Contacts of the helix formed by residues 92 - 106 (chain B) in PDB entry 1M1B
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 92 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288A GLU* 5.4 4.2 + - - -
292A LEU* 5.1 10.2 - - + +
91B GLY* 1.3 74.8 - - - +
93B PHE* 1.3 81.8 + - + +
94B ASN* 2.7 37.8 + - - +
95B ASN* 3.1 14.7 + - - +
96B ALA* 3.0 18.9 + - - +
137B GLU* 6.1 1.3 - - - +
141B LYS* 4.0 7.4 - - - +
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Residues in contact with PHE 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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284A LEU* 4.2 6.7 - - + -
287A ALA* 3.6 28.9 - - + -
288A GLU* 3.7 28.3 - - + -
291A TYR* 3.6 24.2 - + + +
292A LEU* 3.6 39.2 - - + +
92B ASN* 1.3 86.1 - - - +
94B ASN* 1.3 81.0 + - + +
96B ALA* 3.0 3.5 + - - +
97B ARG* 2.8 38.8 + - - +
141B LYS* 3.9 27.8 - - + +
144B ALA* 4.0 20.5 - - + +
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Residues in contact with ASN 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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284A LEU* 3.5 34.3 - - + +
92B ASN* 2.7 23.4 + - - +
93B PHE* 1.3 84.8 - - + +
95B ASN* 1.3 59.0 + - - +
97B ARG* 3.0 36.0 + - - +
98B ARG* 3.0 28.0 + - - +
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Residues in contact with ASN 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B TRP* 5.3 13.0 + - + +
89B GLY 3.9 4.3 - - - +
90B TYR* 3.6 23.2 + - + +
91B GLY* 3.2 10.0 - - - -
92B ASN* 3.1 36.6 + - - +
94B ASN* 1.3 77.9 + - - +
96B ALA* 1.3 65.6 + - - +
98B ARG* 3.4 9.6 + - - +
99B LEU* 3.0 21.7 + - - +
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Residues in contact with ALA 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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89B GLY* 3.9 11.6 + - - +
92B ASN 3.0 5.2 + - - +
93B PHE 3.0 9.5 + - - +
95B ASN* 1.3 77.2 - - - +
97B ARG* 1.3 58.3 + - - +
99B LEU* 2.9 10.5 + - - +
100B VAL* 2.9 28.2 + - - +
113B LEU* 4.0 10.1 - - + -
141B LYS* 3.7 25.4 - - + -
145B CYS* 3.6 24.0 - - - -
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Residues in contact with ARG 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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283A GLU* 2.8 43.2 + - - -
284A LEU* 3.9 9.5 - - - +
287A ALA* 3.6 22.9 - - - +
291A TYR* 5.4 5.3 - - - -
93B PHE* 2.8 25.8 + - + +
94B ASN* 3.0 39.2 + - - +
96B ALA* 1.3 69.9 - - - +
98B ARG* 1.3 64.7 + - - +
100B VAL* 3.4 10.3 + - - +
101B ARG* 3.3 24.2 + - - +
144B ALA* 4.5 10.5 - - + +
145B CYS* 4.4 1.8 - - - -
148B SER* 3.3 33.4 + - - +
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Residues in contact with ARG 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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73A PHE* 3.5 34.8 - - - -
76A ASP* 4.2 13.5 + - - +
64B TRP* 3.8 32.1 - - + -
94B ASN* 3.0 18.7 + - - +
95B ASN* 3.7 10.3 - - - +
96B ALA 3.2 0.2 - - - -
97B ARG* 1.3 79.6 - - - +
99B LEU* 1.3 64.9 + - - +
101B ARG* 3.4 34.4 + - - +
102B LYS* 3.3 35.7 + - + +
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Residues in contact with LEU 99 (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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64B TRP* 4.1 17.7 - - + -
68B VAL* 3.9 23.1 - - + -
84B LEU* 4.5 2.0 - - + -
86B ALA* 3.4 32.3 - - + -
89B GLY* 4.5 7.9 - - - +
90B TYR* 3.6 21.8 - - + -
95B ASN 3.0 12.6 + - - +
96B ALA* 2.9 13.9 + - + +
98B ARG* 1.3 77.7 - - - +
100B VAL* 1.3 62.4 + - + +
102B LYS* 3.2 2.6 + - - -
103B LEU* 2.9 53.4 + - + +
111B ALA* 5.0 4.0 - - + -
113B LEU* 5.5 3.4 - - + -
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Residues in contact with VAL 100 (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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96B ALA 2.9 19.8 + - - +
97B ARG* 3.4 8.3 + - - +
99B LEU* 1.3 77.4 - - + +
101B ARG* 1.3 63.7 + - - +
103B LEU* 3.8 7.4 - - - +
104B GLU* 2.9 29.2 + - + +
111B ALA* 5.3 3.8 - - + -
113B LEU* 6.0 0.4 - - + -
145B CYS* 3.7 36.6 - - + +
148B SER* 5.1 2.2 - - - -
149B GLN* 4.1 27.1 - - + +
154B PHE* 3.9 25.2 - - + -
156B ILE* 4.0 11.4 - - + -
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Residues in contact with ARG 101 (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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76A ASP* 4.2 32.5 + - - +
97B ARG 3.3 10.4 + - - +
98B ARG* 3.7 39.3 - - - +
99B LEU 3.2 0.8 - - - -
100B VAL* 1.3 79.3 - - - +
102B LYS* 1.3 71.5 + - + +
104B GLU* 2.9 27.7 + - - +
105B ASP* 3.0 27.6 + - - +
148B SER* 5.2 7.8 - - - +
150B THR* 5.0 11.4 - - + -
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Residues in contact with LYS 102 (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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72A GLU* 2.6 32.1 + - - +
76A ASP* 2.6 39.0 + - - -
64B TRP* 4.2 23.8 - - + -
68B VAL* 4.7 11.9 - - + -
98B ARG* 3.3 34.6 + - - +
99B LEU 3.2 6.8 + - - +
101B ARG* 1.3 84.5 - - + +
103B LEU* 1.3 64.9 + - - +
105B ASP* 3.1 13.9 + - - +
106B ARG* 2.9 40.3 + - - +
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Residues in contact with LEU 103 (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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68B VAL* 4.7 13.5 - - + -
71B LEU* 4.8 4.9 - - + -
84B LEU* 3.5 34.3 - - + -
99B LEU* 2.9 47.9 + - + +
100B VAL* 3.8 4.0 - - - +
102B LYS* 1.3 74.7 - - - +
104B GLU* 1.3 67.0 + - - +
106B ARG* 3.3 7.3 + - + +
108B VAL* 3.0 48.0 + - + +
110B GLY 4.6 0.7 - - - +
111B ALA* 3.9 23.1 - - + -
154B PHE* 4.0 13.9 - - + -
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Residues in contact with GLU 104 (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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100B VAL* 2.9 21.5 + - + +
101B ARG* 2.9 18.5 + - - +
103B LEU* 1.3 73.5 - - - +
105B ASP* 1.3 58.9 + - - +
107B GLY* 2.7 30.0 + - - -
108B VAL 4.4 2.6 - - - +
149B GLN* 3.6 14.0 - - - +
150B THR* 2.9 36.4 + - - +
151B ASP* 2.8 40.3 + - + +
154B PHE* 3.9 23.5 - - + +
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Residues in contact with ASP 105 (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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76A ASP* 5.3 3.6 - - - +
105A ASP* 3.7 45.6 - - - +
106A ARG* 5.5 3.5 - - - +
101B ARG* 3.0 25.6 + - - +
102B LYS* 3.1 16.5 + - - +
104B GLU* 1.3 79.2 - - - +
106B ARG* 1.3 71.4 + - - +
107B GLY* 3.1 1.4 + - - -
150B THR* 5.6 1.4 + - - -
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Residues in contact with ARG 106 (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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72A GLU* 2.9 40.2 + - - +
105A ASP* 5.8 2.2 - - - +
106A ARG* 3.6 34.6 - - - +
68B VAL* 4.0 26.4 - - + +
69B GLU* 5.8 0.2 - - - +
72B GLU* 3.8 39.7 + - + +
75B SER* 3.0 21.7 + - - -
76B ASP* 4.5 7.1 - - - +
102B LYS* 2.9 45.8 + - - +
103B LEU* 3.8 5.8 - - - +
104B GLU 2.9 0.4 + - - -
105B ASP* 1.3 89.8 + - - +
107B GLY* 1.3 57.3 + - - +
108B VAL* 3.4 10.5 - - + -
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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