Contacts of the helix formed by residues 57 - 69 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55C THR* 3.1 16.9 + - - +
56C PHE* 1.3 74.2 - - - +
58C ARG* 1.3 64.6 + - - +
59C ASP* 3.0 18.2 + - - +
60C LEU* 2.9 38.2 + - + +
61C ILE* 3.0 24.7 + - - +
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Residues in contact with ARG 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C PHE 3.2 9.8 + - - -
57C ASN* 1.3 72.2 + - - +
59C ASP* 1.3 61.8 + - - +
61C ILE* 3.4 9.3 + - + +
62C THR* 2.9 39.5 + - - +
90C ALA* 3.1 34.9 + - + +
91C PHE* 3.9 47.6 + - + +
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Residues in contact with ASP 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C ASN* 3.0 12.3 + - - +
58C ARG* 1.3 81.8 - - - +
60C LEU* 1.3 60.1 + - + +
62C THR* 3.3 8.6 + - - -
63C GLN* 2.9 35.4 + - + +
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Residues in contact with LEU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C VAL* 3.6 24.7 - - - +
49C GLY* 3.7 24.9 - - - +
50C TRP* 4.3 5.8 - - + +
51C PRO* 4.3 4.5 - - + -
55C THR* 3.9 27.1 - - + +
57C ASN* 2.9 30.4 + - + +
59C ASP* 1.3 73.7 - - + +
61C ILE* 1.3 65.2 + - - +
63C GLN* 3.2 6.9 + - + +
64C VAL* 3.1 26.3 + - - +
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Residues in contact with ILE 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C TRP* 3.7 25.1 - - + -
55C THR* 3.8 15.9 - - + +
56C PHE* 4.0 3.1 - - + -
57C ASN 3.0 16.5 + - - +
58C ARG* 3.7 5.2 - - + +
60C LEU* 1.3 74.7 - - - +
62C THR* 1.3 58.7 + - - +
64C VAL* 3.2 4.3 + - - +
65C LYS* 2.9 27.0 + - + +
83C ILE* 3.7 14.1 - - + +
86C TRP* 3.7 16.2 - - + +
87C GLU* 3.7 35.2 - - + +
90C ALA* 3.4 32.1 - - + -
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Residues in contact with THR 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C ARG* 2.9 22.3 + - - +
59C ASP* 3.4 11.8 - - - +
61C ILE* 1.3 79.6 - - - +
63C GLN* 1.3 67.9 + - - +
65C LYS* 3.1 7.9 + - + +
66C ILE* 2.9 42.2 + - + +
87C GLU* 5.1 6.8 + - - -
91C PHE* 6.0 1.4 - - - -
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Residues in contact with GLN 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C VAL* 3.7 39.5 - - + +
59C ASP* 2.9 24.9 + - + +
60C LEU* 3.2 7.8 + - + +
62C THR* 1.3 81.8 - - - +
64C VAL* 1.3 64.5 + - - +
66C ILE* 3.5 22.6 + - - +
67C LYS* 3.4 25.8 + - - +
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Residues in contact with VAL 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C TRP* 3.6 40.8 - - + +
46C PHE* 4.2 8.3 - - + -
48C VAL* 3.9 11.0 - - + -
50C TRP* 3.6 45.3 - - + -
60C LEU 3.1 6.3 + - - +
61C ILE 3.7 7.0 - - - +
63C GLN* 1.3 76.7 - - - +
65C LYS* 1.3 64.7 + - - +
67C LYS* 3.1 4.3 + - - +
68C VAL* 2.9 24.9 + - + +
83C ILE* 3.7 14.6 - - + -
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Residues in contact with LYS 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C ILE* 2.9 17.1 + - + +
62C THR* 3.6 8.3 - - + +
64C VAL* 1.3 75.3 - - - +
66C ILE* 1.3 65.5 + - + +
68C VAL* 4.4 0.2 - - - -
69C PHE* 2.9 68.9 + - + +
83C ILE* 3.8 19.7 - - + +
84C VAL* 4.5 9.0 - - - +
87C GLU* 2.7 43.8 + - + +
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Residues in contact with ILE 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C THR* 2.9 37.3 + - + +
63C GLN* 3.7 25.4 - - - +
64C VAL 3.2 0.2 - - - -
65C LYS* 1.3 76.6 - - + +
67C LYS* 1.3 73.9 + - + +
69C PHE* 3.8 2.8 - - - +
70C SER* 3.1 24.5 + - - -
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Residues in contact with LYS 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C PHE* 3.7 35.7 - - + +
48C VAL* 3.7 26.2 - - + -
63C GLN* 3.5 16.6 - - - +
64C VAL 3.1 7.0 + - - +
66C ILE* 1.3 86.3 - - + +
68C VAL* 1.3 63.9 + - - +
70C SER* 3.2 19.2 + - - -
74C HIS 3.6 6.0 - - - +
75C GLY* 3.6 7.8 - - - -
76C HIS* 4.2 3.3 + - + +
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Residues in contact with VAL 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C TRP* 4.0 3.6 - - - +
46C PHE* 4.1 3.8 - - + -
64C VAL* 2.9 35.6 + - + +
65C LYS 3.2 3.3 + - - +
67C LYS* 1.3 75.9 - - - +
69C PHE* 1.3 60.6 + - + +
70C SER 4.4 0.2 - - - +
75C GLY* 3.5 0.9 - - - -
76C HIS* 2.9 48.8 + - - +
77C PRO* 5.0 0.7 - - - +
79C GLN* 3.6 26.7 - - + +
80C VAL* 3.8 28.2 - - + +
83C ILE* 3.9 17.3 - - + -
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Residues in contact with PHE 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C LYS* 2.9 56.5 + - + +
66C ILE* 3.8 3.6 - - - +
68C VAL* 1.3 80.8 - - + +
70C SER* 1.3 67.7 + - - +
71C PRO* 3.4 4.2 - - - +
80C VAL* 3.7 39.0 - - + -
83C ILE* 4.0 12.1 - - + -
84C VAL* 3.9 8.3 - - + -
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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
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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