Contacts of the helix formed by residues 111 - 121 (chain E) in PDB entry 5FLM
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 THR 111 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81E LYS* 5.8 1.8 - - - +
82E VAL 3.5 21.7 + - - +
83E GLY* 3.9 9.9 - - - -
84E ILE* 4.6 2.2 - - + +
110E MET* 1.3 73.3 - - - +
112E PRO* 1.3 70.3 - - - +
113E SER* 3.9 10.4 + - - +
114E ALA* 2.7 39.7 + - + +
115E LYS* 3.2 7.8 + - - +
38N T 4.2 1.9 + - - -
39N T 3.2 39.3 + - - +
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Residues in contact with PRO 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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110E MET 3.5 4.2 - - - +
111E THR* 1.3 90.3 - - - +
113E SER* 1.3 57.7 + - - +
115E LYS* 3.3 17.0 + - + +
116E GLN* 2.9 36.9 + - - +
4T C 3.8 38.8 - - + +
5T T 3.9 22.7 - - - +
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Residues in contact with SER 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E ILE* 3.5 23.1 - - - +
111E THR* 3.1 10.5 + - - -
112E PRO* 1.3 81.3 - - - +
114E ALA* 1.3 53.0 + - - +
116E GLN* 3.8 14.5 + - - +
117E SER* 2.6 37.5 + - - -
39N T 4.8 13.3 + - - -
4T C 5.0 9.4 - - - -
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Residues in contact with ALA 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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83E GLY 4.3 9.9 - - - -
84E ILE* 4.1 2.9 - - - +
87E ILE* 3.6 23.9 - - + +
110E MET* 3.7 13.9 - - + -
111E THR* 2.7 34.5 + - + +
113E SER* 1.3 71.3 - - - +
115E LYS* 1.3 58.9 + - - +
117E SER* 3.2 8.5 + - - -
118E LEU* 2.9 33.4 + - - +
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Residues in contact with LYS 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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110E MET* 4.0 29.5 + - + +
111E THR 3.2 4.8 + - - +
112E PRO* 3.6 15.2 - - + +
114E ALA* 1.3 73.5 - - - +
116E GLN* 1.3 62.1 + - + +
118E LEU* 2.9 28.3 + - + +
119E VAL* 3.0 18.8 + - + +
129E GLN* 3.4 33.0 - - - +
6T C 6.0 0.4 + - - -
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Residues in contact with GLN 116 (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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112E PRO* 2.9 22.2 + - + +
113E SER* 3.9 13.0 + - - +
115E LYS* 1.3 76.3 - - + +
117E SER* 1.3 55.9 + - - +
119E VAL* 3.2 9.5 + - - +
120E ASP* 2.8 38.1 + - - +
4T C 4.1 27.5 + - - +
5T T 4.7 10.7 + - - +
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Residues in contact with SER 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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84E ILE* 3.6 26.5 - - - +
87E ILE* 5.5 8.8 - - - +
113E SER 2.6 24.5 + - - -
114E ALA* 3.5 9.9 - - - -
115E LYS 3.1 0.2 - - - -
116E GLN* 1.3 74.7 - - - +
118E LEU* 1.3 66.1 + - - +
120E ASP* 3.3 26.5 + - - +
121E MET* 4.4 11.4 + - - +
127E LEU* 5.9 0.7 - - - +
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Residues in contact with LEU 118 (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 ILE* 3.8 25.4 - - + -
104E ILE* 4.6 7.0 - - + -
110E MET* 5.0 6.3 - - + -
114E ALA 2.9 18.0 + - - +
115E LYS* 2.9 16.0 + - + +
117E SER* 1.3 78.6 - - - +
119E VAL* 1.3 62.6 + - + +
120E ASP 3.5 0.2 + - - -
121E MET* 4.1 14.8 + - - +
125E TYR 5.2 0.3 - - - +
126E ILE* 5.6 0.3 - - - -
127E LEU* 3.6 59.3 + - + +
128E GLU 5.1 0.2 - - - -
129E GLN* 4.3 34.8 - - + +
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Residues in contact with VAL 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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115E LYS* 3.0 15.9 + - + +
116E GLN* 3.2 9.8 + - - +
118E LEU* 1.3 77.2 - - + +
120E ASP* 1.3 66.8 + - - +
121E MET 3.4 1.0 + - - -
122E ALA* 4.3 8.7 + - - +
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Residues in contact with ASP 120 (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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116E GLN* 2.8 25.6 + - - +
117E SER* 3.3 28.1 + - - +
118E LEU 3.2 1.2 - - - -
119E VAL* 1.3 80.0 - - - +
121E MET* 1.3 62.7 + - + +
122E ALA* 3.6 2.9 + - - +
123E PRO* 5.4 0.2 - - - +
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Residues in contact with MET 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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91E CYS* 3.7 20.9 - - - -
117E SER 4.5 11.7 - - - +
118E LEU* 4.1 9.6 + - - +
119E VAL 3.4 2.4 - - - -
120E ASP* 1.3 74.8 - - + +
122E ALA* 1.3 60.4 + - - +
123E PRO* 4.4 4.3 - - + -
124E LYS* 3.7 20.9 - - + -
125E TYR* 2.9 76.9 - - + +
126E ILE* 4.6 1.9 - - - +
127E LEU* 6.0 5.4 - - + -
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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