Contacts of the helix formed by residues 108 - 116 (chain A) in PDB entry 1JQI
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 SER 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A PHE 3.9 0.4 + - - -
107A GLY* 1.3 72.4 - - - -
109A SER* 1.3 66.0 + - - +
110A GLN* 3.5 8.3 + - - +
111A GLN* 2.9 36.3 + - - +
112A LYS* 2.9 24.7 + - - +
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Residues in contact with SER 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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108A SER* 1.3 72.6 - - - +
110A GLN* 1.3 62.8 + - - +
112A LYS* 3.3 14.7 + - - +
113A GLN* 3.2 35.9 + - - +
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Residues in contact with GLN 110 (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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108A SER* 3.1 8.3 + - - +
109A SER* 1.3 80.0 - - - +
111A GLN* 1.3 64.0 + - + +
113A GLN* 3.1 29.4 + - - +
114A GLN* 3.1 37.7 + - - +
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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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103A ILE* 4.1 4.0 - - + +
106A PHE 4.6 0.7 - - - +
107A GLY* 3.3 13.3 - - - -
108A SER* 2.9 40.5 + - - +
110A GLN* 1.3 77.4 - - + +
112A LYS* 1.3 57.6 + - - +
114A GLN* 4.1 4.0 - - - +
115A TRP* 2.9 51.1 + - + +
190A LEU* 4.2 18.6 - - + +
227A GLU 3.1 20.2 + - - +
228A ASN 4.2 0.2 - - - -
229A LEU 2.9 30.6 + - - +
230A LEU* 3.8 8.4 - - - +
231A GLY 5.0 1.4 + - - -
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Residues in contact with LYS 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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64A LEU* 4.0 23.3 - - + +
103A ILE* 4.0 12.6 - - - +
104A LEU* 3.4 38.9 + - + +
105A LYS 5.8 0.2 - - - -
107A GLY 3.5 18.8 + - - -
108A SER 2.9 15.9 + - - +
109A SER* 3.5 15.0 + - - +
111A GLN* 1.3 77.3 - - - +
113A GLN* 1.3 58.0 + - + +
116A ILE* 2.9 45.8 + - + +
117A THR 3.5 2.3 + - - -
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Residues in contact with GLN 113 (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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64A LEU* 4.5 11.4 - - + -
109A SER* 3.2 22.8 + - - +
110A GLN* 3.1 25.4 + - - +
112A LYS* 1.3 78.6 - - - +
114A GLN* 1.3 60.0 + - - +
117A THR* 3.5 27.3 - - - +
118A PRO* 3.8 2.8 - - - +
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Residues in contact with GLN 114 (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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110A GLN* 3.1 36.9 + - - +
111A GLN* 4.1 4.2 - - - +
113A GLN* 1.3 78.6 - - - +
115A TRP* 1.3 98.0 + - + +
118A PRO* 3.4 18.8 - - - +
119A PHE* 4.6 3.1 - - - -
227A GLU* 6.2 0.3 - - - +
228A ASN* 5.6 1.4 - - - +
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Residues in contact with TRP 115 (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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99A TYR* 2.8 43.6 + - - +
103A ILE* 3.8 13.9 - - + -
111A GLN* 2.9 31.4 + - - +
114A GLN* 1.3 114.2 + - + +
116A ILE* 1.3 61.7 + - - +
119A PHE* 3.1 17.6 - + - -
170A ALA* 3.8 21.5 - - + -
171A THR 5.5 0.2 - - - -
190A LEU* 3.5 41.4 - - + +
191A VAL 3.9 3.4 - - - -
192A PRO* 3.7 39.3 - - + -
228A ASN* 3.7 23.8 + - - +
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Residues in contact with ILE 116 (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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60A VAL* 4.0 29.4 - - + -
64A LEU* 4.3 8.5 - - + -
100A LEU* 3.7 36.9 - - + +
103A ILE* 3.4 35.7 - - + -
104A LEU* 4.2 8.5 - - + +
112A LYS* 2.9 37.3 + - + +
115A TRP* 1.3 76.3 - - - +
117A THR* 1.3 60.1 + - - +
118A PRO* 3.2 2.0 - - - -
119A PHE* 2.8 24.3 + - - +
120A THR* 3.3 16.1 - - + +
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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
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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