Contacts of the helix formed by residues 48 - 67 (chain M) in PDB entry 3SDI
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 ILE 48 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-3M VAL* 2.8 42.0 + - + +
-2M THR 3.8 7.9 - - - +
-1M GLY 4.1 13.2 - - - +
18M LEU 4.7 2.2 - - - +
19M GLY* 4.7 2.2 - - - -
30M VAL* 4.0 18.2 - - + -
32M ARG* 4.2 9.0 - - - -
46M GLY 4.3 2.0 - - - +
47M ASP* 1.3 69.6 + - - +
49M SER* 1.3 61.0 - - - +
50M ASP 3.2 1.6 - - - -
51M MET* 3.2 31.9 + - + +
52M GLN* 2.9 47.5 + - - +
118N SER* 4.3 1.3 - - - -
120N HIS* 4.1 16.2 - - + -
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Residues in contact with SER 49 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-3M VAL* 4.7 1.4 + - - +
47M ASP* 2.6 20.0 + - - -
48M ILE* 1.3 76.8 - - - +
50M ASP* 1.3 61.4 + - - +
52M GLN* 3.2 5.8 + - - +
53M HIS 3.1 17.0 + - - -
84N LYS* 5.5 1.9 - - - -
88N TYR* 3.5 18.8 - - - -
91N LYS* 2.9 22.5 + - - -
116N GLY* 3.3 21.4 + - - -
117N GLY 3.8 0.9 - - - -
118N SER* 3.6 27.8 - - - +
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Residues in contact with ASP 50 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-7M GLN* 3.3 20.5 + - - +
47M ASP* 2.8 17.9 + - + +
49M SER* 1.3 74.1 + - - +
51M MET* 1.3 65.1 + - - +
53M HIS* 3.2 3.6 + - - +
54M ILE* 2.9 25.5 + - - +
94M ARG* 5.4 0.9 + - - -
100M PRO 4.0 0.4 - - - +
101M LEU* 3.6 16.0 - - + +
102M TRP* 2.8 26.1 + - - +
103M ASN* 3.2 21.5 - - - +
88N TYR* 2.8 29.2 + - - -
91N LYS* 3.6 6.8 + - - -
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Residues in contact with MET 51 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30M VAL* 4.2 7.0 - - + -
31M GLU 3.9 14.4 - - - +
32M ARG* 4.1 28.5 - - - -
34M ILE* 4.6 6.3 - - + -
44M ILE* 3.6 40.3 - - + +
46M GLY 5.6 0.2 - - - +
47M ASP 3.0 15.6 + - - +
48M ILE* 3.4 40.2 - - + +
50M ASP* 1.3 78.0 - - - +
52M GLN* 1.3 61.3 + - + +
54M ILE* 3.1 7.2 + - - +
55M GLU* 2.9 39.9 + - - +
103M ASN* 3.9 4.2 - - - +
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Residues in contact with GLN 52 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30M VAL* 6.2 0.6 - - - +
48M ILE* 2.9 33.9 + - - +
49M SER 3.2 4.5 + - - +
51M MET* 1.3 81.8 - - + +
53M HIS* 1.3 61.8 + - - +
55M GLU* 3.3 22.2 - - - +
56M ARG* 3.2 21.5 + - - +
84N LYS* 3.7 27.6 + - - +
118N SER* 3.4 8.7 - - - -
119N VAL* 2.9 45.8 + - - +
120N HIS* 3.9 5.9 + - - -
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Residues in contact with HIS 53 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49M SER 3.1 5.8 + - - +
50M ASP 3.4 5.6 - - - +
52M GLN* 1.3 74.7 - - - +
54M ILE* 1.3 64.3 + - - +
56M ARG* 3.3 36.1 + - - +
57M LEU* 3.1 51.1 + - + +
94M ARG* 4.4 11.6 + - - -
101M LEU* 3.9 18.6 - - + +
84N LYS* 5.6 1.5 - - - +
88N TYR* 3.2 45.7 - + + +
89N GLU* 5.3 6.4 + - - -
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Residues in contact with ILE 54 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44M ILE* 3.7 22.2 - - + -
50M ASP 2.9 15.2 + - - +
51M MET 3.6 6.1 - - - +
53M HIS* 1.3 72.9 - - + +
55M GLU* 1.3 65.1 + - - +
57M LEU* 3.3 10.1 + - + +
58M LEU* 3.0 31.2 + - + +
87M LEU* 3.9 29.6 - - + -
91M MET* 4.8 1.3 - - - -
101M LEU* 4.1 25.4 - - + -
103M ASN* 3.7 26.7 - - + +
105M ILE* 3.7 24.0 - - + -
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Residues in contact with GLU 55 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31M GLU 5.0 4.2 - - - +
34M ILE* 3.7 40.2 - - + +
51M MET* 2.9 20.4 + - + +
52M GLN* 3.3 29.2 - - - +
54M ILE* 1.3 75.8 - - - +
56M ARG* 1.3 61.9 + - - +
58M LEU* 3.1 8.6 + - - +
59M LYS* 3.0 50.6 + - - +
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Residues in contact with ARG 56 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F LYS* 5.5 1.6 - - + -
101F LYS* 3.8 56.9 + - - +
104F LYS* 6.1 6.5 - - + +
52M GLN 3.2 9.4 + - - +
53M HIS* 3.3 39.5 + - - +
55M GLU* 1.3 77.9 - - - +
57M LEU* 1.3 72.7 + - - +
59M LYS* 3.2 10.5 + - + +
60M ASP* 3.0 53.7 + - - +
84N LYS* 6.0 4.5 - - - +
85N GLU* 5.1 5.8 + - - -
89N GLU* 5.7 1.8 + - - -
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Residues in contact with LEU 57 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53M HIS* 3.1 50.1 + - + +
54M ILE* 3.7 17.0 - - + +
55M GLU 3.3 0.4 - - - -
56M ARG* 1.3 87.3 - - - +
58M LEU* 1.3 59.7 + - + +
60M ASP* 3.4 9.5 + - + +
61M LEU* 3.1 27.9 + - - +
86M TYR* 4.2 32.7 + - + +
87M LEU* 5.4 4.7 - - + -
90M VAL* 4.7 20.4 - - + -
101M LEU* 5.1 0.2 - - + -
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Residues in contact with LEU 58 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34M ILE* 4.0 17.7 - - + -
36M VAL* 3.9 20.7 - - + +
42M VAL* 3.8 28.3 - - + -
54M ILE* 3.0 30.9 + - + +
55M GLU* 3.5 7.9 - - - +
57M LEU* 1.3 77.9 - - - +
59M LYS* 1.3 63.7 + - + +
61M LEU* 3.3 8.6 + - + +
62M VAL* 3.3 26.6 + - - +
83M ILE* 3.9 29.2 - - + -
86M TYR* 5.1 7.6 - - + -
87M LEU* 4.3 15.9 - - + -
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Residues in contact with LYS 59 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F ARG* 3.2 33.6 + - - +
100F LYS* 6.2 4.5 - - - +
104F LYS* 5.8 7.1 - - - +
34M ILE* 6.3 2.7 - - - -
55M GLU* 3.0 40.1 + - - +
56M ARG* 3.2 10.5 + - + +
58M LEU* 1.3 77.0 - - + +
60M ASP* 1.3 66.3 + - - +
62M VAL* 3.4 5.1 + - - +
63M THR* 3.2 8.8 + - - -
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Residues in contact with ASP 60 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F ALA* 5.6 6.7 - - - +
100F LYS* 5.3 9.5 - - - +
56M ARG* 3.0 42.4 + - - +
57M LEU* 3.7 10.6 - - + +
59M LYS* 1.3 77.8 - - - +
61M LEU* 1.3 61.0 + - - +
63M THR* 3.4 8.5 + - - -
64M GLU* 2.9 38.1 + - - +
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Residues in contact with LEU 61 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E PHE* 3.6 35.4 - - + -
36M VAL* 6.1 0.4 - - + -
57M LEU 3.1 11.5 + - - +
58M LEU* 3.4 16.4 - - + +
60M ASP* 1.3 77.6 - - - +
62M VAL* 1.3 56.0 + - - +
64M GLU* 4.0 5.2 - - + +
65M ASN* 3.1 29.6 + - - +
78M LEU* 3.6 37.5 - - + +
83M ILE* 4.3 18.8 - - + -
86M TYR* 4.1 30.3 - - + +
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Residues in contact with VAL 62 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F ARG* 3.9 21.5 - - - +
36M VAL* 3.7 26.2 - - + -
37M GLY* 4.9 5.6 - - - +
58M LEU 3.3 14.9 + - - +
59M LYS* 3.6 9.4 - - - +
60M ASP 3.2 0.4 - - - -
61M LEU* 1.3 74.7 - - - +
63M THR* 1.3 65.4 + - - +
65M ASN* 3.4 3.8 + - - +
66M ALA* 3.3 21.9 + - + +
78M LEU* 4.0 13.7 - - + -
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Residues in contact with THR 63 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F ASP* 4.1 19.9 - - - +
72F ARG* 2.8 37.1 + - - +
100F LYS* 4.6 7.3 + - - +
59M LYS 3.2 6.5 + - - -
60M ASP* 3.5 11.2 + - - +
62M VAL* 1.3 78.4 - - - +
64M GLU* 1.3 58.9 + - + +
66M ALA* 3.2 24.4 + - - +
67M TYR* 3.4 41.9 + - + +
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Residues in contact with GLU 64 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E ARG* 5.7 5.4 + - - +
93F ARG* 5.8 1.6 - - - +
60M ASP* 2.9 22.4 + - - +
61M LEU* 4.3 6.3 - - + +
63M THR* 1.3 74.0 - - - +
65M ASN* 1.3 63.6 + - - +
66M ALA 3.1 1.7 + - - -
67M TYR* 3.5 42.6 + - + +
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Residues in contact with ASN 65 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E ARG* 2.7 38.0 + - - +
61M LEU 3.1 19.1 + - - +
62M VAL 3.9 4.8 + - - +
63M THR 3.3 0.2 - - - -
64M GLU* 1.3 77.4 - - - +
66M ALA* 1.3 58.0 + - - +
67M TYR 3.3 1.5 + - - +
69M ASN* 2.8 36.0 + - - +
72M ALA* 4.3 7.1 + - - +
76M GLU 3.1 19.2 + - - +
77M ALA* 3.9 3.2 - - - +
78M LEU* 3.9 31.0 - - + +
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Residues in contact with ALA 66 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F VAL* 4.5 10.9 - - + +
71F ASP 6.0 0.9 - - - +
72F ARG* 6.1 4.7 - - + -
62M VAL* 3.3 12.0 + - + +
63M THR* 3.3 13.0 - - - +
64M GLU 3.1 0.2 - - - -
65M ASN* 1.3 80.1 - - - +
67M TYR* 1.3 66.0 + - + +
68M ASP 3.3 0.7 + - - -
69M ASN* 3.3 17.7 + - - +
72M ALA* 4.0 16.6 - - + +
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Residues in contact with TYR 67 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E ARG* 5.7 5.7 + - - -
69F VAL* 3.6 22.2 - - + -
71F ASP* 2.8 49.2 + - - -
93F ARG* 3.6 55.7 + - + +
96F ALA* 5.5 1.4 - - - +
97F ALA* 6.2 0.3 - - - +
63M THR* 3.4 23.8 - - + +
64M GLU* 3.5 43.9 - - + +
65M ASN 3.3 2.5 - - - +
66M ALA* 1.3 77.1 - - - +
68M ASP* 1.3 68.2 + - - +
69M ASN* 3.1 6.1 + - - +
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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
------------------------------------------------------------
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