Contacts of the helix formed by residues 102 - 118 (chain F) in PDB entry 5AKM
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8F SER* 5.2 4.2 + - - -
100F LEU 3.4 2.9 + - - +
101F PHE* 1.3 75.0 - - - +
103F MET* 1.3 60.4 + - - +
104F ARG* 3.4 11.4 + - - +
105F GLU* 3.0 42.6 + - - +
106F GLN* 2.8 29.0 + - - +
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Residues in contact with MET 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F ASN* 1.3 75.7 - - - +
104F ARG* 1.3 62.8 + - - +
106F GLN* 3.6 15.2 - - - +
107F ILE* 2.9 47.5 + - + +
144F ASN* 6.2 2.2 - - - -
145F LEU* 3.8 25.1 - - + -
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Residues in contact with ARG 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F ASN* 5.9 5.4 - - - +
8F SER* 4.0 19.1 + - - +
9F GLY* 4.2 20.4 - - - +
102F ASN* 3.3 9.8 + - - +
103F MET* 1.3 76.7 - - - +
105F GLU* 1.3 58.5 + - - +
107F ILE* 3.6 5.3 + - - +
108F ALA* 3.0 27.0 + - - +
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Residues in contact with GLU 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F SER* 3.5 39.9 - - - +
12F ALA* 3.3 12.5 - - + +
94F MET* 4.4 9.6 - - - +
100F LEU 4.5 0.9 - - - +
101F PHE* 3.3 29.6 - - + -
102F ASN* 3.0 45.9 + - - +
104F ARG* 1.3 75.0 - - - +
106F GLN* 1.3 60.9 + - - +
108F ALA* 4.4 0.4 - - - -
109F PHE* 2.9 32.4 + - - +
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Residues in contact with GLN 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F ARG 5.6 0.8 + - - -
101F PHE* 2.7 30.4 + - + -
102F ASN* 2.8 23.1 + - - +
103F MET* 3.2 13.3 + - - +
105F GLU* 1.3 72.0 - - - +
107F ILE* 1.3 60.3 + - + +
109F PHE* 3.2 2.4 + - - +
110F ILE* 2.9 38.6 + - + +
141F TRP* 3.4 67.8 - - + +
144F ASN* 5.5 5.0 + - - +
145F LEU* 5.4 4.9 - - + +
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Residues in contact with ILE 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F MET* 2.9 38.9 + - + +
104F ARG* 4.0 4.7 - - - +
106F GLN* 1.3 75.5 - - + +
108F ALA* 1.3 65.2 + - - +
110F ILE* 3.6 1.3 + - - +
111F LYS* 3.0 23.4 + - + +
145F LEU* 4.2 14.8 - - + -
176F THR* 3.4 45.5 - - + +
177F ILE* 4.1 25.4 - - + +
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Residues in contact with ALA 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F GLY* 3.2 31.9 - - - +
12F ALA* 3.8 9.2 - - + -
13F TYR* 3.4 17.3 - - + +
104F ARG* 3.0 19.6 + - + +
106F GLN 3.3 0.2 - - - -
107F ILE* 1.3 77.5 - - - +
109F PHE* 1.3 58.6 + - - +
111F LYS* 3.3 9.3 + - - +
112F GLY 2.9 23.0 + - - -
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Residues in contact with PHE 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F ALA* 3.5 23.3 - - + +
15F LEU* 4.0 20.2 - - + -
16F GLY* 3.7 20.3 - - - -
19F ILE* 4.4 10.3 - - + -
95F LEU* 5.4 0.2 - - + -
98F ILE* 3.8 23.1 - - + -
101F PHE* 4.1 20.2 - + + -
105F GLU 2.9 19.1 + - - +
106F GLN* 3.7 2.9 - - - +
108F ALA* 1.3 74.5 - - - +
110F ILE* 1.3 66.7 + - - +
112F GLY* 3.2 2.8 + - - -
113F LEU* 2.9 52.1 + - + +
134F LEU* 3.9 16.6 - - + -
138F VAL* 4.3 5.6 - - + -
141F TRP* 4.0 15.5 - + - -
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Residues in contact with ILE 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F GLN* 2.9 26.0 + - + +
107F ILE* 4.0 3.8 - - - +
109F PHE* 1.3 76.1 - - - +
111F LYS* 1.3 61.7 + - - +
113F LEU* 3.2 8.7 + - - +
114F TYR* 3.0 22.3 + - - +
127F ILE* 4.7 7.8 - - + +
138F VAL* 4.1 25.6 - - + -
141F TRP* 4.0 32.1 - - + -
142F LEU* 4.0 21.8 - - + -
145F LEU* 4.9 3.6 - - + -
173F PHE* 4.4 11.9 - - + -
177F ILE* 3.5 30.7 - - + -
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Residues in contact with LYS 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F TYR* 4.1 21.5 - - + -
107F ILE* 3.0 19.7 + - + +
108F ALA* 3.4 8.7 - - - +
109F PHE 3.1 0.2 - - - -
110F ILE* 1.3 74.3 - - - +
112F GLY* 1.3 66.6 + - - +
114F TYR* 3.1 4.4 + - - +
115F VAL* 3.0 36.9 + - + +
177F ILE* 3.4 27.5 + - - +
178F LEU* 3.5 28.6 + - + +
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Residues in contact with GLY 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F TYR* 3.6 34.9 - - - -
16F GLY* 4.1 7.9 - - - -
17F LEU* 3.5 12.1 - - - +
108F ALA 2.9 11.7 + - - -
109F PHE 3.2 3.5 + - - -
111F LYS* 1.3 74.6 - - - +
113F LEU* 1.3 63.2 + - - +
115F VAL 3.3 0.2 + - - -
116F ALA* 3.0 21.7 + - - +
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Residues in contact with LEU 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F GLY* 3.8 16.8 - - - +
19F ILE* 4.3 11.7 - - + -
20F SER* 4.0 11.8 + - - +
109F PHE* 2.9 37.9 + - + +
110F ILE* 3.3 12.3 - - - +
112F GLY* 1.3 76.6 - - - +
114F TYR* 1.3 57.5 + - - +
116F ALA* 3.8 0.9 - - - +
117F GLU* 2.9 33.2 + - - +
118F GLY 3.9 0.3 + - - -
127F ILE* 4.4 27.1 - - + +
129F ASN* 5.6 3.4 - - - +
134F LEU* 4.9 9.6 - - + -
135F LEU* 5.1 4.7 - - + -
138F VAL* 3.8 29.8 - - + -
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Residues in contact with TYR 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F ILE 3.0 15.7 + - - +
111F LYS 3.1 2.7 + - - +
113F LEU* 1.3 74.7 - - - +
115F VAL* 1.3 65.3 + - - +
118F GLY* 2.9 29.6 + - - +
119F ASP 2.6 37.0 + - - -
120F LYS* 4.9 0.2 - - - +
122F LEU* 4.1 11.0 - - + -
125F LEU* 3.4 31.7 - - + +
126F ARG 3.4 21.3 - - - -
127F ILE* 3.5 23.1 - - + -
165F ILE* 4.5 0.9 - - + -
173F PHE* 3.7 23.1 - + + -
178F LEU* 4.2 22.7 - - + -
1180F ACT 3.6 20.8 - - - +
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Residues in contact with VAL 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F TYR* 4.1 24.9 - - + +
17F LEU* 4.2 11.2 - - + -
42F GLN* 5.5 5.8 + - - +
47F LEU* 5.5 10.8 - - + -
51F HIS* 5.5 3.1 - - + +
111F LYS* 3.0 32.4 + - + +
112F GLY 3.7 4.0 - - - +
114F TYR* 1.3 77.3 - - + +
116F ALA* 1.3 63.7 + - - +
120F LYS* 3.8 13.9 + - - -
178F LEU* 5.7 0.2 - - + -
1180F ACT 3.9 27.6 - - + +
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Residues in contact with ALA 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F LEU* 4.1 11.9 - - + -
20F SER* 3.1 28.3 - - - +
21F ASP* 3.6 26.0 - - + +
42F GLN* 5.6 1.6 - - - +
112F GLY 3.0 12.9 + - - +
113F LEU 3.8 0.2 - - - +
115F VAL* 1.3 81.8 - - - +
117F GLU* 1.3 59.3 + - - +
118F GLY 3.9 0.7 - - - -
120F LYS* 3.9 1.3 + - - -
1181F MG 2.4 26.7 - - - -
16J C 3.1 8.1 + - - -
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Residues in contact with GLU 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F SER* 2.8 17.5 - - - +
21F ASP* 3.6 8.7 - - - +
113F LEU* 2.9 17.0 + - - +
116F ALA* 1.3 79.5 - - - +
118F GLY* 1.3 61.7 + - - +
127F ILE* 4.8 3.4 - - + +
128F TRP* 3.1 49.3 + - - +
129F ASN* 3.1 17.0 + - - -
1182F MG 2.3 26.5 - - - -
15H G 2.6 15.1 - - - -
15I C 2.9 27.5 + - - +
16J C 3.9 9.1 - - - +
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Residues in contact with GLY 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F TYR* 2.9 33.8 + - - -
116F ALA 3.9 0.4 - - - -
117F GLU* 1.3 80.1 - - - +
119F ASP* 1.3 61.5 + - - -
120F LYS* 2.9 23.7 + - - +
126F ARG 3.1 10.5 - - - -
127F ILE* 4.5 1.3 - - - -
128F TRP* 3.9 2.7 - - - -
16J C 3.8 4.3 - - - +
17J C 3.8 3.5 + - - -
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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