Contacts of the helix formed by residues 53 - 62 (chain B) in PDB entry 1MF8
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 LEU 53 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356A PHE 4.2 0.2 - - - +
357A VAL* 3.7 29.6 - - + +
360A LYS* 3.2 34.1 - - + -
361A VAL* 4.1 15.5 - - + +
364A MET* 5.1 0.2 - - - -
51B ASN* 2.8 9.6 + - - +
52B PRO* 1.3 84.8 - - + +
54B VAL* 1.3 62.1 + - - +
55B GLN 3.4 2.5 - - - -
56B ARG* 3.2 14.5 + - + +
57B VAL* 2.9 28.1 + - + +
97B ILE* 4.7 13.9 - - + -
114B VAL* 5.3 2.5 - - + +
117B MET* 5.7 1.1 - - + -
118B MET* 3.6 36.3 - - + -
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Residues in contact with VAL 54 (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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364A MET* 3.9 19.3 - - + -
39B VAL* 5.6 0.9 - - + -
42B PHE* 5.0 1.3 - - + -
43B MET* 4.3 21.8 - - + -
48B LEU* 3.5 36.6 - - + +
51B ASN* 3.5 34.9 + - + +
52B PRO 3.6 2.0 - - - -
53B LEU* 1.3 77.0 - - - +
55B GLN* 1.3 64.4 + - - +
56B ARG 3.2 0.3 + - - -
57B VAL* 3.3 2.4 + - - +
58B ILE* 3.0 48.4 + - + +
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Residues in contact with GLN 55 (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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39B VAL* 3.7 39.9 - - - +
43B MET* 6.0 4.4 - - + +
52B PRO 5.0 2.6 + - - +
53B LEU 3.4 0.4 - - - -
54B VAL* 1.3 80.5 - - - +
56B ARG* 1.3 60.6 + - + +
58B ILE* 4.3 10.4 - - - +
59B ASP* 3.1 32.0 + - + +
117B MET* 6.4 3.8 - - + -
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Residues in contact with ARG 56 (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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52B PRO 5.0 0.2 - - - +
53B LEU* 3.2 23.8 + - + +
54B VAL 3.1 0.8 - - - -
55B GLN* 1.3 78.3 + - + +
57B VAL* 1.3 67.2 + - - +
59B ASP* 3.3 24.5 + - - +
60B ILE* 2.9 41.2 + - - +
96B ARG 2.9 26.7 + - - -
97B ILE* 3.4 35.8 + - + +
99B ASP 3.5 13.3 + - - -
100B MET* 3.7 36.7 + - - +
102B LYS* 5.9 2.0 - - - +
114B VAL* 4.7 4.0 - - + -
117B MET* 4.2 34.1 - - - -
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Residues in contact with VAL 57 (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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361A VAL* 4.1 28.0 - - + -
364A MET* 3.6 30.5 - - + -
365A LEU* 4.5 6.3 - - + -
53B LEU* 2.9 19.1 - - + +
54B VAL 3.6 4.3 - - - +
56B ARG* 1.3 76.2 - - - +
58B ILE* 1.3 51.3 + - - +
60B ILE* 2.6 31.8 + - - +
61B PHE* 2.6 46.4 + - + +
81B PHE* 5.4 0.2 - - + -
93B PHE* 4.1 10.5 - - + -
97B ILE* 4.9 2.2 - - + -
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Residues in contact with ILE 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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364A MET* 4.0 12.1 - - + -
37B LEU 5.9 0.7 - - - +
39B VAL* 4.1 31.2 - - + -
42B PHE* 3.6 37.2 - - + -
54B VAL* 3.0 41.7 + - + +
55B GLN* 3.9 11.7 - - - +
57B VAL* 1.3 76.3 - - - +
59B ASP* 1.3 57.5 + - - +
61B PHE* 3.3 9.0 + - + +
62B ASP* 2.9 29.5 + - + +
67B GLY 5.6 6.5 - - - +
68B GLU 6.1 0.2 - - - -
69B VAL* 4.1 13.4 - - + +
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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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55B GLN* 3.1 26.3 + - + +
56B ARG* 3.7 23.9 + - - +
57B VAL 3.2 0.2 - - - -
58B ILE* 1.3 77.0 - - - +
60B ILE* 1.3 59.2 + - - +
62B ASP* 3.5 16.1 - - - +
65B GLY* 6.1 0.3 - - - -
100B MET 4.3 7.0 - - - +
102B LYS* 2.7 37.2 + - - -
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Residues in contact with ILE 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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56B ARG* 2.9 29.5 + - - +
57B VAL* 2.6 18.6 + - - +
59B ASP* 1.3 73.2 - - - +
61B PHE* 1.3 62.2 + - + +
62B ASP 3.2 4.3 + - - -
63B THR* 4.6 4.9 + - - -
93B PHE* 3.7 30.3 - - + +
96B ARG* 3.5 49.5 + - + +
97B ILE* 3.4 33.9 - - + -
102B LYS* 4.5 8.7 + - - +
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Residues in contact with PHE 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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364A MET* 6.0 1.6 - - + -
365A LEU* 3.7 28.5 - - + -
42B PHE* 5.0 9.0 - + - -
57B VAL* 2.6 31.5 + - + +
58B ILE* 3.7 7.6 - - - +
60B ILE* 1.3 79.2 - - + +
62B ASP* 1.3 57.4 + - - +
63B THR* 3.1 13.2 + - - -
69B VAL* 3.8 24.7 - - + -
73B GLU* 3.3 33.0 - - - +
74B PHE* 4.1 11.2 - + - -
77B GLY* 3.5 39.9 - - - -
78B VAL* 3.8 19.3 - - + -
81B PHE* 4.2 2.0 - + - -
93B PHE* 4.1 15.5 - + - -
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Residues in contact with ASP 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 ILE* 2.9 19.7 + - + +
59B ASP* 3.5 13.6 - - - +
60B ILE 3.2 1.2 - - - -
61B PHE* 1.3 73.9 - - - +
63B THR* 1.3 59.8 + - - +
64B ASP* 3.3 2.9 - - - +
65B GLY* 3.1 24.0 + - - -
66B ASN* 3.3 7.0 + - - +
67B GLY* 3.3 15.2 + - - -
68B GLU 3.0 12.3 - - - +
69B VAL* 4.3 3.8 - - + +
73B GLU* 3.8 4.9 - - - -
102B LYS* 2.9 22.6 + - - -
402B CA 2.5 29.8 - - - -
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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