Contacts of the helix formed by residues 108 - 123 (chain E) 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 ALA 108 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E ARG* 6.1 0.6 - - - +
106E LYS 3.3 4.8 + - - -
107E LEU* 1.3 79.4 - - - +
109E VAL* 1.3 65.4 + - - +
110E GLU* 4.3 6.1 - - + +
111E ARG* 3.1 21.1 + - + +
112E ALA* 3.0 18.5 + - - +
142E ASP* 3.5 13.0 - - - +
76M GLU* 3.8 29.1 + - - +
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Residues in contact with VAL 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E HIS* 5.0 1.1 - - - +
74E MET* 3.6 22.0 - - + -
108E ALA* 1.3 67.0 - - - +
110E GLU* 1.3 66.5 + - - +
112E ALA* 3.0 3.8 + - - +
113E GLY 2.9 17.8 + - - -
138E ILE* 4.5 17.9 - - + +
140E GLY* 3.8 31.9 - - - +
142E ASP* 2.9 22.1 + - + +
147E HIS* 3.9 28.0 - - + -
149E LEU* 3.3 23.2 - - + +
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Residues in contact with GLU 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E ALA* 4.3 6.7 - - + +
109E VAL* 1.3 78.5 - - - +
111E ARG* 1.3 57.8 + - - +
113E GLY* 2.9 17.7 + - - -
114E HIS* 3.0 41.2 + - + +
142E ASP* 4.5 1.4 + - - -
147E HIS* 5.5 6.6 + - + -
149E LEU* 4.6 9.8 - - - +
159E GLU* 4.5 16.1 + - - +
63F LYS* 4.7 20.2 - - - +
65F VAL* 5.0 4.3 - - - +
68M ASP 3.6 5.1 - - - +
69M ASN* 5.6 0.2 - - - -
70M PRO* 3.6 34.3 - - - +
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Residues in contact with ARG 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E GLN* 5.8 0.8 + - - -
99E SER* 5.9 0.8 - - - -
107E LEU* 3.3 28.5 - - + +
108E ALA* 3.1 22.8 + - + +
110E GLU* 1.3 79.0 - - - +
112E ALA* 1.3 62.4 + - - +
114E HIS* 3.3 16.9 + - + +
115E LEU* 3.1 45.4 + - + +
64M GLU* 5.7 5.9 + - - +
67M TYR 5.7 5.6 + - - -
68M ASP 6.0 1.6 - - - -
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Residues in contact with ALA 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E MET* 3.8 34.1 - - + -
92E LEU* 3.8 16.9 - - + +
107E LEU* 3.9 12.9 - - + +
108E ALA 3.0 6.4 + - - +
109E VAL* 3.0 9.4 + - + +
111E ARG* 1.3 74.1 - - - +
113E GLY* 1.3 65.5 + - - +
115E LEU* 3.4 5.8 + - - +
116E LEU* 3.2 30.1 + - + +
138E ILE* 5.6 2.5 - - + -
149E LEU* 5.0 1.1 - - + -
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Residues in contact with GLY 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E VAL 2.9 7.3 + - - -
110E GLU 2.9 8.4 + - - -
112E ALA* 1.3 76.8 - - - +
114E HIS* 1.3 62.7 + - - +
116E LEU* 3.2 10.3 + - - +
117E CYS* 2.9 23.3 + - - +
149E LEU* 3.8 20.1 - - - +
157E VAL* 3.9 20.9 - - - +
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Residues in contact with HIS 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E GLU* 3.0 44.7 + - + +
111E ARG* 3.3 19.0 + - + +
113E GLY* 1.3 75.1 - - - +
115E LEU* 1.3 58.0 + - + +
117E CYS* 3.4 6.6 + - - +
118E ASP* 3.1 34.1 + - - +
65F VAL 5.7 4.7 - - - -
86F ARG* 3.5 39.0 + - - +
68M ASP* 3.7 29.0 + - + +
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Residues in contact with LEU 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E TYR* 3.8 33.3 + - + +
92E LEU* 5.3 2.2 - - + -
95E GLN* 4.0 25.1 - - + +
107E LEU* 3.9 26.5 - - + -
111E ARG* 3.1 48.5 + - + +
112E ALA* 3.8 5.6 - - - +
113E GLY 3.2 0.2 - - - -
114E HIS* 1.3 75.0 - - + +
116E LEU* 1.3 64.1 + - - +
118E ASP* 3.4 9.7 + - + +
119E LYS* 3.1 23.0 + - - +
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Residues in contact with LEU 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E LEU* 5.7 0.2 - - + -
88E LEU* 3.9 48.0 - - + +
91E TYR* 4.8 5.8 - - + -
92E LEU* 3.9 27.4 - - + -
112E ALA 3.2 17.1 + - - +
113E GLY* 3.2 7.2 + - - +
115E LEU* 1.3 71.4 - - - +
117E CYS* 1.3 67.9 + - - +
119E LYS* 3.2 4.4 + - - +
120E ALA* 3.0 24.9 + - - +
136E LEU* 4.5 13.9 - - + -
138E ILE* 3.6 31.2 - - + -
151E PHE* 3.7 17.8 - - + -
157E VAL* 5.1 0.4 - - + -
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Residues in contact with CYS 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E GLY 2.9 13.3 + - - +
114E HIS* 3.5 11.9 - - - +
115E LEU 3.3 0.2 - - - -
116E LEU* 1.3 78.0 - - - +
118E ASP* 1.3 66.2 - - - +
120E ALA* 3.3 2.9 + - - +
121E GLN* 3.0 20.6 + - - +
151E PHE* 4.7 0.2 - - - -
155E GLY* 2.9 34.7 - - - +
157E VAL* 4.2 11.3 - - + +
82F ILE* 6.1 1.6 - - - -
83F PRO* 4.3 18.4 - - - -
86F ARG* 3.8 25.4 - - - +
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Residues in contact with ASP 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E HIS 3.1 17.2 + - - +
115E LEU* 3.9 9.0 - - + +
116E LEU 3.3 0.2 - - - -
117E CYS* 1.3 76.9 - - - +
119E LYS* 1.3 62.4 + - - +
121E GLN* 3.4 15.5 + - - +
122E LYS* 3.4 31.6 + - - +
83F PRO 5.3 0.3 - - - +
86F ARG* 2.8 50.6 + - - +
87F HIS* 4.8 2.1 + - - -
90F ASN* 3.0 24.0 - - - +
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Residues in contact with LYS 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87E VAL* 5.0 9.9 - - - +
88E LEU* 3.7 24.9 - - + -
91E TYR* 3.7 50.0 - - + +
115E LEU 3.1 17.4 + - - +
116E LEU* 3.7 6.3 - - - +
117E CYS 3.2 0.4 - - - -
118E ASP* 1.3 76.5 - - - +
120E ALA* 1.3 66.2 + - - +
121E GLN 3.4 0.3 + - - -
122E LYS* 3.5 15.8 + - + +
123E ASN* 3.2 23.1 + - - +
132E TYR* 3.2 20.0 + - - +
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Residues in contact with ALA 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E LEU* 5.3 0.4 - - - +
116E LEU 3.0 16.8 + - - +
117E CYS 3.7 3.4 - - - +
119E LYS* 1.3 77.3 - - - +
121E GLN* 1.3 62.1 + - - +
123E ASN* 3.1 18.2 + - - +
124E THR* 3.4 13.1 - - - +
131E PRO* 5.5 0.3 - - - +
132E TYR* 3.9 17.2 - - + -
151E PHE* 3.8 23.8 - - + -
153E PRO 3.8 18.2 - - - +
154E SER 5.1 0.2 - - - -
155E GLY* 4.0 7.0 - - - -
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Residues in contact with GLN 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E CYS* 3.0 17.5 + - - +
118E ASP* 3.6 10.6 + - - +
119E LYS 3.2 0.2 - - - -
120E ALA* 1.3 76.1 - - - +
122E LYS* 1.3 67.2 + - - +
124E THR* 2.8 38.6 + - - +
125E GLN* 3.4 19.1 + - - +
154E SER 4.9 0.7 - - - -
155E GLY* 4.9 0.6 - - - -
83F PRO* 3.5 39.5 - - + +
84F ASP* 3.0 21.0 - - - +
87F HIS* 3.0 38.7 + - + +
132F PHE* 4.9 0.2 - - - -
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Residues in contact with LYS 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E ASP* 3.4 29.1 + - - +
119E LYS* 3.9 12.9 - - + +
120E ALA 3.3 0.6 - - - -
121E GLN* 1.3 89.7 - - - +
123E ASN* 1.3 65.1 + - - +
125E GLN* 3.6 4.1 + - - +
126E SER* 3.4 31.7 + - - +
87F HIS* 4.6 16.8 - - + +
90F ASN* 5.9 0.2 + - - -
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Residues in contact with ASN 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E THR* 3.7 9.0 + - - -
119E LYS* 3.2 19.8 + - - +
120E ALA 3.1 10.4 + - - +
121E GLN 3.1 0.8 - - - -
122E LYS* 1.3 81.1 - - - +
124E THR* 1.3 56.5 + - - +
125E GLN 3.3 4.8 + - - -
126E SER* 4.6 7.4 + - - +
129E GLY* 4.9 4.7 - - - -
130E ARG* 3.3 31.2 + - - +
131E PRO* 3.7 20.7 - - + -
132E TYR* 3.4 29.8 + - + -
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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