Contacts of the helix formed by residues 112 - 124 (chain x) in PDB entry 5GJQ
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 THR 112 (chain x).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107x THR 4.7 0.9 + - - -
108x ASN* 3.8 2.9 + - - -
109x LEU* 3.0 33.1 + - - +
110x GLY 3.4 12.1 - - - +
111x ASN* 1.3 83.1 - - - +
113x CYS* 1.3 62.5 + - - +
114x TYR* 2.9 13.7 - - + +
115x MET* 3.0 14.0 + - + +
116x ASN* 2.5 40.3 + - - -
175x LEU* 3.7 29.2 - - + +
179x HIS* 6.0 2.0 - - + -
194x TYR* 5.5 3.6 - - + -
195x LEU 5.7 0.4 - - - +
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Residues in contact with CYS 113 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108x ASN* 5.3 1.7 - - - +
112x THR* 1.3 79.2 - - - +
114x TYR* 1.3 53.1 + - - +
116x ASN* 3.2 12.2 - - - +
117x ALA* 2.3 40.9 + - - +
434x HIS* 3.8 8.1 - - + +
435x TYR 3.0 34.9 - - - +
451x ASP* 3.0 26.4 + - - +
75y GLY 3.5 0.2 - - - -
76y GLZ 2.8 39.9 - - - -
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Residues in contact with TYR 114 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111x ASN 3.7 16.3 + - - -
112x THR* 2.9 6.0 - - + +
113x CYS* 1.3 82.7 - - - +
115x MET* 1.3 110.9 + - + +
117x ALA* 3.5 0.7 - - - +
118x THR* 2.8 29.4 + - - -
179x HIS* 4.5 8.0 - - - -
185x PHE* 3.7 30.6 - + - +
195x LEU 5.0 3.0 + - - -
196x GLN* 4.3 0.9 - - - -
197x GLN* 2.9 49.2 - - + +
198x ASP 4.7 1.1 - - - -
199x ALA* 3.9 3.8 - - - +
202x CYS* 4.4 18.4 - - + -
435x TYR* 3.1 38.1 - - + -
75y GLY 3.2 14.6 - - - +
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Residues in contact with MET 115 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112x THR* 3.0 15.7 + - + +
114x TYR* 1.3 108.0 - - + +
116x ASN* 1.3 55.6 + - - +
118x THR* 3.4 0.7 + - - -
119x VAL* 2.7 53.4 + - + +
171x PRO* 5.3 3.1 - - + -
174x LEU* 2.9 44.4 - - + -
175x LEU* 4.0 25.4 - - + -
178x LEU* 3.3 31.6 - - + -
179x HIS* 6.3 0.2 - - + -
202x CYS* 4.3 6.7 - - - -
206x MET* 4.5 7.0 - - + -
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Residues in contact with ASN 116 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106x LEU* 3.3 43.1 + - + +
107x THR 4.2 1.2 - - - +
108x ASN* 4.3 10.1 - - - +
112x THR* 2.5 38.6 + - - -
113x CYS* 3.2 11.6 - - - +
115x MET* 1.3 83.2 - - - +
117x ALA* 1.3 66.8 + - - +
119x VAL* 3.3 1.4 + - - +
120x GLN* 3.0 31.7 + - - +
171x PRO* 3.8 14.4 - - - +
451x ASP* 3.6 14.6 + - - +
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Residues in contact with ALA 117 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113x CYS 2.3 29.9 + - - +
114x TYR* 3.5 4.0 - - - +
116x ASN* 1.3 62.6 - - - +
118x THR* 1.3 58.2 - - - +
120x GLN* 2.5 31.4 + - - +
121x CYS* 3.2 7.6 + - - -
423x LEU* 3.8 20.2 - - + -
435x TYR* 3.9 21.5 - - + +
436x VAL 4.4 0.2 - - - -
437x SER* 3.6 27.6 + - - +
449x PHE 5.9 0.4 - - - -
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Residues in contact with THR 118 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114x TYR 2.8 15.6 + - - -
115x MET 3.8 0.2 - - - -
117x ALA* 1.3 73.4 - - - +
119x VAL* 1.3 61.9 + - - +
120x GLN 3.2 0.5 + - - -
121x CYS* 3.3 2.7 + - - +
122x ILE* 3.2 30.3 + - + +
199x ALA* 3.0 34.8 + - - +
202x CYS* 3.3 26.2 - - - -
203x TRP* 3.5 33.5 - - + +
206x MET* 3.4 12.6 - - + -
423x LEU* 4.0 8.6 - - - +
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Residues in contact with VAL 119 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106x LEU* 4.4 14.4 - - + -
115x MET* 2.7 47.9 + - + +
116x ASN* 3.7 5.4 - - - +
117x ALA 2.8 3.2 + - - -
118x THR* 1.3 71.5 - - - +
120x GLN* 1.3 56.8 + - + +
122x ILE* 4.1 4.5 - - - +
123x ARG* 3.4 20.8 + - - +
155x LEU* 4.7 9.2 - - + -
158x LEU* 4.8 12.1 - - + -
159x PHE* 4.0 22.5 - - + -
162x MET* 5.4 2.2 - - - -
171x PRO* 6.3 0.4 - - + -
174x LEU* 4.5 11.7 - - + -
206x MET* 3.5 24.9 - - + -
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Residues in contact with GLN 120 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104x CYS 3.8 4.8 + - - -
105x GLY* 3.9 6.1 - - - -
106x LEU* 3.7 20.5 + - + +
116x ASN* 3.0 21.4 - - - +
117x ALA* 2.5 14.3 + - - +
119x VAL* 1.3 75.2 - - + +
121x CYS* 1.3 60.2 + - - +
123x ARG* 2.9 26.7 - - - +
124x SER 3.3 3.5 + - - -
162x MET* 3.6 22.5 - - + +
437x SER* 3.8 11.8 - - - +
439x VAL* 3.5 12.0 - - - +
449x PHE* 2.8 61.7 - - + +
451x ASP* 5.4 3.3 + - - +
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Residues in contact with CYS 121 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117x ALA 3.2 7.0 + - - -
118x THR 3.7 2.7 - - - +
120x GLN* 1.3 72.7 - - - +
122x ILE* 1.3 65.6 + - - +
123x ARG 2.9 2.2 + - - -
124x SER* 2.2 33.3 + - - -
125x VAL* 4.1 2.3 + - - +
203x TRP* 3.2 29.8 - - + -
421x ALA* 4.1 14.6 - - + -
422x VAL 3.0 29.8 - - - -
423x LEU* 3.3 25.8 - - - -
437x SER* 3.4 9.2 - - - -
439x VAL* 4.6 0.2 - - - -
478x LEU* 4.4 1.9 - - - +
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Residues in contact with ILE 122 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118x THR* 3.2 25.8 - - + +
119x VAL* 4.1 5.8 - - - +
121x CYS* 1.3 78.4 - - - +
123x ARG* 1.3 63.5 + - - +
125x VAL* 3.2 24.4 + - - +
128x LEU* 3.1 33.2 - - + +
132x LEU* 6.1 0.7 - - + -
155x LEU* 5.3 6.7 - - + -
159x PHE* 4.8 9.8 - - + -
203x TRP* 4.3 11.4 - - + +
206x MET* 3.8 37.2 - - + -
207x MET* 4.1 25.1 - - + -
210x LEU* 4.3 11.9 - - + -
246x PHE* 6.3 0.2 - - - -
478x LEU* 6.3 0.2 - - - -
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Residues in contact with ARG 123 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104x CYS* 4.9 3.8 + - - +
119x VAL 3.4 13.1 + - - +
120x GLN* 2.9 20.9 - - - +
122x ILE* 1.3 79.4 - - - +
124x SER* 1.3 50.7 + - - +
125x VAL 2.9 11.1 + - - -
129x LYS* 3.0 52.4 - - - +
159x PHE* 3.5 27.4 - - + -
162x MET* 2.9 61.5 + - - +
163x ASP* 3.4 24.5 + - - +
441x ARG* 3.8 25.0 - - - +
449x PHE* 4.1 16.9 - - - -
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Residues in contact with SER 124 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120x GLN 3.3 0.4 + - - -
121x CYS 2.2 27.4 + - - -
123x ARG* 1.3 74.4 - - - +
125x VAL* 1.3 49.8 + - - +
126x PRO* 2.6 24.0 - - - +
129x LYS* 5.2 2.0 - - - +
420x GLN* 4.2 16.4 + - - +
421x ALA* 3.7 5.3 - - - +
439x VAL* 3.5 38.6 - - - -
441x ARG* 4.6 7.4 - - - +
478x LEU* 3.6 16.3 - - - +
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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