Contacts of the helix formed by residues 100 - 115 (chain E) in PDB entry 1SSP
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 PRO 100 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98E GLY 3.7 4.9 - - - +
99E LYS* 1.3 86.5 - - + +
101E TYR* 1.3 57.2 + - - +
103E ILE* 3.4 10.9 + - + +
104E LYS* 2.9 46.6 + - + +
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Residues in contact with TYR 101 (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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96E GLU* 2.6 38.7 + - - +
99E LYS* 3.2 22.8 + - + -
100E PRO* 1.3 79.0 - - - +
102E PHE* 1.3 72.0 + + + +
104E LYS* 3.5 8.5 + - - +
105E LEU* 2.8 35.1 + - + +
220E ARG 4.6 2.6 - - - +
221E GLY* 3.4 33.9 - - - -
224E GLN* 3.3 43.1 - - + +
225E PHE* 3.3 29.8 - - + -
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Residues in contact with PHE 102 (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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85E PHE* 5.1 0.7 - + - -
96E GLU 3.1 23.6 - - - +
97E PHE* 3.6 45.5 - + + +
99E LYS 3.0 3.4 + - - +
101E TYR* 1.3 90.7 - - + +
103E ILE* 1.3 61.4 + - - +
105E LEU* 3.5 11.7 - - + +
106E MET* 2.9 66.6 + - + +
126E PHE* 4.6 9.0 - + - -
222E TRP* 4.8 2.0 - + - -
225E PHE* 3.7 40.6 - + - -
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Residues in contact with ILE 103 (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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97E PHE 3.7 12.6 - - - +
98E GLY* 3.6 23.8 - - - +
99E LYS 3.1 11.1 + - - +
100E PRO* 3.8 10.3 - - + +
102E PHE* 1.3 78.2 - - - +
104E LYS* 1.3 65.1 + - + +
106E MET* 3.5 4.9 + - - +
107E GLY* 3.1 19.8 + - - -
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Residues in contact with LYS 104 (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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100E PRO* 2.9 32.0 + - + +
101E TYR* 3.7 7.0 - - - +
103E ILE* 1.3 78.6 - - + +
105E LEU* 1.3 58.6 + - - +
107E GLY* 3.2 2.6 + - - -
108E PHE* 2.9 28.6 + - - +
220E ARG 5.1 2.5 - - - +
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Residues in contact with LEU 105 (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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101E TYR* 2.8 23.1 + - + +
102E PHE* 3.2 16.8 + - + +
104E LYS* 1.3 73.3 - - - +
106E MET* 1.3 75.5 + - + +
108E PHE* 3.0 7.5 + - + +
109E VAL* 3.0 29.4 + - + +
220E ARG* 3.6 31.4 + - + +
221E GLY* 3.7 16.4 - - - +
222E TRP* 3.5 63.5 - - + +
225E PHE* 4.7 1.8 - - + -
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Residues in contact with MET 106 (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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102E PHE* 2.9 55.0 + - + +
103E ILE* 3.9 4.5 - - - +
105E LEU* 1.3 82.5 - - + +
107E GLY* 1.3 57.8 + - - +
109E VAL* 3.5 8.1 + - + +
110E ALA* 2.9 30.0 + - - +
126E PHE* 4.6 10.1 - - + -
222E TRP* 3.5 38.1 - - + -
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Residues in contact with GLY 107 (chain E).
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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103E ILE 3.1 14.8 + - - -
104E LYS* 3.6 4.7 - - - -
105E LEU 3.1 0.4 - - - -
106E MET* 1.3 75.2 - - - +
108E PHE* 1.3 58.8 + - - +
110E ALA* 3.3 6.6 + - - +
111E GLU* 2.9 30.5 + - - +
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Residues in contact with PHE 108 (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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104E LYS 2.9 12.5 + - - +
105E LEU* 3.4 10.8 - - + +
107E GLY* 1.3 74.1 - - - +
109E VAL* 1.3 70.5 + - + +
111E GLU* 3.3 7.6 + - + +
112E GLU* 2.9 56.6 + - + +
210E ARG* 5.7 0.9 - - - -
216E SER 4.8 1.3 - - - -
217E HIS* 3.6 38.1 - + + -
220E ARG* 3.5 67.3 - - + +
222E TRP* 6.0 0.2 - - - -
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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
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105E LEU* 3.0 17.2 + - + +
106E MET* 3.9 11.0 - - + +
108E PHE* 1.3 87.3 - - + +
110E ALA* 1.3 57.4 + - - +
112E GLU* 3.3 5.4 + - - +
113E ARG* 3.0 52.0 + - - +
118E VAL* 4.4 5.8 - - + -
125E VAL* 5.9 0.2 - - + -
208E THR* 3.8 35.7 - - + +
217E HIS* 4.8 1.1 - - - +
222E TRP* 4.0 21.3 - - + +
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Residues in contact with ALA 110 (chain E).
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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106E MET 2.9 18.6 + - - +
107E GLY* 3.4 8.5 - - - +
108E PHE 3.2 0.2 - - - -
109E VAL* 1.3 76.1 - - - +
111E GLU* 1.3 63.3 + - - +
113E ARG* 3.3 19.0 + - - +
114E LYS* 3.4 30.6 + - - +
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Residues in contact with GLU 111 (chain E).
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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107E GLY 2.9 18.3 + - - +
108E PHE* 3.6 8.5 - - + +
110E ALA* 1.3 76.4 - - - +
112E GLU* 1.3 64.6 + - + +
114E LYS* 3.1 26.6 + - - +
115E HIS* 2.9 53.0 + - + -
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Residues in contact with GLU 112 (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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108E PHE* 2.9 48.6 + - + +
109E VAL 3.5 4.9 - - - +
111E GLU* 1.3 78.0 - - + +
113E ARG* 1.3 52.0 + - - +
114E LYS 3.1 0.2 - - - -
115E HIS* 3.0 4.4 + - - -
116E TYR* 2.7 47.4 + - - +
118E VAL* 3.7 12.7 - - + +
210E ARG* 2.8 46.4 + - - +
217E HIS* 2.8 28.2 + - + +
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Residues in contact with ARG 113 (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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109E VAL* 3.0 35.5 + - - +
110E ALA* 3.3 10.2 + - - +
112E GLU* 1.3 75.1 - - - +
114E LYS* 1.3 61.6 + - + +
115E HIS 3.3 0.2 - - - -
116E TYR 3.2 16.3 - - - +
118E VAL* 3.0 49.8 + - + +
120E PRO 2.8 22.2 + - - -
121E PRO* 4.1 1.0 - - - +
122E PRO* 3.6 36.2 - - - +
125E VAL* 3.5 20.4 - - - +
208E THR* 4.1 0.8 - - - +
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Residues in contact with LYS 114 (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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110E ALA* 3.4 30.2 + - - +
111E GLU* 3.1 27.5 + - - +
112E GLU 3.1 0.8 - - - -
113E ARG* 1.3 78.4 - - + +
115E HIS* 1.3 73.3 + - + +
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Residues in contact with HIS 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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111E GLU* 2.9 53.4 + - + -
112E GLU* 3.0 2.9 + - - +
114E LYS* 1.3 92.7 + - + +
116E TYR* 1.3 87.2 + + + +
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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