Contacts of the helix formed by residues 105 - 117 (chain a) in PDB entry 3J7Y
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 GLU 105 (chain a).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189T PRO* 5.9 2.8 - - - +
195T HIS* 5.4 2.8 + - - -
104a GLU* 1.3 80.1 - - - +
106a GLY* 1.3 62.9 + - - +
108a MET* 3.2 23.4 + - - +
109a ILE* 2.9 41.3 + - + +
123a TRP 5.6 0.5 - - - +
124a TYR* 5.2 12.0 - - + -
125a PRO* 4.8 16.8 - - - +
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Residues in contact with GLY 106 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104a GLU* 5.1 0.4 + - - +
105a GLU* 1.3 78.7 - - - +
107a PRO* 1.3 67.1 - - - +
109a ILE* 3.2 14.1 + - - +
110a GLU* 2.9 33.7 + - - +
124a TYR* 5.3 7.2 - - - -
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Residues in contact with PRO 107 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104a GLU* 3.8 30.3 - - + +
105a GLU 3.5 2.5 - - - -
106a GLY* 1.3 90.1 - - - +
108a MET* 1.3 55.7 + - - +
110a GLU* 3.2 16.3 + - - +
111a GLN* 2.9 29.2 + - - +
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Residues in contact with MET 108 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190T LYS 3.6 23.6 - - - +
191T THR* 4.7 0.9 - - - -
192T ALA* 3.4 28.9 - - + +
195T HIS* 3.6 19.1 - - + +
104a GLU 3.0 24.7 + - - +
105a GLU* 3.4 26.5 - - - +
107a PRO* 1.3 76.4 - - - +
109a ILE* 1.3 68.3 + - - +
111a GLN* 3.2 13.9 + - - +
112a LEU* 2.9 51.8 + - - +
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Residues in contact with ILE 109 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195T HIS* 5.2 1.3 - - - +
105a GLU* 2.9 24.6 + - + +
106a GLY* 3.2 16.1 + - - +
108a MET* 1.3 93.0 - - + +
110a GLU* 1.3 66.4 + - + +
112a LEU* 3.2 8.5 + - + +
113a SER* 2.9 31.9 + - - +
120a LYS* 4.1 28.3 - - + +
123a TRP* 3.4 44.9 - - + +
124a TYR* 4.5 22.7 - - + +
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Residues in contact with GLU 110 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106a GLY 2.9 17.9 + - - +
107a PRO* 3.4 17.0 - - - +
109a ILE* 1.3 82.2 - - + +
111a GLN* 1.3 57.9 + - - +
113a SER* 3.2 8.6 + - - -
114a LYS* 2.9 32.8 + - + +
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Residues in contact with GLN 111 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192T ALA* 4.2 22.8 - - - +
107a PRO 2.9 12.4 + - - +
108a MET* 3.3 12.8 + - - +
110a GLU* 1.3 77.5 - - - +
112a LEU* 1.3 57.7 + - - +
114a LYS* 3.2 9.0 + - + +
115a MET* 2.9 40.7 + - + +
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Residues in contact with LEU 112 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192T ALA* 3.6 26.7 - - + +
195T HIS* 3.8 22.9 - - + -
196T ALA* 4.0 11.7 - - + +
108a MET* 2.9 42.2 + - + +
109a ILE* 3.2 12.3 + - + +
111a GLN* 1.3 78.2 - - - +
113a SER* 1.3 56.4 + - - +
115a MET* 3.2 12.3 + - - +
116a PHE* 2.9 40.2 + - + +
123a TRP* 3.9 37.9 - - + -
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Residues in contact with SER 113 (chain a).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123K GLU* 5.7 0.4 - - - -
109a ILE 2.9 15.6 + - - -
110a GLU* 3.4 11.8 - - - -
112a LEU* 1.3 76.9 - - - +
114a LYS* 1.3 55.0 + - - +
117a PHE* 2.7 37.2 + - - -
118a THR* 3.0 27.3 + - - +
119a THR 3.8 13.5 + - - -
120a LYS* 3.9 6.2 + - - +
123a TRP* 3.9 8.0 + - - +
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Residues in contact with LYS 114 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110a GLU* 2.9 15.4 + - + +
111a GLN* 3.4 12.1 - - - +
113a SER* 1.3 78.3 - - - +
115a MET* 1.3 62.3 + - - +
117a PHE* 4.0 22.3 + - + -
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Residues in contact with MET 115 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196T ALA* 4.4 19.5 - - + -
200T ILE* 6.0 2.7 - - + -
111a GLN* 2.9 24.5 + - + +
112a LEU* 3.2 15.7 - - - +
114a LYS* 1.3 79.2 - - - +
116a PHE* 1.3 81.4 + - + +
117a PHE* 3.9 5.9 - - - -
265c THR* 3.1 25.1 - - - +
266c ALA* 4.1 24.5 - - + +
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Residues in contact with PHE 116 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K ARG* 2.7 34.8 + - - -
196T ALA* 3.7 44.4 - - + -
199T TYR* 3.3 33.2 - + + -
200T ILE* 4.1 11.7 - - + -
112a LEU* 2.9 24.9 + - + +
115a MET* 1.3 96.1 - - + +
117a PHE* 1.3 62.9 - - - +
118a THR* 3.9 14.5 - - + +
123a TRP* 3.6 16.4 - + - -
265c THR* 6.4 0.2 - - - -
266c ALA* 4.8 5.4 - - + -
267c LEU* 3.9 34.9 - - + +
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Residues in contact with PHE 117 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K ARG* 3.5 2.0 + - - +
18K TRP* 3.7 27.1 - + - -
56K HIS* 3.5 23.8 - + + -
123K GLU* 3.9 20.0 - - - +
124K ARG* 2.7 34.2 + - + -
126K HIS* 3.6 30.5 - + - -
137K ILE* 6.1 1.1 - - + -
140K ASN* 5.4 1.6 - - - -
113a SER 2.7 17.4 + - - -
114a LYS* 4.0 13.2 + - + -
115a MET 3.6 13.4 - - - -
116a PHE* 1.3 79.9 - - - +
118a THR* 1.3 54.6 + - - +
265c THR* 4.0 17.5 - - + -
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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