Contacts of the helix formed by residues 108 - 122 (chain K) in PDB entry 3Q2K
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 ARG 108 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113J LYS* 5.6 11.5 - - - +
350J ASP* 5.4 8.2 + - - -
106K ALA* 3.8 3.1 - - - +
107K THR* 1.3 88.7 + - - +
109K TRP* 1.3 66.9 + - - +
110K GLU* 4.7 2.9 - - + +
111K ASP* 2.9 42.5 + - - +
112K GLY 3.0 9.7 + - - -
178K TRP* 5.3 4.4 + - - +
179K GLU* 3.8 50.3 + - - +
329K LEU* 4.5 3.4 - - - -
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Residues in contact with TRP 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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107K THR 4.2 0.8 + - - -
108K ARG* 1.3 69.5 - - - +
110K GLU* 1.3 68.8 + - + +
112K GLY* 3.1 11.3 + - - -
113K LYS* 3.2 45.5 + - + +
326K LEU* 3.5 44.2 - - + -
329K LEU* 3.9 14.5 - - + +
330K ALA* 3.6 30.1 - - + -
333K THR* 3.5 27.2 + - + +
337K ARG* 4.0 17.3 - - - +
349K LEU* 3.9 26.5 - - + +
350K ASP 3.0 27.3 + - - -
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Residues in contact with GLU 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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108K ARG* 3.4 3.4 - - + +
109K TRP* 1.3 83.0 - - + +
111K ASP* 1.3 65.4 + - - +
113K LYS* 2.9 35.8 + - - +
114K ARG* 3.2 35.3 + - - +
337K ARG* 5.5 3.6 + - - +
350K ASP 4.2 3.1 - - - +
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Residues in contact with ASP 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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83K GLY 5.3 1.4 - - - +
86K PRO* 3.4 27.9 - - + +
87K TRP* 3.7 35.6 + - + -
106K ALA* 4.2 0.9 - - + -
107K THR* 5.2 1.6 + - - -
108K ARG* 2.9 39.2 + - - +
110K GLU* 1.3 79.7 - - - +
112K GLY* 1.3 68.7 + - - +
114K ARG* 3.0 9.7 + - - +
115K MET* 2.9 25.6 + - - +
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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
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105K MET* 4.0 2.0 - - - +
106K ALA* 3.8 9.4 - - - +
108K ARG 3.0 10.7 + - - -
109K TRP 3.1 4.6 + - - -
111K ASP* 1.3 78.7 - - - +
113K LYS* 1.3 59.3 + - - +
115K MET* 3.4 11.2 + - - +
116K VAL* 3.3 24.1 + - - +
326K LEU* 3.7 8.6 - - - +
329K LEU* 3.8 19.7 - - - -
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Residues in contact with LYS 113 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109K TRP* 3.2 47.8 + - + +
110K GLU* 2.9 43.6 + - - +
111K ASP 3.2 0.6 - - - -
112K GLY* 1.3 72.4 - - - +
114K ARG* 1.3 60.9 + - - +
116K VAL* 3.3 5.1 + - - +
117K LYS* 3.0 29.6 + - - +
326K LEU* 3.9 12.5 - - + +
350K ASP* 3.1 29.6 + - - +
108M ARG* 6.2 2.5 - - - +
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Residues in contact with ARG 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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87K TRP* 4.3 25.2 - - - -
90K ILE* 4.0 16.4 - - + +
110K GLU* 3.2 23.9 + - - +
111K ASP* 3.0 12.9 + - - +
113K LYS* 1.3 75.8 - - - +
115K MET* 1.3 68.7 + - - +
117K LYS* 3.3 29.5 + - - +
118K ALA* 2.9 23.7 + - - +
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Residues in contact with MET 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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85K HIS 3.9 6.3 - - - +
86K PRO* 3.1 30.3 - - + +
89K ALA* 3.8 22.7 - - + -
90K ILE* 4.1 10.9 - - - +
101K SER* 4.1 16.6 - - - +
105K MET* 3.4 57.0 - - + +
111K ASP 2.9 12.7 + - - +
112K GLY* 3.4 12.8 - - - +
114K ARG* 1.3 78.4 - - - +
116K VAL* 1.3 60.9 + - - +
118K ALA* 3.2 1.9 + - - +
119K CYS* 3.2 28.9 + - - -
126K LEU* 4.3 13.7 - - + -
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Residues in contact with VAL 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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105K MET* 3.9 14.4 - - + -
112K GLY 3.3 14.2 + - - +
113K LYS* 3.8 6.1 - - - +
114K ARG 3.1 0.6 - - - -
115K MET* 1.3 76.6 - - - +
117K LYS* 1.3 65.7 + - - +
119K CYS* 3.6 1.6 + - - +
120K ASP* 3.0 30.4 + - - +
126K LEU* 4.2 10.5 - - + -
322K GLY* 4.1 11.2 - - - -
323K ARG* 3.4 43.5 - - + +
326K LEU* 3.8 29.6 - - + -
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Residues in contact with LYS 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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113K LYS 3.0 17.2 + - - +
114K ARG* 3.6 33.4 - - - +
116K VAL* 1.3 79.0 - - - +
118K ALA* 1.3 55.6 + - - +
120K ASP* 3.4 10.2 - - + +
121K GLU* 3.0 61.9 + - - +
87M TRP* 5.7 13.0 - - + -
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Residues in contact with ALA 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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90K ILE* 4.1 33.4 - - + +
93K ALA* 3.9 8.0 - - + +
94K GLN* 5.7 4.5 - - + +
114K ARG 2.9 16.7 + - - +
115K MET 3.2 4.2 + - - +
117K LYS* 1.3 76.1 - - - +
119K CYS* 1.3 65.4 + - - +
121K GLU* 3.4 8.6 + - - +
122K ALA* 3.1 25.6 + - - +
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Residues in contact with CYS 119 (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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89K ALA* 4.6 6.5 - - - -
93K ALA* 3.9 11.0 - - - -
99K VAL* 4.4 14.4 - - - -
115K MET 3.2 16.0 + - - +
116K VAL 4.1 2.9 - - - +
118K ALA* 1.3 71.9 - - - +
120K ASP* 1.3 67.9 + - - +
122K ALA 3.5 0.5 + - - -
123K GLY* 3.0 3.5 + - - -
124K VAL* 2.9 59.8 + - - +
125K ARG 4.6 0.2 - - - -
126K LEU* 4.0 31.9 - - + -
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Residues in contact with ASP 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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116K VAL* 3.0 28.0 + - - +
117K LYS* 3.4 10.9 - - + +
119K CYS* 1.3 76.2 - - - +
121K GLU* 1.3 56.0 + - - +
123K GLY* 2.8 25.2 + - - -
323K ARG* 3.0 41.9 + - - -
180M TRP* 5.6 0.5 - - - -
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Residues in contact with GLU 121 (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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117K LYS* 3.0 45.5 + - - +
118K ALA* 3.9 8.6 - - - +
119K CYS 3.3 0.2 - - - -
120K ASP* 1.3 78.7 - - - +
122K ALA* 1.3 57.9 + - + +
123K GLY 3.4 0.4 + - - -
87M TRP* 5.4 7.4 - - - -
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Residues in contact with ALA 122 (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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93K ALA* 3.7 28.0 - - + +
94K GLN* 5.0 3.1 - - + +
96K GLY* 5.7 2.9 - - - -
118K ALA 3.1 16.1 + - - +
119K CYS 4.4 0.7 - - - +
120K ASP 3.1 0.4 - - - -
121K GLU* 1.3 78.3 - - - +
123K GLY* 1.3 65.4 + - - +
124K VAL* 3.3 7.3 + - + +
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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