Contacts of the helix formed by residues 103 - 119 (chain E) in PDB entry 5GJQ
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 103 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69E VAL* 4.8 0.2 - - - -
94E HIS* 5.6 5.8 - - + -
101E PRO 5.8 0.2 - - - -
102E VAL* 1.3 92.8 - - - +
104E VAL* 1.3 64.6 + - - +
105E GLU* 3.2 17.5 + - - +
106E TYR* 3.1 27.8 + - + +
107E ILE 3.3 3.8 + - - -
137E ASP* 3.1 20.2 + - - -
70e ASN* 6.1 0.9 - - - +
72e GLU* 5.9 3.6 - - - +
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Residues in contact with VAL 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E ASN* 4.2 1.1 - - - +
69E VAL* 4.0 17.5 - - + +
102E VAL 4.2 0.2 + - - -
103E THR* 1.3 72.0 + - - +
105E GLU* 1.3 58.0 + - - +
107E ILE* 3.2 8.5 - - - +
108E THR* 2.5 35.3 + - - +
133E ILE* 3.7 30.5 - - + +
134E VAL 4.1 1.8 - - - +
135E GLY* 3.7 41.3 - - - +
137E ASP* 2.9 21.4 + - - +
143E ARG* 4.7 6.3 - - + +
145E TYR* 4.5 12.6 - - + -
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Residues in contact with GLU 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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103E THR* 3.2 7.7 + - - +
104E VAL* 1.3 78.8 - - - +
106E TYR* 1.3 63.5 + - - +
108E THR* 3.5 6.0 + - - -
109E ARG* 2.9 41.3 + - - +
137E ASP* 4.5 4.0 + - - +
143E ARG* 5.9 0.7 - - - -
145E TYR* 3.0 38.6 + - + +
153E TYR* 4.9 13.3 + - + -
69e ARG 5.4 2.3 - - - +
70e ASN 5.5 3.6 - - - +
71e LYS* 5.5 7.4 - - - +
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Residues in contact with TYR 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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90E GLU* 3.2 37.0 + - + -
91E CYS* 6.4 0.2 - - - -
94E HIS* 3.4 43.6 - + + -
102E VAL* 4.7 10.1 - - + -
103E THR* 3.1 29.8 + - + +
105E GLU* 1.3 77.8 - - - +
107E ILE* 1.3 63.9 + - + +
109E ARG* 3.1 30.2 + - - +
110E TYR* 3.0 28.4 + + + +
66e TYR* 6.1 0.9 - + - -
70e ASN* 3.6 24.9 - - - +
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Residues in contact with ILE 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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65E LEU* 3.6 19.5 - - + -
69E VAL* 4.1 21.8 - - + -
87E ALA* 3.3 37.2 - - + +
90E GLU* 4.4 7.2 - - + -
91E CYS* 3.5 12.3 - - - +
102E VAL* 4.2 9.0 - - + -
103E THR 3.3 5.2 + - - +
104E VAL* 3.2 22.0 - - - +
106E TYR* 1.3 79.9 - - + +
108E THR* 1.3 68.3 + - - +
110E TYR* 3.3 14.4 + - + +
111E ILE* 3.0 26.6 + - + +
133E ILE* 4.2 7.9 - - + -
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Residues in contact with THR 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 VAL 2.5 25.7 + - - -
105E GLU* 3.5 8.3 - - - -
107E ILE* 1.3 78.3 - - - +
109E ARG* 1.3 57.1 + - - +
111E ILE* 3.4 2.4 + - - +
112E ALA* 2.9 27.5 + - - +
133E ILE* 3.4 30.5 - - + +
145E TYR* 3.7 31.9 - - + +
147E THR* 3.8 13.0 - - + +
153E TYR* 3.8 22.2 - - + -
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Residues in contact with ARG 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 GLU* 2.9 30.3 + - - +
106E TYR* 3.1 39.3 + - - +
108E THR* 1.3 75.9 - - - +
110E TYR* 1.3 61.8 + - - +
112E ALA* 3.6 5.6 - - + +
113E SER* 3.0 30.3 + - - -
153E TYR* 3.9 28.6 + - + +
69e ARG* 3.7 34.4 + - - +
70e ASN* 2.8 33.9 + - - +
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Residues in contact with TYR 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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86E ARG* 3.3 50.5 + - + -
87E ALA* 4.2 9.4 - - - -
89E VAL* 5.7 2.1 - - - +
90E GLU* 3.4 55.1 + - + +
106E TYR* 3.0 17.0 + + + +
107E ILE* 3.5 13.2 - - + +
108E THR 3.3 0.2 - - - -
109E ARG* 1.3 74.9 - - - +
111E ILE* 1.3 70.5 + - + +
113E SER* 2.6 23.3 + - - -
114E LEU* 3.0 19.6 + - + +
117E ARG* 5.0 10.1 - - - -
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Residues in contact with ILE 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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65E LEU* 4.3 7.6 - - + -
71E MET* 4.3 17.7 - - - -
83E VAL* 3.6 26.0 - - + -
87E ALA* 4.0 30.3 - - + -
107E ILE* 3.0 17.4 + - + +
108E THR 3.8 4.0 - - - +
110E TYR* 1.3 79.9 - - + +
112E ALA* 1.3 63.7 + - - +
114E LEU* 3.2 8.5 + - + +
115E LYS* 3.0 41.3 + - + +
131E ALA* 5.4 3.4 - - + -
133E ILE* 3.6 23.1 - - + -
147E THR* 4.6 6.7 - - + +
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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
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108E THR 2.9 18.7 + - - +
109E ARG* 3.6 5.6 - - + +
111E ILE* 1.3 76.7 - - - +
113E SER* 1.3 64.4 + - - +
115E LYS* 3.3 7.6 + - - +
116E GLN* 3.0 23.7 + - - +
147E THR* 4.7 6.9 - - + +
151E GLY* 3.3 28.4 - - - +
153E TYR* 4.0 23.8 - - + -
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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
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109E ARG 3.0 14.9 + - - -
110E TYR* 2.6 27.5 + - - -
112E ALA* 1.3 77.2 - - - +
114E LEU* 1.3 56.4 + - - +
116E GLN* 3.7 8.8 - - - +
117E ARG* 2.9 46.1 + - - +
86F LYS* 6.4 2.5 - - - -
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Residues in contact with LEU 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 VAL* 4.1 32.8 - - + +
86E ARG* 3.6 55.6 - - + +
110E TYR* 3.0 23.9 + - + +
111E ILE* 3.3 10.3 - - + +
113E SER* 1.3 78.4 + - - +
115E LYS* 1.3 64.4 + - - +
117E ARG* 3.1 22.4 + - - +
118E TYR* 3.0 35.8 + - + -
127E PHE* 3.8 8.5 - - + -
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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 VAL* 4.7 4.3 - - + -
111E ILE* 3.0 27.9 + - + +
112E ALA* 3.6 7.6 - - - +
114E LEU* 1.3 79.5 - - + +
116E GLN* 1.3 64.7 + - - +
118E TYR* 3.0 14.9 + - - +
119E THR* 3.0 17.0 + - - +
126E PRO* 5.3 0.9 - - - +
127E PHE* 4.0 24.3 + - + +
129E ILE* 3.5 40.1 + - - +
130E SER* 4.0 1.6 - - - +
131E ALA* 3.9 14.1 - - - +
147E THR* 2.6 33.6 + - - +
148E ASP 3.4 26.3 - - - +
149E PRO* 4.5 7.8 - - + +
151E GLY* 4.3 3.1 - - - +
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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 ALA 3.0 16.8 + - - +
113E SER* 3.7 8.9 - - - +
115E LYS* 1.3 76.6 - - - +
117E ARG* 1.3 64.3 + - - +
119E THR* 2.4 35.9 + - - +
120E GLN* 2.7 36.4 + - - +
150E SER 3.9 9.2 - - - +
151E GLY* 4.2 3.7 - - - -
83F ALA* 3.3 40.3 + - + +
84F ASP* 3.7 17.3 + - - +
87F THR* 3.5 13.3 + - - -
135F ARG* 4.6 0.2 - - - +
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Residues in contact with ARG 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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86E ARG* 3.9 24.2 - - - +
110E TYR* 5.0 10.9 - - - -
113E SER* 2.9 35.2 + - - +
114E LEU* 3.3 30.7 - - - +
115E LYS 3.1 0.2 - - - -
116E GLN* 1.3 83.6 + - - +
118E TYR* 1.3 64.6 + - + +
120E GLN* 3.2 11.8 + - + +
121E SER* 2.7 32.7 + - - +
124E ARG* 5.8 6.0 - - - +
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Residues in contact with TYR 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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123D GLN* 3.4 31.1 + - + -
124D PHE* 3.6 19.2 - + - -
8E THR* 4.7 1.2 + - - -
82E ILE* 5.6 2.4 - - - +
86E ARG* 4.5 10.9 + - - -
114E LEU* 3.0 25.4 + - + +
115E LYS 3.0 10.1 + - - +
117E ARG* 1.3 81.6 - - + +
119E THR* 1.3 59.2 + - - +
120E GLN 3.3 1.5 + - - -
121E SER* 4.4 3.0 + - - +
124E ARG* 3.8 55.7 + - + +
125E ARG 3.7 22.7 + - - +
126E PRO* 3.8 18.4 - - + +
127E PHE* 3.4 35.5 - + + -
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Residues in contact with THR 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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8E THR* 3.2 22.1 - - - +
16E LEU* 5.1 1.7 - - - +
19E VAL* 4.2 15.5 - - + -
115E LYS 3.3 12.8 - - - +
116E GLN* 2.4 37.4 + - - +
118E TYR* 1.3 77.6 - - - +
120E GLN* 1.3 53.0 + - - +
121E SER 3.8 1.1 - - - -
126E PRO* 4.1 13.7 - - + -
149E PRO 3.3 23.6 - - - +
150E SER* 4.2 6.7 + - - +
84F ASP* 5.0 1.0 + - - -
135F ARG* 2.5 34.9 + - - -
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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
------------------------------------------------------------
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