Contacts of the helix formed by residues 97 - 111 (chain E) in PDB entry 2FL0
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 GLY 97 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17E ASN* 4.3 16.7 - - - +
93E LEU 3.5 11.7 + - - -
94E GLU* 4.3 3.4 - - - -
95E GLN 2.7 1.6 - - - -
96E ALA* 1.3 80.8 - - - +
98E LEU* 1.3 66.5 + - - +
99E PRO 3.5 1.6 - - - -
100E ASP* 3.2 15.4 + - - +
101E LEU* 3.2 17.6 + - - +
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Residues in contact with LEU 98 (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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94E GLU 3.7 14.5 + - - +
95E GLN* 3.1 6.8 + - + +
97E GLY* 1.3 73.8 - - - +
99E PRO* 1.3 75.5 - - + +
101E LEU* 2.7 19.9 + - + +
102E LYS* 2.9 32.0 + - + +
124E LEU* 3.5 28.7 - - + -
127E GLU* 4.0 20.9 - - + -
128E GLU* 4.8 15.9 - - + +
131E ILE* 3.7 20.0 - - + -
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Residues in contact with PRO 99 (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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95E GLN 3.0 28.3 - - - +
96E ALA* 4.2 4.7 - - - +
97E GLY 3.6 4.3 - - - +
98E LEU* 1.3 81.0 - - + +
100E ASP* 1.3 58.8 + - - +
102E LYS* 3.8 7.3 - - + +
103E ALA* 2.9 31.2 + - - +
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Residues in contact with ASP 100 (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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10E HIS* 5.0 1.9 + - - -
13E LYS* 3.0 39.0 + - + +
14E ILE* 4.1 11.9 - - + +
17E ASN* 3.5 22.5 + - - +
96E ALA 3.8 15.2 - - - +
97E GLY 3.2 8.0 + - - +
98E LEU 3.0 1.2 - - - -
99E PRO* 1.3 78.8 - - - +
101E LEU* 1.3 64.9 + - - +
103E ALA* 3.3 6.4 + - - +
104E ALA* 2.9 24.8 + - - +
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Residues in contact with LEU 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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14E ILE* 3.7 27.5 - - + +
18E GLU* 5.5 0.9 - - - +
97E GLY 3.2 11.6 + - - +
98E LEU* 2.7 21.5 + - + +
100E ASP* 1.3 74.4 - - - +
102E LYS* 1.3 56.8 + - - +
104E ALA* 3.3 3.5 + - - +
105E ILE* 2.9 34.0 + - - +
120E LEU* 4.1 19.3 - - + +
123E ILE* 3.8 26.2 - - + -
124E LEU* 3.9 26.9 - - + -
127E GLU* 3.5 32.3 - - + -
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Residues in contact with LYS 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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98E LEU* 2.9 33.3 + - + +
99E PRO* 4.0 6.1 - - + +
101E LEU* 1.3 71.6 - - - +
103E ALA* 1.3 61.7 + - - +
104E ALA 3.1 1.3 - - - -
105E ILE* 3.9 7.1 - - + +
106E ALA* 3.0 31.0 + - - +
124E LEU* 4.5 31.0 - - + -
128E GLU* 4.6 13.3 + - - -
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Residues in contact with ALA 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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10E HIS* 4.0 14.2 - - + -
99E PRO 2.9 19.8 + - - +
100E ASP* 3.7 7.6 - - - +
102E LYS* 1.3 77.1 - - - +
104E ALA* 1.3 56.9 + - - +
106E ALA* 3.8 6.3 - - - +
107E TYR* 3.1 25.6 + - - +
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Residues in contact with ALA 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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10E HIS* 3.9 27.1 - - + +
11E LEU 5.7 0.2 - - - +
14E ILE* 3.8 13.5 - - + -
100E ASP 2.9 17.2 + - - +
101E LEU 3.5 2.9 - - - +
102E LYS 3.1 0.2 - - - -
103E ALA* 1.3 76.4 - - - +
105E ILE* 1.3 66.4 + - - +
107E TYR* 3.1 3.3 + - - +
108E CYS* 2.9 28.0 + - - -
120E LEU* 3.4 21.1 - - + -
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Residues in contact with ILE 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 LEU* 2.9 24.9 + - + +
102E LYS* 3.9 7.2 - - + +
104E ALA* 1.3 74.2 - - - +
106E ALA* 1.3 65.2 + - - +
108E CYS* 3.2 7.0 + - - +
109E GLU* 3.0 21.5 + - - +
117E ARG* 3.5 42.6 - - + +
120E LEU* 3.7 23.3 - - + +
121E GLU* 4.2 20.9 - - + +
124E LEU* 3.5 33.9 - - + -
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Residues in contact with ALA 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 LYS 3.0 17.8 + - - +
103E ALA* 3.8 7.9 - - - +
105E ILE* 1.3 79.0 - - - +
107E TYR* 1.3 61.6 + - - +
109E GLU* 3.2 22.1 - - - +
110E SER* 3.2 8.7 + - - -
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Residues in contact with TYR 107 (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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4E ASP* 3.2 9.9 + - - -
6E ILE* 3.1 45.9 - - + +
7E VAL* 3.6 25.8 - - + -
10E HIS* 3.7 28.3 - + + +
103E ALA 3.1 18.2 + - - +
104E ALA 3.1 7.0 + - - +
106E ALA* 1.3 74.3 - - - +
108E CYS* 1.3 68.2 + - - +
110E SER* 2.6 35.6 + - - -
111E VAL* 3.1 29.0 + - + +
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Residues in contact with CYS 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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7E VAL* 4.1 18.6 - - - -
10E HIS* 6.2 1.6 - - - -
11E LEU* 5.2 1.3 - - - -
104E ALA* 2.9 18.5 + - - -
105E ILE 3.6 7.2 - - - +
107E TYR* 1.3 80.6 - - - +
109E GLU* 1.3 63.6 + - - +
111E VAL* 3.3 5.9 + - - -
112E GLY* 2.9 4.5 + - - -
113E ASP* 2.9 42.8 + - - +
116E SER* 3.8 26.0 - - - -
117E ARG* 4.0 11.9 - - + -
120E LEU* 4.1 14.6 - - - -
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Residues in contact with GLU 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 ILE 3.0 11.1 + - - +
106E ALA* 3.2 15.7 - - - +
108E CYS* 1.3 76.9 - - - +
110E SER* 1.3 62.0 + - - +
112E GLY* 3.2 12.0 + - - -
114E TYR* 3.4 20.0 + - - -
117E ARG* 2.6 37.0 + - - +
109G GLU* 4.5 13.3 - - - +
117G ARG* 2.6 31.0 + - - -
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Residues in contact with SER 110 (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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106E ALA 3.2 7.1 + - - -
107E TYR* 2.6 31.9 + - - -
109E GLU* 1.3 80.8 - - - +
111E VAL* 1.3 67.9 + - - +
112E GLY 3.7 0.5 + - - -
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Residues in contact with VAL 111 (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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4E ASP* 3.9 20.2 - - + +
7E VAL* 3.6 27.1 - - + -
107E TYR* 3.1 42.6 + - + +
108E CYS 3.8 3.1 - - - +
110E SER* 1.3 84.5 - - - +
112E GLY* 1.3 59.8 + - - +
113E ASP* 3.3 12.9 + - + +
102G LYS* 5.7 0.3 - - - +
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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