Contacts of the helix formed by residues 101 - 116 (chain C) in PDB entry 1SDS
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 ASP 101 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C LYS* 4.1 6.1 - - - +
99C GLU* 3.8 6.0 - - - +
100C GLY* 1.3 80.7 - - - +
102C ALA* 1.3 64.4 + - - +
103C GLU* 2.8 14.8 + - - +
104C GLU* 2.8 57.8 + - + +
105C LEU* 3.1 20.6 + - - +
215D G 3.7 5.2 - - - -
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Residues in contact with ALA 102 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99C GLU* 3.3 12.3 + - - -
101C ASP* 1.3 70.6 + - - +
103C GLU* 1.3 65.4 + - - +
105C LEU* 3.2 4.8 + - - +
106C LYS* 3.0 23.8 + - - +
215D G 3.0 41.4 + - - +
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Residues in contact with GLU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ASP* 2.8 13.8 + - - +
102C ALA* 1.3 76.5 - - - +
104C GLU* 1.3 62.0 + - + +
106C LYS* 3.3 8.6 + - - +
107C VAL* 3.0 30.9 + - + +
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Residues in contact with GLU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C LYS* 2.8 40.6 + - - +
101C ASP* 2.8 36.2 + - + +
103C GLU* 1.3 73.1 - - + +
105C LEU* 1.3 58.3 + - - +
107C VAL* 3.2 9.1 + - - +
108C LEU* 2.8 30.7 + - - +
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Residues in contact with LEU 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ALA* 5.1 7.6 - - + -
44C LYS* 4.1 21.1 - - + +
45C LEU* 4.0 28.0 - - + -
96C ILE* 4.4 12.6 - - + -
99C GLU* 3.1 45.8 - - + +
101C ASP 3.1 6.7 + - - +
102C ALA* 3.6 7.4 - - - +
104C GLU* 1.3 78.2 - - - +
106C LYS* 1.3 55.5 + - - +
108C LEU* 3.1 6.9 + - + +
109C ILE* 2.7 57.3 + - + +
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Residues in contact with LYS 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C ALA 3.0 12.3 + - - +
103C GLU* 3.6 12.1 - - - +
105C LEU* 1.3 77.2 - - - +
107C VAL* 1.3 63.2 + - + +
109C ILE* 3.6 9.6 + - - +
110C GLU* 3.2 18.7 + - - -
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Residues in contact with VAL 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C GLU* 6.0 0.2 - - - +
103C GLU* 3.0 24.1 + - + +
104C GLU* 3.5 10.3 - - - +
106C LYS* 1.3 76.2 - - + +
108C LEU* 1.3 63.8 + - - +
110C GLU* 3.4 2.1 + - - +
111C LYS* 3.2 43.1 + - + +
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Residues in contact with LEU 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ILE* 4.2 17.9 - - + -
16C GLU* 3.4 53.2 - - + +
17C LEU* 3.7 28.7 - - + -
20C ALA* 3.9 17.3 - - + -
45C LEU* 4.5 9.2 - - + -
104C GLU 2.8 16.4 + - - +
105C LEU* 3.6 6.7 - - + +
107C VAL* 1.3 75.8 - - - +
109C ILE* 1.3 65.9 + - + +
110C GLU 3.1 0.2 - - - -
111C LYS* 3.2 9.0 + - + +
112C VAL* 3.0 28.7 + - + +
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Residues in contact with ILE 109 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C LYS* 3.9 18.8 - - + +
45C LEU* 4.6 10.3 - - + -
71C PRO* 3.7 27.6 - - + -
105C LEU* 2.7 55.3 + - + +
106C LYS* 3.9 7.2 - - - +
108C LEU* 1.3 72.3 - - - +
110C GLU* 1.3 58.3 + - - +
112C VAL* 3.4 5.7 + - - +
113C ASN* 2.9 51.5 + - - +
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Residues in contact with GLU 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C LYS 3.2 13.5 + - - -
107C VAL 3.4 4.2 + - - -
108C LEU 3.1 0.6 - - - -
109C ILE* 1.3 75.5 - - - +
111C LYS* 1.3 64.9 + - - +
113C ASN* 3.1 16.7 + - - +
114C VAL* 3.2 21.3 + - - +
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Residues in contact with LYS 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ILE* 4.1 23.0 - - + +
16C GLU* 3.3 38.0 + - - +
107C VAL* 3.2 33.6 + - + +
108C LEU* 3.5 10.8 - - + +
110C GLU* 1.3 75.0 - - - +
112C VAL* 1.3 57.2 + - + +
114C VAL* 2.8 27.8 - - - +
115C LEU* 3.1 15.8 - - - +
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Residues in contact with VAL 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C PHE* 4.0 11.3 - - + -
9C VAL* 5.6 0.9 - - + -
13C ILE* 4.3 20.6 - - + -
17C LEU* 4.3 11.4 - - + -
45C LEU* 5.7 4.5 - - + -
71C PRO* 6.1 0.7 - - + -
72C TYR 3.6 25.6 - - - +
73C ALA* 3.7 22.0 - - + -
108C LEU* 3.0 18.4 + - + +
109C ILE* 3.8 6.7 - - - +
111C LYS* 1.3 74.4 - - - +
113C ASN* 1.3 64.6 + - - +
114C VAL 3.1 5.2 - - - -
115C LEU* 3.0 26.2 + - + +
116C LYS* 3.2 11.0 + - + +
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Residues in contact with ASN 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C PRO* 4.2 18.3 - - - +
72C TYR 5.4 0.8 + - - +
109C ILE* 2.9 42.0 + - - +
110C GLU* 3.1 7.3 + - - +
112C VAL* 1.3 83.4 - - - +
114C VAL* 1.3 61.0 + - + +
115C LEU 3.4 0.2 - - - -
116C LYS* 3.8 19.9 + - - +
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Residues in contact with VAL 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C GLU* 3.2 13.7 - - - +
111C LYS* 2.8 31.4 - - - +
113C ASN* 1.3 77.2 - - + +
115C LEU* 1.3 71.2 + - + +
116C LYS 3.1 6.3 + - - -
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Residues in contact with LEU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C PHE* 3.9 18.5 - - + +
8C LYS 4.3 11.3 - - - +
9C VAL* 4.3 15.3 - - + -
10C PRO* 3.4 37.9 - - + -
13C ILE* 3.5 22.0 - - + -
111C LYS 3.1 19.3 - - - +
112C VAL* 3.0 14.5 + - + +
114C VAL* 1.3 83.7 - - + +
116C LYS* 1.3 59.1 + - - +
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Residues in contact with LYS 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C PHE* 3.6 35.9 - - + -
112C VAL* 3.2 9.1 + - + +
113C ASN* 4.0 15.6 - - - +
114C VAL 3.1 6.6 - - - -
115C LEU* 1.3 82.6 - - - +
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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