66B ILE* 3.5 5.7 + - - +
67B LYS* 3.4 15.9 + - - +
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Residues in contact with VAL 64 (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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43B TRP* 3.6 38.8 - - + -
46B PHE* 4.3 4.0 - - + -
48B VAL* 4.0 13.5 - - + -
50B TRP* 3.5 45.5 - - + -
60B LEU 3.3 2.2 + - - +
61B ILE 3.2 7.6 + - - +
63B GLN* 1.3 75.3 - - - +
65B LYS* 1.3 65.8 + - - +
67B LYS* 3.1 6.0 + - - +
68B VAL* 2.8 29.5 + - + +
83B ILE* 3.6 15.9 - - + -
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Residues in contact with LYS 65 (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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61B ILE* 2.9 18.4 + - + +
62B THR* 3.5 12.1 - - + +
64B VAL* 1.3 76.1 - - - +
66B ILE* 1.3 67.2 + - + +
68B VAL 3.3 0.5 + - - -
69B PHE* 2.9 62.8 + - + +
83B ILE* 3.8 21.7 - - + +
84B VAL* 5.4 4.0 - - + -
87B GLU* 3.0 41.5 + - + +
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Residues in contact with ILE 66 (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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62B THR* 3.0 29.9 + - + +
63B GLN* 4.0 5.8 - - - +
65B LYS* 1.3 79.1 - - + +
67B LYS* 1.3 62.0 + - - +
69B PHE* 3.5 5.4 + - + -
70B SER* 2.8 29.8 + - - +
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Residues in contact with LYS 67 (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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46B PHE* 3.7 43.9 - - + +
48B VAL* 4.9 8.3 - - + -
63B GLN 3.4 10.4 + - - +
64B VAL* 3.1 9.0 + - - +
66B ILE* 1.3 79.1 - - - +
68B VAL* 1.3 63.0 + - - +
70B SER* 3.1 22.2 + - - +
73B PRO 5.5 0.6 + - - -
74B HIS* 3.0 19.4 + - - +
75B GLY* 3.4 5.9 - - - -
76B HIS* 2.7 36.1 + - + +
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Residues in contact with VAL 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B TRP* 4.0 3.6 - - - +
46B PHE* 4.2 5.4 - - + -
64B VAL* 2.8 34.8 + - + +
65B LYS 3.7 3.1 - - - +
67B LYS* 1.3 74.8 - - - +
69B PHE* 1.3 60.8 + - + +
70B SER 3.5 0.7 + - - +
75B GLY* 3.6 0.3 - - - -
76B HIS* 2.9 50.7 + - - +
77B PRO* 5.0 0.5 - - - +
79B GLN* 3.7 26.5 - - + +
80B VAL* 3.7 29.8 - - + +
83B ILE* 4.0 14.1 - - + -
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Residues in contact with PHE 69 (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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65B LYS* 2.9 55.0 + - + +
66B ILE* 3.8 7.2 - - + +
67B LYS 3.3 0.2 - - - -
68B VAL* 1.3 79.1 - - + +
70B SER* 1.3 66.1 + - - +
71B PRO* 3.7 2.4 - - - +
80B VAL* 3.7 33.2 - - + -
83B ILE* 4.0 15.9 - - + -
84B VAL* 3.9 14.4 - - + -
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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