Contacts of the helix formed by residues 63 - 77 (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 SER 63 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B GLU 3.4 4.5 + - - -
62B ALA* 1.3 77.6 - - - +
64B TRP* 1.3 65.6 + - - +
65B THR* 3.1 18.2 + - - -
66B GLN* 2.7 40.1 + - - +
67B VAL* 3.3 10.2 + - - +
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Residues in contact with TRP 64 (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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62B ALA 3.7 0.6 + - - -
63B SER* 1.3 77.1 - - - +
65B THR* 1.3 83.9 + - + +
67B VAL* 3.5 5.1 + - - +
68B VAL* 3.0 44.7 + - + +
90B TYR* 3.4 57.5 - + + -
95B ASN* 5.3 12.2 + - + -
98B ARG* 3.8 42.4 - - + -
99B LEU* 4.1 19.1 - - + -
102B LYS* 4.2 20.6 - - + -
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Residues in contact with THR 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLU* 5.5 8.1 - - - +
63B SER* 3.1 13.2 + - - -
64B TRP* 1.3 116.3 - - + +
66B GLN* 1.3 59.5 + - - +
68B VAL* 3.0 8.3 + - + +
69B GLU* 2.9 30.6 + - - +
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Residues in contact with GLN 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LEU* 5.4 5.6 - - + -
62B ALA* 3.3 16.6 - - + +
63B SER* 2.7 44.2 + - - +
65B THR* 1.3 77.8 + - - +
67B VAL* 1.3 63.5 + - - +
69B GLU* 3.5 10.8 + - - +
70B VAL* 3.2 27.2 + - - +
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Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLY* 6.2 2.9 - - - -
50B VAL* 4.4 22.4 - - + -
54B LEU* 5.7 1.3 - - + -
62B ALA* 4.3 18.2 - - + +
63B SER 3.3 14.3 + - - +
64B TRP* 3.6 9.2 - - - +
65B THR 3.2 0.4 - - - -
66B GLN* 1.3 75.8 - - - +
68B VAL* 1.3 64.6 + - + +
70B VAL* 3.2 8.6 + - - +
71B LEU* 3.0 22.4 + - + +
84B LEU* 4.0 23.3 - - + -
85B ASP 5.5 0.4 - - - +
87B ASP* 6.1 0.2 - - - +
90B TYR* 3.6 26.7 - - + +
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Residues in contact with VAL 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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64B TRP* 3.0 38.0 + - + +
65B THR* 3.0 12.0 + - + +
67B VAL* 1.3 78.2 - - + +
69B GLU* 1.3 57.3 + - - +
71B LEU* 3.2 8.1 + - - +
72B GLU* 2.8 25.8 + - - +
84B LEU* 5.6 1.8 - - + -
90B TYR* 6.0 0.2 - - + -
99B LEU* 3.9 17.7 - - + -
102B LYS* 4.7 9.6 - - + -
103B LEU* 4.7 12.5 - - + +
106B ARG* 4.0 37.2 - - + +
108B VAL* 6.0 0.2 - - - +
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Residues in contact with GLU 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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65A THR* 5.3 9.9 - - - +
65B THR 2.9 14.1 + - - +
66B GLN* 3.8 9.8 - - - +
67B VAL 3.3 0.4 - - - -
68B VAL* 1.3 74.5 - - - +
70B VAL* 1.3 67.4 + - + +
72B GLU* 3.0 28.8 + - - +
73B PHE* 3.0 36.4 + - + -
106B ARG* 5.8 0.2 - - - +
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Residues in contact with VAL 70 (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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27B HIS 3.7 23.6 - - - +
28B ASN* 4.7 2.2 - - - -
29B GLY 4.9 0.5 + - - -
50B VAL* 4.0 15.7 - - + -
53B GLN* 3.8 14.6 - - - +
54B LEU* 4.5 17.7 - - + -
66B GLN 3.2 15.1 + - - +
67B VAL 3.2 8.8 + - - +
69B GLU* 1.3 76.9 - - + +
71B LEU* 1.3 77.9 + - + +
73B PHE* 3.4 9.3 + - - +
74B MET* 3.1 23.5 + - + +
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Residues in contact with LEU 71 (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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45B GLY* 4.9 2.9 - - - -
50B VAL* 4.1 13.0 - - + -
67B VAL* 3.0 18.5 + - + +
68B VAL* 3.6 10.1 - - - +
69B GLU 3.2 0.2 - - - -
70B VAL* 1.3 84.0 - - + +
72B GLU* 1.3 53.6 - - - +
74B MET* 3.3 30.2 - - + +
75B SER* 2.7 35.5 + - - -
82B ILE* 4.4 14.6 - - + +
84B LEU* 3.0 55.4 - - + -
103B LEU* 4.8 1.3 - - + -
108B VAL* 4.5 15.9 - - + +
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Residues in contact with GLU 72 (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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102A LYS* 3.1 30.6 + - - +
106A ARG* 3.0 35.8 + - - -
68B VAL 2.8 13.9 + - - +
69B GLU* 3.0 26.4 + - - +
71B LEU* 1.3 73.4 - - - +
73B PHE* 1.3 70.6 + - + +
74B MET 3.2 0.2 + - - -
75B SER* 3.2 5.1 + - - -
76B ASP* 2.9 32.8 + - - +
106B ARG* 3.8 29.6 + - + +
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Residues in contact with PHE 73 (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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98A ARG* 3.3 29.6 - - - -
29B GLY* 3.9 13.7 - - - +
69B GLU* 3.0 46.4 + - + -
70B VAL* 3.7 9.4 - - - +
72B GLU* 1.3 80.6 - - + +
74B MET* 1.3 63.0 + - - +
76B ASP* 3.5 10.0 + - + +
77B ALA* 3.1 23.2 + - - +
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Residues in contact with MET 74 (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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26B ALA* 3.7 36.6 - - + +
27B HIS* 3.7 6.7 - - - -
28B ASN* 3.2 37.7 - - - +
29B GLY* 3.9 6.1 - - - -
32B ALA* 4.0 7.5 - - + +
43B ILE* 4.2 12.6 - - + -
45B GLY* 4.6 3.4 - - - -
50B VAL* 4.8 0.4 - - - -
70B VAL* 3.1 13.9 + - - +
71B LEU* 3.3 34.3 - - + +
72B GLU 3.0 0.8 - - - -
73B PHE* 1.3 75.4 - - - +
75B SER* 1.3 64.0 + - - +
77B ALA* 3.2 10.7 + - - +
78B SER* 2.9 19.2 + - - -
82B ILE* 3.8 20.4 - - + +
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Residues in contact with SER 75 (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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7B LYS* 2.9 37.4 + - - +
71B LEU 2.7 19.4 + - - -
72B GLU* 3.8 2.7 - - - -
74B MET* 1.3 73.1 - - - +
76B ASP* 1.3 63.6 + - - +
77B ALA 3.1 0.5 + - - -
78B SER* 3.1 9.2 + - - +
82B ILE* 3.6 15.2 - - - +
106B ARG 3.0 27.2 + - - -
107B GLY* 3.4 14.6 + - - -
108B VAL* 4.5 5.2 - - - -
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Residues in contact with ASP 76 (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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98A ARG* 4.6 11.2 + - - +
102A LYS* 2.5 33.5 + - - -
105A ASP* 5.5 2.1 - - - +
33B ARG* 4.6 3.5 + - - -
72B GLU* 2.9 27.0 + - - +
73B PHE* 3.5 11.5 - - + +
75B SER* 1.3 77.9 - - - +
77B ALA* 1.3 59.0 + - + +
78B SER 3.5 1.7 + - - +
106B ARG 4.5 7.6 - - - +
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Residues in contact with ALA 77 (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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29B GLY* 3.6 26.2 - - - +
33B ARG* 3.2 57.9 - - - +
36B GLN* 4.9 0.9 + - - +
73B PHE 3.1 15.9 + - - +
74B MET 3.2 2.4 + - - +
75B SER 3.1 1.2 - - - -
76B ASP* 1.3 77.2 - - + +
78B SER* 1.3 59.5 + - - +
280B ARG* 5.2 0.2 + - - -
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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
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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