Contacts of the helix formed by residues 75 - 90 (chain N) 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 SER 75 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F THR* 5.3 2.4 - - - +
143F LYS* 6.4 2.0 - - - -
41N ILE* 4.0 4.2 - - - +
66N TYR* 5.3 0.8 + - - -
73N THR 3.7 2.4 + - - -
74N PRO* 1.3 77.1 - - - +
76N THR* 1.3 63.9 + - - +
77N GLU* 3.6 10.9 + - - +
78N THR* 3.1 29.6 + - - -
79N ALA 3.2 16.6 + - - -
105N ASP* 4.4 17.3 - - - -
106N ASN* 5.4 7.9 - - - -
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Residues in contact with THR 76 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41N ILE* 4.4 8.5 - - + +
74N PRO 4.0 0.2 + - - -
75N SER* 1.3 73.1 - - - +
77N GLU* 1.3 58.8 + - - +
79N ALA* 3.1 9.0 + - - +
80N ALA* 2.9 27.2 + - - +
101N VAL* 4.2 11.2 - - + +
102N ALA* 4.0 4.7 - - - -
103N GLY* 3.6 44.9 + - - +
104N TYR 4.4 1.4 + - - -
105N ASP* 4.5 12.6 + - - +
106N ASN* 6.2 0.2 - - - +
107N LYS 5.4 0.2 + - - -
109N GLU* 3.9 21.9 + - + +
111N TYR* 4.0 16.6 - - + -
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Residues in contact with GLU 77 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F TYR 5.4 0.4 - - - +
104F LYS* 3.3 43.8 + - + +
105F THR* 5.6 5.9 - - - +
75N SER* 3.8 9.9 + - - +
76N THR* 1.3 77.8 - - - +
78N THR* 1.3 56.8 + - - +
80N ALA* 3.2 4.2 + - - +
81N SER* 2.8 28.2 + - - -
109N GLU* 4.1 3.0 + - - +
111N TYR* 3.4 34.9 + - + +
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Residues in contact with THR 78 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F TYR* 3.0 51.7 + - + -
105F THR* 3.6 14.9 - - - +
63N LEU* 4.5 5.6 - - + -
66N TYR* 4.0 16.4 + - + -
74N PRO* 4.2 10.1 - - + -
75N SER* 3.1 29.8 + - - -
77N GLU* 1.3 74.3 - - - +
79N ALA* 1.3 62.7 + - - +
81N SER* 3.2 3.9 + - - -
82N VAL* 3.0 23.0 + - - +
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Residues in contact with ALA 79 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37N VAL* 5.0 2.2 - - + -
41N ILE* 3.7 35.0 - - + -
59N VAL* 4.5 0.7 - - - +
63N LEU* 3.8 28.4 - - + +
75N SER 3.2 4.9 + - - -
76N THR 3.1 9.0 + - - +
78N THR* 1.3 75.5 - - - +
80N ALA* 1.3 63.7 + - - +
82N VAL* 3.1 5.7 + - - +
83N PHE* 3.1 29.3 + - + -
101N VAL* 4.3 3.8 - - + -
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Residues in contact with ALA 80 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76N THR 2.9 12.9 + - - +
77N GLU* 3.5 8.3 - - - +
79N ALA* 1.3 74.3 - - - +
81N SER* 1.3 57.0 + - - +
83N PHE* 3.4 3.2 + - - +
84N LYS* 2.9 30.0 + - - +
101N VAL* 4.2 16.9 - - + +
111N TYR* 3.7 38.6 - - + -
113N ILE* 3.8 4.2 - - + +
119N VAL* 4.3 10.4 - - + +
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Residues in contact with SER 81 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F LYS 4.2 5.4 + - - -
102F LEU 3.0 19.9 + - - +
103F TYR 4.0 1.8 - - - -
104F LYS* 3.4 29.1 + - - +
77N GLU 2.8 13.4 + - - -
78N THR 3.3 9.4 - - - -
80N ALA* 1.3 72.9 - - - +
82N VAL* 1.3 65.8 + - - +
84N LYS* 3.4 10.4 + - - +
85N GLU* 3.0 27.7 + - - +
119N VAL* 5.9 1.1 - - - -
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Residues in contact with VAL 82 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F LEU* 3.9 21.1 - - + +
103F TYR* 4.0 22.9 - - + -
59N VAL* 4.0 22.2 - - + -
62N HIS* 4.0 31.0 - - + -
63N LEU* 4.2 13.2 - - + -
78N THR 3.0 15.3 + - - +
79N ALA 3.1 6.2 + - - +
81N SER* 1.3 78.6 - - - +
83N PHE* 1.3 62.3 + - - +
85N GLU* 3.4 5.5 + - - +
86N LEU* 3.2 25.7 + - + +
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Residues in contact with PHE 83 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37N VAL* 4.0 21.5 - - + -
43N CYS* 3.7 26.2 - - + -
55N ILE* 3.6 24.9 - - + -
56N ALA* 4.4 7.0 - - - -
59N VAL* 3.7 29.6 - - + +
79N ALA 3.1 24.0 + - - -
80N ALA 3.5 7.6 - - - +
82N VAL* 1.3 72.9 - - - +
84N LYS* 1.3 66.1 + - - +
86N LEU* 3.4 5.0 + - - +
87N CYS* 3.0 30.1 + - - -
99N ILE* 3.5 31.0 - - + -
101N VAL* 3.6 25.4 - - + -
113N ILE* 3.7 13.7 - - + -
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Residues in contact with LYS 84 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104F LYS* 5.8 6.3 - - - +
49M SER 5.5 2.7 - - - -
52M GLN* 3.7 35.2 + - - +
53M HIS* 6.2 0.9 - - - +
56M ARG* 6.0 4.4 - - - +
80N ALA 2.9 20.1 + - - +
81N SER* 3.6 9.9 - - - +
82N VAL 3.3 0.2 - - - -
83N PHE* 1.3 72.2 - - - +
85N GLU* 1.3 68.3 + - - +
87N CYS* 2.9 5.6 + - - -
88N TYR* 2.6 44.5 + - + +
113N ILE* 4.4 7.6 - - + +
117N GLY 3.3 22.2 - - - +
118N SER* 5.1 0.2 - - - +
119N VAL* 3.4 32.9 - - + +
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Residues in contact with GLU 85 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F LYS* 2.7 57.8 + - - +
102F LEU* 3.9 23.3 - - + -
56M ARG* 5.1 6.7 + - - -
81N SER* 3.0 14.0 + - - +
82N VAL 3.4 9.9 - - - +
84N LYS* 1.3 88.5 - - - +
86N LEU* 1.3 66.1 + - + +
88N TYR* 4.8 2.7 - - - -
89N GLU* 3.0 41.6 + - + +
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Residues in contact with LEU 86 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F LEU* 6.5 1.1 - - + -
55N ILE* 4.1 25.8 - - + +
58N ILE* 3.7 38.6 - - + -
59N VAL* 3.8 26.0 - - + -
62N HIS* 5.6 4.3 - - + +
82N VAL* 3.2 14.4 + - + +
83N PHE 3.7 4.9 - - - +
85N GLU* 1.3 78.0 - - + +
87N CYS* 1.3 62.9 + - - +
89N GLU* 5.1 0.7 - - - -
90N ASN* 3.2 41.8 + - - +
95N LEU* 3.6 3.9 - - + +
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Residues in contact with CYS 87 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55N ILE* 4.1 23.3 - - - -
83N PHE* 3.0 20.4 + - - +
84N LYS 2.9 6.6 + - - +
86N LEU* 1.3 71.2 - - - +
88N TYR* 1.3 65.1 + - - +
90N ASN 3.7 0.7 - - - -
91N LYS* 3.2 24.6 + - - +
95N LEU* 4.1 9.3 - - + +
97N ALA* 4.5 16.8 - - + +
99N ILE* 4.7 11.2 - - - -
113N ILE* 4.0 17.7 - - + -
115N LEU 5.2 1.9 - - - +
116N GLY 4.9 0.2 - - - -
117N GLY* 4.1 19.4 + - - +
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Residues in contact with TYR 88 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49M SER* 3.5 37.2 - - - -
50M ASP* 2.8 28.5 + - - -
53M HIS* 3.2 44.8 - + + +
94M ARG* 5.0 4.2 + - - -
101M LEU* 3.8 7.8 - - - +
84N LYS* 2.6 30.2 + - + +
85N GLU* 4.1 3.4 - - - +
87N CYS* 1.3 71.2 - - - +
89N GLU* 1.3 90.7 + - - +
90N ASN 3.0 1.4 + - - -
91N LYS* 3.1 33.5 + - - +
116N GLY 4.3 1.6 - - - -
117N GLY* 4.0 14.7 - - - +
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Residues in contact with GLU 89 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F LYS* 4.2 10.1 + - - +
53M HIS* 5.3 6.6 + - - -
56M ARG* 5.7 1.4 + - - -
85N GLU* 3.0 38.2 + - + +
86N LEU 4.5 0.9 - - - +
88N TYR* 1.3 103.1 - - - +
90N ASN* 1.3 67.0 + - - +
91N LYS* 3.5 1.4 + - - +
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Residues in contact with ASN 90 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86N LEU* 3.2 37.0 + - - +
87N CYS 3.7 2.9 - - - -
88N TYR 3.0 1.0 - - - -
89N GLU* 1.3 87.5 - - - +
91N LYS* 1.3 54.9 + - - +
92N ASP* 2.9 12.4 + - - -
94N ASN* 3.0 28.6 + - + +
95N LEU* 3.2 26.3 + - + +
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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