Contacts of the helix formed by residues 117 - 132 (chain K) in PDB entry 1IA0
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 GLY 117 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70K GLN* 3.6 12.6 - - - -
106K THR 3.5 11.9 - - - -
108K MET 2.7 25.1 + - - -
115K GLN 3.6 1.4 + - - -
116K GLN* 1.3 74.7 - - - +
118K ILE* 1.3 66.4 + - - -
119K ILE 3.4 2.9 - - - -
120K PRO* 3.2 2.5 - - - +
121K GLN* 3.1 27.0 + - - +
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Residues in contact with ILE 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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70K GLN 5.8 0.4 - - - +
73K VAL* 4.0 23.6 - - + +
74K TYR* 3.9 27.6 - - + -
77K ILE* 5.3 3.4 - - + -
78K GLY* 4.6 1.6 - - - +
93K ILE* 4.1 34.8 - - + -
106K THR* 3.0 37.5 + - + +
107K MET* 3.3 23.5 + - + +
117K GLY* 1.3 71.6 - - - -
119K ILE* 1.3 60.4 + - - +
121K GLN 3.8 0.2 - - - -
122K LEU* 2.9 32.5 + - + +
246K LEU* 4.8 5.8 - - + -
328K VAL* 4.5 6.7 - - + -
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Residues in contact with ILE 119 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107K MET* 2.9 42.0 + - + +
108K MET* 4.0 18.6 - - + -
118K ILE* 1.3 71.3 - - - +
120K PRO* 1.3 70.1 - - + +
122K LEU* 3.9 0.9 - - - +
123K CYS* 3.0 24.3 + - - -
146K TYR* 5.5 1.3 - - + +
196K MET* 3.7 25.6 - - + -
221K PHE* 3.9 34.3 - - + -
246K LEU* 3.8 37.7 - - + +
248K ASP* 5.7 4.7 - - + -
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Residues in contact with PRO 120 (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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107K MET 3.5 7.9 - - - +
108K MET* 3.4 31.4 - - + +
116K GLN* 3.9 22.2 - - + -
117K GLY 3.2 13.0 - - - +
119K ILE* 1.3 96.6 - - + +
121K GLN* 1.3 60.3 + - - +
123K CYS* 3.4 0.8 + - + -
124K GLU* 3.0 25.1 + - - +
189K TYR* 3.6 19.6 + - - +
193K GLN* 4.0 12.8 - - - +
196K MET* 4.0 9.6 - - + -
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Residues in contact with GLN 121 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70K GLN* 3.2 26.9 + - - +
71K LYS* 3.4 34.0 + - - +
74K TYR* 3.2 39.9 - - + +
114K ASP* 5.3 2.4 + - - +
116K GLN* 3.0 30.5 + - + +
117K GLY 3.1 16.3 + - - +
120K PRO* 1.3 79.9 - - - +
122K LEU* 1.3 58.1 + - - +
124K GLU* 3.4 13.7 + - - +
125K ASP* 2.9 30.8 + - - +
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Residues in contact with LEU 122 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74K TYR* 3.5 16.1 - - + +
78K GLY* 3.9 22.9 - - - +
81K MET* 5.1 4.7 - - + -
82K LEU* 4.0 31.8 - - + +
93K ILE* 5.1 2.0 - - + -
118K ILE* 2.9 20.9 + - + +
119K ILE* 3.9 3.6 - - - +
121K GLN* 1.3 74.2 - - - +
123K CYS* 1.3 66.3 + - - +
125K ASP* 3.3 1.7 + - - +
126K LEU* 2.8 28.1 + - + +
223K ILE* 4.2 20.2 - - + -
244K ILE* 4.4 21.5 - - + -
246K LEU* 4.5 20.0 - - + -
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Residues in contact with CYS 123 (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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119K ILE* 3.0 24.6 + - - +
120K PRO 3.7 3.6 - - - +
122K LEU* 1.3 81.4 - - - +
124K GLU* 1.3 62.4 + - - +
126K LEU* 3.2 8.9 + - - +
127K PHE* 3.1 28.3 + - - -
189K TYR* 3.9 7.2 - - + -
192K ILE* 3.9 33.2 - - + -
196K MET* 3.7 20.0 - - + -
221K PHE* 3.9 21.3 - - - -
223K ILE* 3.9 8.5 - - - -
246K LEU* 5.5 0.2 - - - -
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Residues in contact with GLU 124 (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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71K LYS* 4.9 10.0 + - - -
120K PRO 3.0 17.2 + - - +
121K GLN* 3.7 13.1 - - - +
123K CYS* 1.3 76.3 - - - +
125K ASP* 1.3 63.9 + - - +
126K LEU 3.3 0.2 + - - -
127K PHE* 3.3 3.5 + - - +
128K SER* 2.9 32.9 + - - +
189K TYR* 3.6 37.7 - - + +
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Residues in contact with ASP 125 (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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74K TYR* 2.7 40.6 + - + +
79K GLU* 4.2 15.1 - - - +
82K LEU* 3.6 10.4 - - + +
121K GLN 2.9 13.0 + - - +
122K LEU 3.6 1.6 - - - +
124K GLU* 1.3 76.6 - - - +
126K LEU* 1.3 63.4 + - - +
128K SER* 3.3 6.5 + - - -
129K ARG* 3.0 38.5 + - - +
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Residues in contact with LEU 126 (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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82K LEU* 3.7 17.7 - - + +
86K PHE* 3.8 22.7 - - + -
122K LEU* 2.8 19.7 + - + +
123K CYS* 3.4 6.3 - - - +
125K ASP* 1.3 78.1 - - - +
127K PHE* 1.3 67.8 + - + +
129K ARG* 3.4 3.1 + - - +
130K ILE* 3.1 46.0 + - + +
142K VAL* 4.4 14.4 - - + -
192K ILE* 5.7 0.2 - - + -
223K ILE* 4.2 37.5 - - + -
225K PHE* 4.0 15.3 - - + -
244K ILE* 4.7 7.2 - - + -
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Residues in contact with PHE 127 (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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123K CYS 3.1 26.2 + - - +
124K GLU 4.0 2.7 - - - +
126K LEU* 1.3 79.0 - - + +
128K SER* 1.3 61.1 + - - +
130K ILE* 3.3 12.3 + - + +
131K ASN* 2.9 46.0 + - - +
142K VAL* 4.0 22.0 - - + -
186K VAL* 3.7 27.6 - - + -
187K THR* 3.5 10.3 - - - -
188K SER* 3.4 37.7 - - - -
189K TYR* 3.6 26.7 - - + +
192K ILE* 3.9 22.9 - - + -
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Residues in contact with SER 128 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124K GLU* 2.9 25.9 + - - +
125K ASP* 3.6 10.5 - - - -
126K LEU 3.3 0.2 - - - -
127K PHE* 1.3 76.9 - - - +
129K ARG* 1.3 62.5 + - - +
131K ASN* 3.4 5.6 + - - +
132K ASP* 3.1 32.8 + - - +
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Residues in contact with ARG 129 (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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79K GLU* 5.2 3.4 + - - +
82K LEU* 4.1 8.5 - - - +
83K GLN* 3.8 30.7 - - - +
86K PHE* 3.5 58.2 - - + +
125K ASP* 3.0 37.3 + - - +
126K LEU 3.8 0.7 - - - +
128K SER* 1.3 76.2 - - - +
130K ILE* 1.3 62.5 + - - +
132K ASP* 3.3 16.1 + - - +
133K THR* 3.5 10.4 + - - -
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Residues in contact with ILE 130 (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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86K PHE* 4.4 3.4 - - + -
126K LEU* 3.1 27.5 + - + +
127K PHE* 3.7 16.4 - - + +
129K ARG* 1.3 76.9 - - - +
131K ASN* 1.3 64.7 + - - +
132K ASP 3.1 0.2 - - - -
133K THR* 2.7 29.2 + - - -
140K TYR* 3.7 34.4 - - + -
142K VAL* 3.8 22.0 - - + -
225K PHE* 3.7 30.7 - - + -
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Residues in contact with ASN 131 (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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127K PHE* 2.9 37.6 + - - +
128K SER* 3.8 4.9 - - - +
130K ILE* 1.3 81.6 - - - +
132K ASP* 1.3 57.4 + - - +
133K THR 3.2 6.0 + - - +
187K THR 5.3 4.3 + - - +
188K SER* 5.8 2.0 - - - +
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Residues in contact with ASP 132 (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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128K SER* 3.1 22.7 + - - +
129K ARG* 3.6 9.4 - - - +
130K ILE 3.1 0.6 - - - -
131K ASN* 1.3 75.0 - - - +
133K THR* 1.3 66.0 + - - +
134K THR* 3.4 13.9 + - - +
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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
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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