Contacts of the helix formed by residues 84 - 98 (chain B) in PDB entry 1M4C
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 ASP 84 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83B ARG* 1.3 90.7 - - - +
85B LEU* 1.3 65.1 + - - +
86B ILE 3.4 1.1 - - - -
87B SER* 3.3 7.9 + - - -
88B ASN* 3.3 23.9 + - - +
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Residues in contact with LEU 85 (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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20B ASP* 4.0 29.8 - - - +
23B MET* 4.9 11.7 - - + -
24B ILE* 3.2 43.5 - - + +
70B LEU* 6.1 1.3 - - + -
83B ARG 4.5 2.0 - - - +
84B ASP* 1.3 78.4 - - - +
86B ILE* 1.3 64.3 + - + +
88B ASN* 3.2 18.1 + - + +
89B ILE* 3.3 15.9 + - + +
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Residues in contact with ILE 86 (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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24B ILE* 3.7 27.1 - - + -
63B LEU* 4.2 34.0 - - + +
66B LEU* 4.1 18.4 - - + -
67B GLU* 3.5 36.1 - - + +
70B LEU* 3.8 20.2 - - + -
83B ARG 5.1 7.9 - - - +
84B ASP 3.4 0.8 - - - +
85B LEU* 1.3 75.5 - - + +
87B SER* 1.3 66.5 + - - +
89B ILE* 3.2 9.3 + - + +
90B ASN* 3.0 24.1 + - + +
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Residues in contact with SER 87 (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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67B GLU* 5.0 1.7 + - - -
83B ARG 3.3 21.9 + - - -
84B ASP* 3.3 12.5 + - - -
85B LEU 3.2 0.6 - - - -
86B ILE* 1.3 79.2 - - - +
88B ASN* 1.3 60.1 + - - +
90B ASN* 3.4 8.9 - - - +
91B VAL* 3.3 25.2 + - - +
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Residues in contact with ASN 88 (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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20B ASP* 3.7 18.3 + - - +
84B ASP 3.3 8.5 + - - +
85B LEU* 3.2 12.8 + - + +
86B ILE 3.2 0.2 - - - -
87B SER* 1.3 75.3 - - - +
89B ILE* 1.3 66.3 + - - +
90B ASN 3.0 1.6 - - - -
91B VAL* 3.0 22.5 + - - +
92B ILE* 3.0 24.2 + - + +
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Residues in contact with ILE 89 (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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17B LEU* 3.6 23.3 - - + -
20B ASP* 4.0 25.3 + - + -
21B LEU* 4.5 15.7 - - + -
24B ILE* 3.8 28.9 - - + -
59B LEU* 4.4 4.9 - - + -
63B LEU* 4.1 23.3 - - + -
66B LEU* 5.3 1.3 - - + -
85B LEU 3.3 14.1 - - - +
86B ILE* 3.2 15.9 + - + +
88B ASN* 1.3 74.8 - - - +
90B ASN* 1.3 62.3 - - - +
92B ILE* 3.4 7.5 + - - +
93B VAL* 3.0 30.0 + - + +
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Residues in contact with ASN 90 (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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60B GLU* 3.2 25.1 + - - -
63B LEU* 3.8 20.6 - - + +
86B ILE* 3.0 14.5 + - - +
87B SER* 3.4 13.5 - - - +
88B ASN 3.0 0.2 - - - -
89B ILE* 1.3 78.2 - - - +
91B VAL* 1.3 62.9 + - + +
93B VAL* 3.5 1.1 + - - +
94B LEU* 2.9 37.4 + - + +
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Residues in contact with VAL 91 (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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87B SER* 3.3 14.5 + - - +
88B ASN* 3.0 14.6 + - - +
90B ASN* 1.3 77.3 - - + +
92B ILE* 1.3 69.1 + - + +
94B LEU* 3.4 7.8 + - + +
95B GLU* 3.0 51.0 + - + +
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Residues in contact with ILE 92 (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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13B GLN* 3.5 44.2 - - + +
16B HIS* 4.4 13.7 - - + -
17B LEU* 3.8 20.2 - - + +
20B ASP* 4.9 4.0 - - - +
88B ASN* 3.0 24.5 + - + +
89B ILE* 3.7 9.2 - - - +
91B VAL* 1.3 81.2 - - + +
93B VAL* 1.3 53.6 + - - +
95B GLU* 3.2 4.0 + - - +
96B LEU* 2.7 57.9 + - + +
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Residues in contact with VAL 93 (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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17B LEU* 4.4 6.7 - - + -
56B LEU* 3.5 32.3 - - + +
59B LEU* 3.8 30.5 - - + -
60B GLU* 3.9 21.5 - - + +
63B LEU* 4.9 3.8 - - + -
89B ILE* 3.0 25.9 + - + +
90B ASN* 3.9 4.7 - - - +
92B ILE* 1.3 76.7 - - - +
94B LEU* 1.3 65.8 + - - +
96B LEU* 3.1 5.2 + - - -
97B LYS* 3.1 40.2 + - + +
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Residues in contact with LEU 94 (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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60B GLU* 3.8 26.7 - - - +
90B ASN* 2.9 35.8 + - - +
91B VAL* 3.7 7.2 - - + +
93B VAL* 1.3 77.9 - - - +
95B GLU* 1.3 63.2 + - + +
97B LYS* 4.1 5.8 - - - +
98B GLY* 3.4 18.7 + - - -
99B SER* 3.4 29.8 + - - +
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Residues in contact with GLU 95 (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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9B LYS* 5.5 9.1 + - - +
13B GLN* 3.1 29.8 + - - +
91B VAL* 3.0 38.5 + - + +
92B ILE* 3.9 2.5 - - - +
94B LEU* 1.3 78.4 - - + +
96B LEU* 1.3 64.7 + - - +
98B GLY* 4.0 6.2 + - - -
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Residues in contact with LEU 96 (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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10B THR* 3.9 29.4 - - + +
13B GLN* 3.7 29.4 - - + +
14B LEU* 3.8 33.9 - - + +
17B LEU* 4.2 3.8 - - + -
53B LEU* 4.5 17.8 - - + +
56B LEU* 3.9 20.4 - - + -
92B ILE* 2.7 40.6 + - + +
93B VAL 3.8 2.5 - - - +
95B GLU* 1.3 75.2 - - - +
97B LYS* 1.3 59.8 + - - +
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Residues in contact with LYS 97 (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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53B LEU* 3.9 23.8 - - - +
54B LYS* 4.6 13.9 - - - +
56B LEU* 4.3 5.4 - - + -
57B GLN* 3.8 40.9 - - + +
60B GLU* 4.2 13.0 + - - -
93B VAL* 3.1 34.6 + - + +
94B LEU* 4.1 9.6 - - - +
96B LEU* 1.3 77.7 - - - +
98B GLY* 1.3 70.6 + - - +
99B SER* 3.4 26.1 + - - +
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Residues in contact with GLY 98 (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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94B LEU 3.4 10.2 + - - -
95B GLU 4.0 5.5 + - - -
96B LEU 3.4 2.8 - - - -
97B LYS* 1.3 96.8 + - - +
99B SER* 1.3 64.0 + - - -
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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