Contacts of the helix formed by residues 110 - 122 (chain K) in PDB entry 3J0O
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 PRO 110 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35K ALA* 4.9 0.4 - - + -
36K THR 3.3 18.2 - - - +
37K TRP* 4.4 24.2 - - + -
40K THR* 5.1 0.4 - - - +
69K SER* 3.0 21.8 - - - +
70K SER* 5.0 5.6 - - - +
71K PRO* 5.6 8.3 - - + +
109K GLY* 1.3 84.1 - - - +
111K GLY* 1.3 63.6 + - - +
112K ALA* 2.7 17.1 + - - -
113K GLN* 3.8 13.0 + - - +
114K SER* 4.0 8.0 + - - -
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Residues in contact with GLY 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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33K ILE* 4.8 0.2 - - - +
35K ALA* 4.2 2.0 - - - +
40K THR* 3.4 34.9 + - - +
70K SER 4.0 17.9 - - - -
74K ALA* 3.9 3.6 - - - +
109K GLY* 4.7 0.2 - - - -
110K PRO* 1.3 84.7 - - - +
112K ALA* 1.3 60.4 + - - +
114K SER* 4.0 11.9 - - - -
115K ALA* 3.5 14.2 + - - +
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Residues in contact with ALA 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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33K ILE* 5.0 5.7 - - - +
35K ALA* 3.7 22.1 - - + +
97K LEU* 4.5 15.5 - - + -
108K PRO* 4.2 15.9 - - + -
109K GLY 4.0 13.0 - - - +
110K PRO 2.7 4.4 + - - -
111K GLY* 1.3 76.0 - - - +
113K GLN* 1.3 58.2 + - - +
114K SER 2.7 12.6 + - - -
115K ALA* 2.9 15.1 + - - +
116K LEU* 3.3 11.5 + - - +
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Residues in contact with GLN 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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110K PRO 3.8 8.2 + - - +
112K ALA* 1.3 78.2 - - - +
114K SER* 1.3 66.5 + - - +
116K LEU* 4.4 7.2 - - - +
117K ARG* 3.2 46.9 + - - +
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Residues in contact with SER 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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71K PRO* 3.1 34.3 + - - +
74K ALA* 3.6 16.4 - - - +
75K MET* 4.8 5.4 + - - +
110K PRO 4.0 13.5 - - - -
111K GLY* 4.0 2.5 - - - -
112K ALA 2.7 1.2 + - - +
113K GLN* 1.3 88.9 + - - +
115K ALA* 1.3 64.6 + - - -
117K ARG* 3.5 4.8 + - - +
118K ALA* 3.1 22.0 + - - +
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Residues in contact with ALA 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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33K ILE* 4.0 15.0 - - + -
40K THR* 5.3 0.2 - - + -
42K ILE* 3.4 30.7 - - + -
74K ALA* 3.8 15.0 - - + +
111K GLY 3.5 17.5 + - - +
112K ALA 2.9 5.3 + - - +
114K SER* 1.3 75.1 - - - +
116K LEU* 1.3 70.7 + - - +
118K ALA* 3.0 11.6 + - - +
119K LEU* 3.2 16.2 + - - +
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Residues in contact with LEU 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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33K ILE* 4.5 7.2 - - + +
95K ILE* 4.4 24.0 - - + -
112K ALA 3.3 10.3 + - - +
113K GLN* 4.4 7.0 - - - +
115K ALA* 1.3 76.0 - - - +
117K ARG* 1.3 61.9 - - + +
119K LEU* 2.7 39.5 + - + +
120K ALA* 3.1 9.0 + - + +
126K ILE* 3.6 27.6 - - + -
129K ILE* 5.5 4.3 - - + -
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Residues in contact with ARG 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 GLN* 3.2 34.5 + - - +
114K SER* 3.5 7.0 - - - +
115K ALA 3.3 0.2 - - - -
116K LEU* 1.3 84.8 - - + +
118K ALA* 1.3 56.0 + - - +
120K ALA* 3.5 4.5 + - - +
121K ARG* 3.0 31.6 + - - +
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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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75K MET* 4.1 7.9 - - + +
78K ALA* 3.2 31.4 - - + -
79K ILE* 4.6 1.6 - - - +
114K SER 3.1 9.0 + - - +
115K ALA 3.0 4.1 + - - +
116K LEU 2.8 3.6 + - - -
117K ARG* 1.3 74.4 - - - +
119K LEU* 1.3 58.2 + - - +
121K ARG* 2.9 49.1 + - - +
122K SER* 3.0 17.7 + - - -
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Residues in contact with LEU 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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31K CYS* 4.3 25.1 - - + -
33K ILE* 4.5 9.6 - - + -
42K ILE* 5.0 5.2 - - + -
78K ALA* 3.3 45.8 - - + +
81K VAL* 5.3 4.7 - - + -
82K VAL* 3.8 9.6 - - + -
93K LEU* 4.8 11.4 - - + -
95K ILE* 5.9 2.0 - - + -
115K ALA 3.2 9.2 + - - +
116K LEU* 2.7 21.5 + - + +
118K ALA* 1.3 71.3 - - - +
120K ALA* 1.3 63.2 + - - +
122K SER* 3.6 7.5 + - - -
123K GLY 3.7 0.2 - - - -
124K MET* 2.8 36.9 + - + +
126K ILE* 5.5 3.8 - - + -
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Residues in contact with ALA 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 LEU* 3.1 13.9 + - + +
117K ARG* 3.8 8.7 - - - +
119K LEU* 1.3 75.7 - - - +
121K ARG* 1.3 67.3 + - - +
123K GLY* 3.2 18.4 + - - +
124K MET 4.1 9.1 - - - +
126K ILE* 3.8 24.6 - - + +
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Residues in contact with ARG 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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75K MET* 2.9 72.8 + - - +
79K ILE* 4.1 23.5 - - - +
117K ARG* 3.0 15.3 + - - +
118K ALA* 2.9 25.4 + - - +
120K ALA* 1.3 73.8 - - - +
122K SER* 1.3 65.6 + - - +
123K GLY* 2.6 18.5 + - - -
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Residues in contact with SER 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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79K ILE* 3.7 28.9 - - - -
82K VAL* 2.9 50.6 - - - +
83K ASN* 6.2 0.2 - - - -
86K LYS* 4.1 11.9 + - - -
118K ALA 3.0 14.0 + - - -
119K LEU 3.6 1.3 + - - -
120K ALA 3.4 0.2 - - - -
121K ARG* 1.3 78.8 - - - +
123K GLY* 1.3 56.1 + - - +
124K MET 3.6 0.4 + - - -
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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