Contacts of the helix formed by residues 77 - 93 (chain B) in PDB entry 3M0V
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 GLY 77 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B PRO 4.1 1.6 + - - -
76B ARG* 1.3 74.2 - - - +
78B ILE* 1.3 65.8 + - - -
79B PHE* 3.3 4.2 + - - -
80B ASP 3.3 0.7 + - - -
81B LYS* 3.2 34.8 + - - +
104B TRP 5.6 3.1 - - - -
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Residues in contact with ILE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B SER* 5.4 1.3 - - - -
77B GLY* 1.3 70.4 - - - -
79B PHE* 1.3 71.9 + - + +
81B LYS* 3.3 12.2 + - + +
82B LEU* 2.8 41.1 + - + +
100B LEU* 3.6 24.9 - - + -
104B TRP 5.2 2.8 + - - -
105B ASP* 3.3 48.9 + - + +
106B LYS 4.7 1.8 - - - +
107B ALA* 4.2 10.1 - - + -
112B LEU* 3.2 36.1 - - + -
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Residues in contact with PHE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLY* 3.3 1.9 - - - -
78B ILE* 1.3 78.5 - - + +
80B ASP* 1.3 68.2 + - - +
82B LEU* 3.4 8.0 + - + +
83B ASP* 3.1 28.5 + - - +
107B ALA* 4.2 21.3 - - + -
111B GLU* 4.2 47.3 - - + -
112B LEU* 4.2 16.2 - - + -
115B ARG* 4.2 24.3 + - + +
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Residues in contact with ASP 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B PRO* 3.5 9.5 - - + +
76B ARG* 2.9 49.8 + - - +
77B GLY 3.3 1.8 + - - -
78B ILE 3.3 0.2 - - - -
79B PHE* 1.3 78.3 - - - +
81B LYS* 1.3 63.8 + - - +
83B ASP* 3.3 7.4 + - - +
84B ASP* 3.2 18.7 + - - -
419B ARG* 3.4 38.6 + - - +
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Residues in contact with LYS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B SER* 3.3 29.4 + - - +
57B TRP* 4.6 10.6 - - - +
59B VAL* 3.7 23.1 - - + +
60B GLY* 5.5 4.9 - - - +
75B PRO* 4.1 23.6 - - + -
77B GLY* 3.2 24.6 + - - +
78B ILE* 3.5 8.5 - - + +
80B ASP* 1.3 76.4 - - - +
82B LEU* 1.3 61.3 + - - +
84B ASP* 3.2 3.6 + - - +
85B CYS* 2.9 33.4 + - - -
104B TRP* 5.0 12.3 + - - +
105B ASP* 4.0 19.2 + - - +
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B SER* 6.0 0.9 - - - -
78B ILE* 2.8 45.9 + - + +
79B PHE* 3.8 7.2 - - + +
80B ASP 3.3 0.2 - - - -
81B LYS* 1.3 73.8 - - + +
83B ASP* 1.3 64.2 + - - +
85B CYS* 3.0 4.6 + - + +
86B ALA* 2.9 23.7 + - - +
98B VAL* 4.2 33.2 - - + -
100B LEU* 4.8 0.9 - - + -
112B LEU* 4.5 15.3 - - + +
115B ARG* 4.1 24.2 - - + -
116B GLY* 4.8 3.1 - - - +
119B LEU* 3.7 14.8 - - + -
121B LEU* 3.7 9.8 - - + +
123B PHE* 4.3 17.7 - - + -
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Residues in contact with ASP 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ARG* 3.3 43.7 + - - +
79B PHE* 3.1 19.7 + - - +
80B ASP* 3.5 14.3 - - - +
82B LEU* 1.3 76.0 - - - +
84B ASP* 1.3 64.5 + - - +
86B ALA* 3.3 15.5 - - - +
87B VAL* 3.6 1.4 + - - +
115B ARG* 2.6 40.2 + - - -
119B LEU* 3.7 8.7 - - - +
411B TYR* 3.6 2.6 + - - +
419B ARG* 4.2 4.3 + - - +
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Residues in contact with ASP 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B VAL* 4.2 17.1 - - + +
73B GLY 4.5 0.5 - - - +
75B PRO* 3.4 18.0 - - - +
80B ASP 3.2 6.7 + - - +
81B LYS 3.6 7.4 - - - +
82B LEU 3.1 0.6 - - - -
83B ASP* 1.3 74.5 - - - +
85B CYS* 1.3 65.9 + - - +
86B ALA 3.1 0.4 - - - -
87B VAL* 3.1 19.7 + - - +
88B ILE* 3.6 8.1 + - - +
336B ILE* 3.9 24.0 - - + +
411B TYR* 2.7 31.5 + - - -
412B ARG* 4.7 3.6 + - - -
419B ARG* 2.9 36.7 + - - -
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Residues in contact with CYS 85 (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 24.6 - - + +
55B PRO 4.5 3.4 - - - -
56B SER* 4.6 2.5 - - - -
59B VAL* 3.7 21.3 - - - -
81B LYS 2.9 22.6 + - - +
82B LEU* 3.0 9.4 + - - +
84B ASP* 1.3 76.4 - - - +
86B ALA* 1.3 62.7 + - - +
88B ILE* 3.1 22.9 + - - +
89B GLN* 3.1 12.8 + - - +
95B THR* 4.7 1.4 + - - +
98B VAL* 3.8 32.8 - - + -
121B LEU* 4.0 5.4 - - + +
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ARG* 3.6 16.8 - - + -
82B LEU 2.9 11.5 + - - +
83B ASP 3.3 13.0 - - - +
85B CYS* 1.3 78.6 - - - +
87B VAL* 1.3 56.3 + - - +
89B GLN* 3.3 2.6 + - - +
90B GLN* 2.8 30.5 + - - +
119B LEU* 3.9 32.0 - - + +
121B LEU* 3.8 11.9 - - + +
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Residues in contact with VAL 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ARG* 3.5 21.3 - - + -
6B ILE* 4.0 8.5 - - + -
83B ASP 3.9 1.6 - - - +
84B ASP 3.1 10.6 + - - +
86B ALA* 1.3 78.5 - - - +
88B ILE* 1.3 62.8 + - - +
90B GLN* 3.3 4.8 + - - +
91B LEU* 3.0 36.8 + - + +
336B ILE* 4.0 10.8 - - + -
406B TYR* 3.8 28.7 - - + -
411B TYR* 3.5 40.6 - - + +
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Residues in contact with ILE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B VAL* 4.1 10.1 - - + -
59B VAL* 4.0 15.5 - - + -
84B ASP 3.9 7.0 - - - +
85B CYS* 3.1 8.9 + - - +
87B VAL* 1.3 77.8 - - - +
89B GLN* 1.3 56.8 + - - +
92B THR* 2.8 41.9 + - + +
95B THR* 3.4 23.3 - - + +
336B ILE* 3.9 28.0 - - + +
339B LEU* 3.5 40.4 - - + +
340B ILE* 4.1 27.8 - - + +
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Residues in contact with GLN 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B PHE* 5.9 0.8 - - - -
85B CYS 3.1 3.9 + - - +
86B ALA 3.8 4.7 - - - +
88B ILE* 1.3 76.2 - - - +
90B GLN* 1.3 63.3 + - - +
93B ARG* 2.7 63.4 + - - +
95B THR* 3.0 42.0 + - - +
96B PRO* 3.1 21.5 - - + +
119B LEU 5.5 2.0 - - - +
120B GLY 4.2 8.5 + - - +
121B LEU* 3.7 26.2 - - + -
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Residues in contact with GLN 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE* 3.8 19.9 - - + +
5B ARG* 3.2 14.9 + - - +
6B ILE* 2.9 55.9 + - - +
7B ALA 5.0 0.4 - - - -
8B GLN* 5.1 1.0 - - - +
11B VAL* 3.8 16.4 - - - +
86B ALA 2.8 17.6 + - - +
87B VAL* 3.3 5.6 + - - +
89B GLN* 1.3 79.1 - - - +
91B LEU* 1.3 61.5 + - + +
93B ARG* 3.1 40.0 + - - +
397B GLY 3.5 2.0 - - - +
398B GLY* 3.5 9.2 - - - -
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 4.3 14.8 - - + -
11B VAL* 4.2 17.3 - - + -
87B VAL* 3.0 32.0 + - + +
88B ILE 4.3 1.1 - - - +
90B GLN* 1.3 84.3 - - + +
92B THR* 1.3 58.7 + - - +
340B ILE* 4.1 8.5 - - + -
393B ARG* 3.6 9.0 - - - -
398B GLY* 3.6 1.3 - - - -
399B ALA* 3.0 31.4 + - + +
402B PRO* 3.7 32.3 - - + +
405B THR* 4.1 20.9 - - + -
406B TYR* 3.8 23.3 - - + -
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Residues in contact with THR 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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88B ILE* 2.8 28.5 + - + +
91B LEU* 1.3 78.8 - - - +
93B ARG* 1.3 73.2 + - - +
94B ALA* 2.9 21.2 + - - +
95B THR* 3.8 7.6 + - - +
340B ILE* 3.6 42.8 - - + +
343B ALA* 4.9 2.0 - - + -
344B ASN* 3.9 18.8 - - - +
347B ARG* 3.7 8.8 + - - -
393B ARG* 3.5 19.9 - - - +
402B PRO* 4.3 1.3 - - + -
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Residues in contact with ARG 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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4B PHE* 4.9 11.7 - - - -
48B GLU 4.6 0.5 - - - +
51B PHE* 3.5 13.9 - - - -
89B GLN* 2.7 53.2 + - - +
90B GLN* 3.1 35.5 + - - +
92B THR* 1.3 73.3 + - - +
94B ALA* 1.3 55.7 + - - +
347B ARG* 3.1 15.6 + - - +
393B ARG* 4.7 0.4 - - - +
396B THR* 3.2 47.9 + - - +
397B GLY* 3.2 21.2 + - - -
398B GLY* 3.7 11.4 - - - +
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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