Contacts of the helix formed by residues 55 - 70 (chain B) in PDB entry 3MI9
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 SER 55 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ASN 3.9 0.4 + - - -
54B VAL* 1.3 79.0 - - - +
56B GLN* 1.3 65.2 + - - +
57B LEU* 3.6 10.4 + - - +
58B THR* 3.2 32.1 + - - -
59B ILE* 3.4 8.0 + - - +
95B GLU* 5.2 0.7 - - - +
97B GLN* 2.9 24.7 + - - +
10C PRO 4.7 1.4 + - - -
13C HIS* 3.6 21.1 - - - +
14C PRO 3.2 25.1 + - - -
15C GLY* 4.3 0.2 - - - -
16C SER* 4.1 0.9 - - - +
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Residues in contact with GLN 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLN* 3.0 41.3 + - - +
55B SER* 1.3 71.2 - - - +
57B LEU* 1.3 61.1 + - - +
59B ILE* 3.0 16.0 + - - +
60B ASN* 2.8 62.6 + - - +
175B TYR* 4.1 22.2 - - + +
179B THR* 4.0 18.3 - - - +
183B HIS* 4.8 0.4 + - - -
1C MET 5.1 7.1 + - - +
4C VAL* 5.1 8.5 - - + +
14C PRO 4.3 2.0 + - - -
16C SER* 4.0 12.8 - - - +
35C GLN* 5.3 0.5 - - - +
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Residues in contact with LEU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B SER* 3.6 5.8 - - - +
56B GLN* 1.3 80.5 - - - +
58B THR* 1.3 55.1 + - - +
60B ASN* 3.8 7.6 - - - +
61B THR* 3.0 25.8 + - - -
95B GLU* 3.3 37.9 - - + +
150B ILE 5.5 1.8 - - - +
152B HIS* 3.8 22.9 - - + -
10C PRO* 3.8 24.2 - - + +
13C HIS* 3.6 38.1 + - + +
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Residues in contact with THR 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B VAL* 3.8 21.2 - - + +
55B SER* 3.2 24.7 + - - -
56B GLN 3.1 0.6 - - - -
57B LEU* 1.3 75.7 - - - +
59B ILE* 1.3 60.4 + - - +
61B THR 3.5 0.3 + - - -
62B ALA* 2.9 27.5 + - - +
88B LEU* 4.1 7.6 - - + -
91B ALA* 3.5 6.6 - - + +
92B ALA* 3.5 38.6 - - + +
95B GLU* 3.7 20.8 - - - +
97B GLN* 4.1 7.1 + - - +
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Residues in contact with ILE 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 3.7 7.9 - - + +
46B GLN* 3.6 58.1 - - - +
49B GLY* 3.9 17.0 - - - -
54B VAL* 3.8 11.7 - - + -
55B SER 3.5 10.3 - - - +
56B GLN* 3.0 11.1 + - - +
58B THR* 1.3 75.0 - - - +
60B ASN* 1.3 57.9 + - - +
62B ALA* 3.1 7.1 + - - +
63B ILE* 2.9 43.3 + - + +
88B LEU* 4.4 2.7 - - + -
16C SER* 3.4 31.9 - - - +
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Residues in contact with ASN 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLN* 2.8 49.7 + - - +
57B LEU* 3.8 4.5 - - - +
59B ILE* 1.3 76.1 - - - +
61B THR* 1.3 61.3 + - - +
63B ILE* 3.3 9.6 + - - +
64B VAL* 3.2 19.6 + - - +
152B HIS* 3.2 26.3 - - + +
154B HIS* 3.3 36.5 + - - +
175B TYR* 5.2 0.2 + - - -
179B THR* 4.5 3.3 - - - +
182B LEU* 3.6 26.2 - - + +
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Residues in contact with THR 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU 3.0 16.1 + - - -
58B THR 3.8 3.6 - - - -
60B ASN* 1.3 75.8 - - - +
62B ALA* 1.3 57.6 + - - +
64B VAL* 3.3 2.8 + - - +
65B TYR* 3.0 63.2 + - + +
91B ALA* 4.1 6.7 - - + -
94B VAL* 5.0 0.7 - - + -
95B GLU* 2.8 30.8 + - + +
148B LEU 4.6 0.4 - - - +
150B ILE* 4.0 11.5 - - + +
152B HIS* 2.9 23.0 + - - -
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Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 3.8 13.6 - - + +
58B THR 2.9 18.7 + - - +
59B ILE* 3.1 5.6 + - - +
61B THR* 1.3 78.0 - - - +
63B ILE* 1.3 55.7 + - - +
65B TYR* 3.3 9.0 + - - +
66B MET* 3.0 26.9 + - - +
87B ALA* 4.0 5.2 - - - +
88B LEU* 3.9 27.8 - - + +
91B ALA* 3.7 16.6 - - + -
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Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ALA* 4.1 14.6 - - + +
45B LEU* 3.7 22.4 - - + -
59B ILE* 2.9 31.2 + - + +
60B ASN* 3.6 12.1 - - - +
61B THR 3.3 0.2 - - - -
62B ALA* 1.3 75.3 - - - +
64B VAL* 1.3 59.4 + - - +
66B MET* 3.2 10.4 + - + +
67B HIS* 2.8 38.7 + - + +
182B LEU* 3.5 38.1 - - + +
183B HIS* 4.0 30.7 - - + +
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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
----------------------------------------------------------
60B ASN 3.2 4.2 + - - +
61B THR 3.7 5.2 - - - +
63B ILE* 1.3 73.4 - - - +
65B TYR* 1.3 66.8 + - - +
67B HIS* 3.8 6.7 - - + +
68B ARG* 2.9 53.0 + - + +
150B ILE* 3.9 22.4 - - + -
151B ASP 5.5 0.4 - - - +
152B HIS* 3.4 31.9 - - + +
182B LEU* 4.1 17.7 - - + -
188B SER* 4.4 15.5 - - - +
189B LEU* 5.9 0.4 - - + -
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Residues in contact with TYR 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B THR* 3.0 30.9 + - + +
62B ALA* 3.4 8.1 - - - +
64B VAL* 1.3 74.8 - - + +
66B MET* 1.3 58.6 + - - +
68B ARG* 3.8 2.7 - - - +
69B PHE* 2.8 31.8 + - - +
87B ALA* 4.1 24.7 - - + -
90B LEU* 4.0 27.8 - - + -
91B ALA* 4.0 10.5 - - + -
94B VAL* 3.4 20.7 - - + +
140B ILE* 4.9 3.5 - - + +
144B LEU* 3.4 32.4 - - + +
147B GLU 4.1 6.3 - - - -
148B LEU* 2.7 38.3 + - + +
150B ILE* 3.8 21.3 - - + -
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Residues in contact with MET 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ARG* 3.3 35.0 - - - +
41B ALA* 3.7 23.8 - - + -
42B ALA* 4.3 4.0 - - + +
45B LEU* 4.1 11.0 - - + -
62B ALA 3.0 13.8 + - - +
63B ILE* 3.2 21.1 - - + +
64B VAL 3.1 0.2 - - - -
65B TYR* 1.3 75.7 - - - +
67B HIS* 1.3 95.0 + - + +
69B PHE* 3.2 6.3 + - - +
70B TYR* 3.1 52.3 + - + -
83B VAL* 5.3 8.7 - - + -
84B ALA* 6.1 2.2 - - - +
87B ALA* 5.0 5.1 - - + +
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Residues in contact with HIS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ARG* 2.9 68.7 + - + +
63B ILE* 2.8 36.7 + - + +
64B VAL* 3.2 4.0 + - - +
66B MET* 1.3 83.0 - - + +
68B ARG* 1.3 60.4 - - - +
70B TYR 3.6 3.6 + - - -
71B MET* 3.7 5.2 + - - +
182B LEU* 3.0 22.9 + - + -
183B HIS 4.9 2.4 + - - -
185B THR 3.4 17.2 + - - -
186B THR* 4.0 6.6 - - + +
188B SER* 3.7 20.0 - - - +
189B LEU* 3.5 26.8 - - + +
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Residues in contact with ARG 68 (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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12B TRP* 3.4 76.8 + - + +
13B TYR* 4.6 16.2 + - - -
64B VAL* 2.9 39.5 + - + +
65B TYR* 5.4 1.1 - - - +
67B HIS* 1.3 74.1 - - - +
69B PHE* 1.3 70.0 + - - +
70B TYR 3.1 0.2 - - - -
71B MET* 3.0 13.5 + - - +
72B ILE* 3.7 2.3 + - - +
144B LEU* 3.5 19.5 - - + +
147B GLU* 3.6 21.2 + - - +
149B THR 5.3 0.2 + - - -
150B ILE* 3.7 24.2 - - - +
188B SER 5.0 5.9 + - - -
189B LEU* 3.8 16.7 - - + +
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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 TYR 2.8 18.8 + - - +
66B MET* 3.3 9.0 - - - +
68B ARG* 1.3 75.9 - - - +
70B TYR* 1.3 79.8 + + - +
72B ILE* 3.0 9.4 + - - +
73B GLN* 2.9 49.2 + - + +
78B PHE* 3.7 36.8 - + + -
83B VAL* 3.7 17.7 - - + -
136B LEU* 6.0 1.3 - - + -
139B ILE* 4.1 7.6 - - + -
140B ILE* 3.8 35.0 - - + -
143B THR* 3.8 35.1 - - + +
144B LEU* 4.1 3.5 - - + +
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Residues in contact with TYR 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PRO* 3.6 10.0 - - - +
24B SER* 4.8 1.6 + - - -
34B GLU* 4.0 3.8 - - - +
38B ARG* 3.3 30.8 + - - +
66B MET* 3.1 39.4 + - + +
67B HIS 3.6 0.4 + - - -
68B ARG 3.1 0.6 - - - -
69B PHE* 1.3 95.8 - + - +
71B MET* 1.3 54.7 + - - +
72B ILE 3.1 4.5 - - - -
73B GLN 3.3 22.8 - - - +
74B SER 3.9 2.9 - - - -
75B PHE* 3.3 57.2 - + + -
78B PHE 2.4 30.2 + - - -
80B GLY* 3.5 10.9 + - - -
83B VAL* 3.2 21.2 - - + +
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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
------------------------------------------------------------
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