Contacts of the helix formed by residues 104 - 118 (chain E) in PDB entry 5LEZ
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 104 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101E ARG* 3.9 17.0 - - - +
102E PRO 3.3 9.4 - - - +
103E LEU* 1.4 93.7 - - + +
105E VAL* 1.3 66.7 + - - +
106E SER* 3.3 7.4 - - - +
107E ARG* 3.2 37.4 + - + +
108E LEU* 3.1 17.0 + - - +
138E ASP* 3.7 16.8 - - + +
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Residues in contact with VAL 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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69E HIS* 4.3 5.8 - - + -
70E ILE* 4.1 22.9 - - + -
103E LEU 4.2 0.9 - - - -
104E PRO* 1.3 71.0 - - - +
106E SER* 1.3 58.6 + - - +
108E LEU* 3.2 5.4 + - + +
109E VAL* 3.0 26.7 + - + +
134E ILE* 4.3 20.6 - - + -
136E GLY* 3.9 27.4 - - - +
137E TYR 4.1 3.4 - - - +
138E ASP* 2.9 23.1 + - - +
143E HIS* 3.9 17.5 - - + -
145E PHE* 3.8 23.8 - - + -
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Residues in contact with SER 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E PRO* 4.6 6.9 - - - +
105E VAL* 1.3 76.5 - - - +
107E ARG* 1.3 63.7 + - - +
109E VAL* 3.5 3.8 + - - +
110E SER* 3.1 29.7 + - - -
138E ASP* 4.5 2.2 + - - -
143E HIS* 5.6 5.4 + - - -
145E PHE* 4.0 26.5 - - - -
153E TYR* 5.5 1.6 - - - -
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Residues in contact with ARG 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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101E ARG* 4.1 22.0 - - - +
103E LEU* 4.0 13.7 - - + -
104E PRO* 3.2 34.7 + - + +
106E SER* 1.3 78.1 + - - +
108E LEU* 1.3 65.6 + - - +
110E SER* 3.3 9.2 + - - -
111E LEU* 3.1 29.3 + - + +
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Residues in contact with LEU 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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66E VAL* 4.3 1.6 - - + -
70E ILE* 3.6 27.4 - - + -
87E PHE* 5.3 0.7 - - + -
88E MET* 3.6 57.0 - - + +
91E GLU* 4.0 12.8 - - + -
92E CYS* 3.8 11.0 - - - -
103E LEU* 3.7 26.9 - - + +
104E PRO 3.1 9.7 + - - +
105E VAL* 3.5 11.0 - - + +
107E ARG* 1.3 75.0 - - - +
109E VAL* 1.3 65.2 + - + +
111E LEU* 3.2 10.5 + - + +
112E ILE* 3.0 20.7 + - + +
134E ILE* 5.5 1.8 - - + -
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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
----------------------------------------------------------
105E VAL* 3.0 17.5 + - + +
106E SER* 3.7 8.1 - - - +
107E ARG 3.2 0.4 - - - -
108E LEU* 1.3 78.0 - - + +
110E SER* 1.3 57.8 + - - +
112E ILE* 3.0 10.6 + - - +
113E GLY* 2.9 24.3 + - - -
134E ILE* 4.0 16.2 - - + -
145E PHE* 3.6 39.0 - - + -
147E THR* 4.4 8.5 - - + -
153E TYR* 3.3 43.9 - - + -
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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 SER 3.1 15.4 + - - -
107E ARG* 3.5 11.7 - - - -
109E VAL* 1.3 74.0 - - - +
111E LEU* 1.3 61.1 + - - +
113E GLY* 3.2 1.9 + - - -
114E SER* 3.0 29.9 + - - -
153E TYR* 3.3 26.1 + - - -
89F ASP* 5.6 0.2 - - - +
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Residues in contact with LEU 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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87E PHE* 3.9 18.3 - - + -
91E GLU* 3.5 39.3 - - + +
103E LEU* 4.3 18.6 - - + -
107E ARG* 3.1 19.9 + - + +
108E LEU* 3.2 8.7 + - + +
110E SER* 1.3 74.4 - - - +
112E ILE* 1.3 63.9 + - - +
114E SER* 3.9 6.1 - - - -
115E LYS* 2.9 25.6 + - - +
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Residues in contact with ILE 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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84E LEU* 4.4 13.2 - - + -
87E PHE* 4.3 12.8 - - + -
88E MET* 3.6 48.9 - - + -
108E LEU* 3.0 15.2 + - + +
109E VAL* 3.0 12.4 + - - +
111E LEU* 1.3 76.6 - - - +
113E GLY* 1.3 52.6 + - - +
115E LYS* 3.3 1.7 + - - -
116E THR* 2.8 57.5 + - + +
132E LEU* 4.6 2.5 - - + -
134E ILE* 3.8 18.2 - - + -
147E THR* 4.2 22.0 - - + -
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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
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109E VAL 2.9 13.4 + - - -
110E SER 3.2 4.2 + - - -
112E ILE* 1.3 76.3 - - - +
114E SER* 1.3 61.8 + - - +
116E THR* 4.0 1.3 - - - -
117E GLN* 3.1 27.2 + - - +
151E ALA* 3.4 25.3 - - - +
153E TYR* 4.3 11.9 - - - -
82F ALA* 5.3 0.6 - - - +
85F ARG* 6.1 2.9 - - - -
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Residues in contact with SER 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 SER 3.0 15.2 + - - -
111E LEU* 3.9 7.6 - - - -
113E GLY* 1.3 79.6 - - - +
115E LYS* 1.3 63.1 + - - +
117E GLN* 3.5 10.3 + - - +
118E ILE* 3.5 21.5 + - - +
86F SER* 6.0 6.3 - - - +
89F ASP* 4.3 19.2 + - - +
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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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83E LEU* 6.3 1.6 - - - -
84E LEU* 4.9 3.8 - - + -
87E PHE* 3.6 53.0 - - + -
111E LEU 2.9 17.7 + - - +
112E ILE* 3.8 2.9 - - - +
114E SER* 1.3 79.4 + - - +
116E THR* 1.3 62.7 + - + +
117E GLN 3.4 0.5 + - - -
118E ILE* 3.5 14.7 + - + +
119E PRO* 3.4 15.6 - - - +
128E TYR* 3.4 28.3 - - + +
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Residues in contact with THR 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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84E LEU* 3.8 28.5 - - + -
112E ILE* 2.8 37.7 + - + +
113E GLY* 4.0 0.2 - - - -
115E LYS* 1.3 72.3 - - + +
117E GLN* 1.3 62.8 + - - +
118E ILE 3.3 0.2 - - - -
119E PRO* 3.5 10.5 - - - +
120E THR* 3.6 13.9 - - - +
128E TYR* 3.5 39.2 + - + -
148E 6V1 4.6 4.6 + - - +
149E PRO 4.8 3.1 - - - +
151E ALA* 3.4 26.3 - - - +
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Residues in contact with GLN 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 3.1 19.8 + - - +
114E SER* 3.9 6.1 - - - +
115E LYS 3.2 0.6 - - - -
116E THR* 1.3 78.3 - - - +
118E ILE* 1.3 77.7 + - - +
119E PRO 3.4 0.2 - - - -
120E THR* 2.6 32.9 + - - +
121E GLN* 2.9 29.7 + - - +
151E ALA* 3.4 11.8 - - + +
82F ALA* 3.6 30.7 - - + +
83F ASP* 3.0 24.7 + - - +
86F SER* 3.9 20.4 + - - -
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Residues in contact with ILE 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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114E SER* 3.5 20.6 - - - +
115E LYS* 3.7 13.9 - - + +
117E GLN* 1.3 87.4 + - - +
119E PRO* 1.3 74.0 - - + +
120E THR 3.1 1.2 + - - -
121E GLN* 3.3 11.7 + - - +
122E ARG* 3.6 27.3 - - + +
125E ARG* 4.7 9.4 - - - +
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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