Contacts of the helix formed by residues 102 - 118 (chain K) in PDB entry 5O6I
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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8K SER* 5.2 1.8 + - - -
100K LEU 3.5 2.4 + - - -
101K CYS* 1.3 72.6 - - - +
103K MET* 1.3 65.6 + - - +
104K ARG* 3.1 11.7 + - - +
105K GLU* 2.8 46.1 + - - +
106K GLN* 2.9 25.1 + - - +
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Residues in contact with MET 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102K ASN* 1.3 76.0 - - - +
104K ARG* 1.3 59.1 + - + +
106K GLN* 3.4 16.0 + - - +
107K ILE* 3.0 45.7 + - + +
144K ASN* 5.8 4.5 - - - +
145K LEU* 3.7 30.3 - - + -
176K THR* 5.3 4.3 - - + -
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Residues in contact with ARG 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K GLU 3.1 23.2 - - - +
6K ASN* 2.7 34.0 - - - +
8K SER* 3.9 4.4 + - - -
9K GLY* 2.9 35.2 - - - +
102K ASN* 3.1 8.0 + - - +
103K MET* 1.3 78.4 - - + +
105K GLU* 1.3 64.0 + - - +
107K ILE* 3.5 7.0 + - - +
108K ALA* 3.1 22.2 + - - +
182K LEU* 3.4 44.7 + - + +
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Residues in contact with GLU 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8K SER* 3.3 40.4 - - - +
9K GLY* 4.9 1.8 - - - +
12K ALA* 3.3 22.8 - - + +
94K MET* 4.5 8.2 - - + +
100K LEU 4.8 0.9 - - - +
101K CYS* 3.8 20.3 - - + -
102K ASN* 2.8 49.0 + - - +
104K ARG* 1.3 77.6 - - - +
106K GLN* 1.3 59.8 + - - +
108K ALA* 4.3 1.3 - - - -
109K PHE* 2.8 28.1 + - - +
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Residues in contact with GLN 106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99K ARG 5.5 1.0 + - - -
101K CYS* 2.7 29.8 + - + -
102K ASN* 2.9 21.0 + - - +
103K MET* 3.4 13.6 - - - +
105K GLU* 1.3 76.5 - - - +
107K ILE* 1.3 58.2 + - + +
109K PHE* 3.3 1.7 + - - +
110K ILE* 2.9 37.0 + - + +
141K TRP* 3.5 66.0 - - + +
144K ASN* 4.4 14.9 + - - +
145K LEU* 5.2 5.6 - - + +
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Residues in contact with ILE 107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103K MET* 3.0 49.0 + - + +
104K ARG* 3.8 7.2 - - - +
105K GLU 3.3 0.2 - - - -
106K GLN* 1.3 75.0 - - - +
108K ALA* 1.3 57.0 + - - +
110K ILE* 3.4 2.9 + - - +
111K LYS* 2.9 28.4 + - - +
145K LEU* 4.0 19.1 - - + -
176K THR* 3.6 33.4 - - + +
177K ILE* 4.0 15.4 - - + +
180K SER* 3.6 18.4 - - - +
182K LEU* 3.8 13.2 - - + -
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Residues in contact with ALA 108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K GLY* 3.3 28.9 - - - +
12K ALA* 3.9 2.2 - - + -
13K TYR* 3.3 20.5 - - + +
104K ARG 3.1 17.4 + - - +
105K GLU* 3.8 4.3 - - - +
106K GLN 3.3 0.2 - - - -
107K ILE* 1.3 76.7 - - - +
109K PHE* 1.3 58.8 + - - +
111K LYS* 3.4 8.4 + - - +
112K GLY 2.9 22.9 + - - -
182K LEU* 3.8 15.9 - - + +
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Residues in contact with PHE 109 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K ALA* 3.5 16.8 - - + +
15K LEU* 4.1 18.4 - - + -
16K GLY* 3.7 30.1 - - - -
19K ILE* 4.4 9.2 - - + -
98K ILE* 3.5 31.0 - - + -
101K CYS* 5.8 2.7 - - - -
105K GLU 2.8 19.0 + - - +
106K GLN 3.7 2.7 - - - +
108K ALA* 1.3 74.8 - - - +
110K ILE* 1.3 66.4 + - + +
112K GLY* 3.2 1.4 + - - -
113K LEU* 2.8 41.0 + - + +
134K LEU* 3.7 26.0 - - + -
138K VAL* 4.1 14.4 - - + -
141K TRP* 3.7 21.3 - + + -
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Residues in contact with ILE 110 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106K GLN 2.9 25.6 + - - +
107K ILE 4.0 2.7 - - - +
109K PHE* 1.3 77.4 - - + +
111K LYS* 1.3 58.2 + - - +
113K LEU* 3.2 6.9 + - - +
114K TYR* 2.8 29.1 + - - +
127K ILE* 4.8 8.3 - - + -
138K VAL* 4.0 24.2 - - + -
141K TRP* 4.1 33.2 - - + -
142K LEU* 4.0 19.7 - - + -
145K LEU* 4.7 5.2 - - + -
173K PHE* 4.2 12.8 - - + -
177K ILE* 3.8 27.8 - - + -
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Residues in contact with LYS 111 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K TYR* 3.9 27.7 - - + +
107K ILE 2.9 19.0 + - - +
108K ALA* 3.6 7.6 - - - +
110K ILE* 1.3 77.5 - - - +
112K GLY* 1.3 57.9 + - - +
114K TYR* 3.4 4.0 + - - +
115K VAL* 3.0 38.4 + - + +
177K ILE* 3.4 21.2 - - - +
178K LEU* 3.7 17.8 - - + +
180K SER* 3.3 39.0 + - - +
181K HIS* 4.3 10.9 + - - +
182K LEU* 5.9 0.8 - - + +
183K ASN* 5.2 2.8 - - - +
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Residues in contact with GLY 112 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13K TYR* 3.6 35.1 - - - -
16K GLY* 3.6 9.9 - - - +
17K LEU* 3.4 14.6 - - - +
108K ALA 2.9 11.7 + - - -
109K PHE 3.7 2.2 - - - -
111K LYS* 1.3 76.7 - - - +
113K LEU* 1.3 62.4 + - - +
115K VAL 3.4 0.3 + - - -
116K ALA 3.2 16.5 + - - -
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Residues in contact with LEU 113 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K GLY* 3.7 19.0 - - - +
19K ILE* 4.4 14.1 - - + -
20K GLY* 4.2 7.6 - - - +
109K PHE* 2.8 32.1 + - + +
110K ILE* 3.7 6.7 - - - +
112K GLY* 1.3 73.2 - - - +
114K TYR* 1.3 51.7 + - - +
116K ALA 3.3 0.2 + - - -
117K GLU* 2.7 56.3 + - + +
127K ILE* 4.2 27.1 - - + +
129K ASN* 5.0 2.0 - - + +
134K LEU* 4.3 13.7 - - + -
135K LEU* 4.8 4.3 - - + -
138K VAL* 4.0 27.8 - - + -
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Residues in contact with TYR 114 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110K ILE 2.8 17.9 + - - +
111K LYS 3.9 4.0 - - - +
113K LEU* 1.3 73.8 - - - +
115K VAL* 1.3 62.4 + - - +
116K ALA 3.1 1.6 - - - -
117K GLU 4.7 0.2 - - - -
118K GLY* 2.7 36.0 + - - +
119K ASP 2.8 36.1 + - - -
120K LYS* 3.9 7.0 + - + +
122K LEU* 3.9 13.9 - - + -
125K LEU* 3.4 29.0 - - + +
126K ARG 3.5 18.8 - - - -
127K ILE* 3.5 24.7 - - + +
165K ILE* 4.2 2.9 - - + -
173K PHE* 3.7 25.6 - + + -
178K LEU* 3.9 24.7 - - + -
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Residues in contact with VAL 115 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K TYR* 4.0 18.4 - - + +
17K LEU* 3.7 18.8 - - + -
21K ASP* 4.4 2.5 - - - +
42K GLN* 4.6 7.4 - - - +
47K LEU* 5.4 5.8 - - + -
52K PHE* 4.1 15.9 - - + -
111K LYS* 3.0 28.2 + - + +
112K GLY 3.7 5.6 - - - +
114K TYR* 1.3 76.9 - - + +
116K ALA* 1.3 58.6 + - - +
120K LYS* 3.1 27.3 + - + +
178K LEU* 5.8 4.3 - - + -
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Residues in contact with ALA 116 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K GLY 4.1 3.4 - - - +
17K LEU* 4.2 6.7 - - + +
20K GLY* 3.6 23.8 - - - -
21K ASP* 3.3 29.5 - - + +
112K GLY 3.2 15.6 + - - +
113K LEU 3.7 2.0 - - - +
114K TYR 3.1 0.4 - - - -
115K VAL* 1.3 78.8 - - - +
117K GLU* 1.3 59.8 + - - +
118K GLY 3.6 0.4 - - - -
120K LYS* 3.4 4.0 + - - -
201K MN 2.4 25.3 + - - -
16N C 3.0 6.1 + - - -
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Residues in contact with GLU 117 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K GLY* 3.5 12.3 - - - +
21K ASP* 4.0 0.3 - - - +
113K LEU* 2.7 40.0 + - + +
116K ALA* 1.3 80.0 - - - +
118K GLY* 1.3 57.9 + - - +
127K ILE* 3.8 10.3 - - + -
128K TRP* 3.3 48.7 + - - +
129K ASN* 2.4 31.6 + - - +
202K MN 2.5 27.1 + - - -
15L G 3.4 6.8 + - - -
15N C 3.2 11.7 + - - +
16N C 4.0 8.1 - - - +
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Residues in contact with GLY 118 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114K TYR* 2.7 41.9 + - - -
116K ALA 3.6 0.8 - - - -
117K GLU* 1.3 75.6 - - - +
119K ASP* 1.3 62.5 + - - -
120K LYS* 2.9 24.8 + - - -
126K ARG 3.2 9.0 - - - -
127K ILE* 4.5 0.4 - - - -
128K TRP* 4.1 1.6 - - - -
16N C 3.9 3.6 - - - +
17N C 3.8 3.1 + - - -
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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