Contacts of the helix formed by residues 102 - 118 (chain E) in PDB entry 5AKF
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 ASN 102 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8E SER* 5.2 4.6 + - - -
100E LEU 3.3 4.5 + - - +
101E PHE* 1.3 78.0 - - - +
103E MET* 1.3 64.9 + - - +
104E ARG* 3.0 15.2 + - - +
105E GLU* 2.7 47.0 + - - +
106E GLN* 3.0 16.9 + - - +
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Residues in contact with MET 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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102E ASN* 1.3 74.4 - - - +
104E ARG* 1.3 63.2 + - - +
106E GLN* 3.1 26.5 + - - +
107E ILE* 3.1 32.5 + - + +
144E ASN* 3.7 27.1 - - - +
145E LEU* 3.7 29.6 - - + -
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Residues in contact with ARG 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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5E GLU 3.2 48.8 + - - +
6E ASN* 4.5 11.1 + - - +
8E SER* 4.7 5.6 - - - -
9E GLY* 5.0 9.2 - - - +
102E ASN* 3.0 14.7 + - - +
103E MET* 1.3 79.5 - - - +
105E GLU* 1.3 61.1 + - + +
107E ILE* 3.4 8.3 + - - +
108E ALA* 3.2 22.4 + - - +
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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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8E SER* 4.3 28.9 - - - +
9E GLY* 5.2 0.7 - - - +
12E ALA* 3.5 12.1 - - + +
94E MET* 4.0 18.5 - - - +
100E LEU 4.3 1.9 - - - +
101E PHE* 3.4 31.0 - - + -
102E ASN* 2.7 49.1 + - - +
104E ARG* 1.3 75.9 - - + +
106E GLN* 1.3 58.6 + - - +
108E ALA* 4.4 0.9 - - - -
109E PHE* 2.8 33.3 + - - +
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Residues in contact with GLN 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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99E ARG 5.7 0.4 + - - -
101E PHE* 2.8 23.9 + - + +
102E ASN* 3.0 18.6 + - - +
103E MET* 3.1 26.3 + - - +
105E GLU* 1.3 76.1 - - - +
107E ILE* 1.3 59.3 + - + +
109E PHE* 3.9 0.7 - - - +
110E ILE* 2.9 39.1 + - + +
141E TRP* 3.3 69.5 - - + +
144E ASN* 5.0 4.6 + - - +
145E LEU* 4.8 3.9 - - + +
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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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103E MET* 3.1 23.8 + - + +
104E ARG* 3.6 8.7 - - - +
106E GLN* 1.3 75.1 - - - +
108E ALA* 1.3 55.6 + - - +
110E ILE* 3.0 6.5 + - - +
111E LYS* 2.8 35.9 + - - +
145E LEU* 3.7 25.4 - - + -
176E THR* 3.8 13.2 - - + +
177E ILE* 3.4 34.8 - - + +
180E SER* 3.8 32.5 - - - +
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Residues in contact with ALA 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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9E GLY* 3.2 34.1 - - - +
12E ALA* 3.6 8.5 - - + -
13E TYR* 3.3 15.8 - - + +
104E ARG 3.2 14.1 + - - +
107E ILE* 1.3 80.0 - - - +
109E PHE* 1.3 62.3 - - - +
111E LYS* 3.3 11.0 + - - +
112E GLY 3.0 18.5 + - - -
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Residues in contact with PHE 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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12E ALA* 3.3 22.1 - - + +
15E LEU* 4.0 17.0 - - + -
16E GLY* 3.6 21.0 - - - -
19E ILE* 4.4 10.3 - - + -
98E ILE* 3.8 24.2 - - + -
101E PHE* 3.9 21.8 - + + -
105E GLU 2.8 18.1 + - - +
106E GLN 4.0 2.0 - - - +
108E ALA* 1.3 76.4 - - - +
110E ILE* 1.3 63.6 + - + +
112E GLY* 3.4 0.9 + - - -
113E LEU* 3.0 49.5 + - + +
134E LEU* 4.0 13.2 - - + -
138E VAL* 4.2 13.2 - - + -
141E TRP* 3.8 16.4 - + + -
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Residues in contact with ILE 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 GLN 2.9 30.0 + - - +
107E ILE* 3.5 4.0 - - - +
109E PHE* 1.3 79.0 - - + +
111E LYS* 1.3 59.0 + - - +
113E LEU* 3.9 4.4 - - - +
114E TYR* 2.9 27.9 + - - +
127E ILE* 5.2 7.5 - - + +
138E VAL* 4.0 24.2 - - + -
141E TRP* 4.2 26.2 - - + -
142E LEU* 4.0 23.1 - - + -
145E LEU* 4.5 9.2 - - + -
173E PHE* 4.4 15.9 - - + -
177E ILE* 3.2 23.3 - - + -
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Residues in contact with LYS 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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13E TYR* 4.0 18.2 - - + -
107E ILE* 2.8 20.9 + - - +
108E ALA* 3.5 10.3 - - - +
110E ILE* 1.3 73.9 - - - +
112E GLY* 1.3 57.6 + - - +
114E TYR* 3.2 6.1 + - - +
115E VAL* 2.9 37.8 + - + +
177E ILE* 2.9 27.8 - - - +
178E LEU* 3.9 22.9 + - + +
180E SER* 2.8 44.2 + - - +
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Residues in contact with GLY 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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13E TYR* 3.5 36.7 - - - -
16E GLY 3.8 7.2 - - - -
17E LEU* 3.5 12.6 - - - +
108E ALA 3.0 11.3 + - - -
109E PHE 3.8 1.6 - - - -
111E LYS* 1.3 76.8 - - - +
113E LEU* 1.3 62.2 + - - +
114E TYR 3.2 0.2 + - - -
115E VAL* 3.3 2.0 + - - +
116E ALA* 3.0 19.8 + - - +
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Residues in contact with LEU 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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16E GLY* 3.5 21.4 - - - +
19E ILE* 4.2 16.6 - - + -
20E GLY* 4.1 5.8 - - - -
109E PHE* 3.0 37.8 + - + +
110E ILE* 4.0 4.7 - - - +
112E GLY* 1.3 74.0 - - - +
114E TYR* 1.3 57.0 + - - +
116E ALA* 4.5 0.7 - - - +
117E GLU* 2.8 56.2 + - + +
118E GLY 3.8 0.2 + - - -
127E ILE* 4.1 26.4 - - + +
129E ASN* 4.5 5.4 - - - +
134E LEU* 4.5 10.3 - - + -
135E LEU* 4.8 4.0 - - + -
138E VAL* 4.2 17.0 - - + -
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Residues in contact with TYR 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 ILE 2.9 20.0 + - - +
111E LYS 3.7 3.8 - - - +
112E GLY 3.1 0.2 - - - -
113E LEU* 1.3 74.5 - - - +
115E VAL* 1.3 63.4 + - - +
118E GLY* 2.6 32.4 + - - +
119E ASP* 2.6 44.5 + - - +
120E MET* 3.9 11.5 - - - +
122E LEU* 3.6 15.9 - - + -
124E ARG 3.6 0.5 + - - -
125E LEU* 3.5 16.7 - - + +
126E ARG 3.2 31.2 + - - -
127E ILE* 3.4 28.4 - - + +
165E ILE* 4.5 0.9 - - + -
173E PHE* 3.9 20.0 - + + -
178E LEU* 4.1 24.9 - - + -
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Residues in contact with VAL 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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13E TYR* 3.8 20.0 - - + +
17E LEU* 3.9 17.9 - - + -
21E ASP* 4.7 0.7 - - - +
47E LEU* 5.9 10.1 - - + -
51E HIS* 5.9 2.5 - - + +
111E LYS* 2.9 24.5 + - + +
112E GLY 3.5 7.0 - - - +
114E TYR* 1.3 76.6 - - + +
116E ALA* 1.3 62.5 + - - +
118E GLY 4.7 0.2 + - - -
120E MET* 4.2 28.8 - - + +
178E LEU* 5.9 2.7 - - + -
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Residues in contact with ALA 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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16E GLY 4.2 5.2 - - - +
17E LEU* 4.3 7.9 - - + -
20E GLY* 3.9 20.0 - - - -
21E ASP* 3.3 30.5 - - + +
112E GLY 3.0 16.2 + - - +
113E LEU 3.9 1.8 - - - +
114E TYR 3.1 0.2 - - - -
115E VAL* 1.3 79.7 - - - +
117E GLU* 1.3 59.5 + - - +
118E GLY 3.6 0.4 - - - -
1182E MN 2.4 27.5 + - - -
16H C 2.9 8.2 + - - +
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Residues in contact with GLU 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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19E ILE 4.2 0.9 - - - +
20E GLY* 3.2 41.9 - - - +
113E LEU* 2.8 26.6 + - + +
116E ALA* 1.3 72.9 - - - +
118E GLY* 1.3 60.7 + - - +
127E ILE* 4.2 7.6 - - + -
128E TRP* 3.2 47.2 + - - +
129E ASN* 2.9 24.9 + - - -
15H C 2.9 38.9 + - - +
16H C 3.7 10.2 + - - +
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Residues in contact with GLY 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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113E LEU 3.8 0.2 + - - -
114E TYR* 2.6 32.8 + - - -
116E ALA 3.6 1.0 - - - -
117E GLU* 1.3 83.3 - - - +
119E ASP* 1.3 61.7 + - - -
120E MET* 3.2 13.3 + - - +
126E ARG 3.1 11.4 - - - -
127E ILE* 4.4 0.7 - - - -
128E TRP* 3.7 2.9 - - - -
16H C 3.6 17.2 - - - +
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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