Contacts of the helix formed by residues 106 - 124 (chain D) 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 PRO 106 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97D TYR* 3.5 14.6 - - + +
103D GLU* 5.8 2.5 - - - +
104D PRO 3.5 8.5 - - - +
105D ILE* 1.3 89.9 - - + +
107D CYS* 1.3 67.3 + - - +
108D GLU* 3.4 2.0 - - + +
109D GLN* 3.2 38.0 + - + +
110D LEU* 3.3 8.8 + - - +
140D ASP* 4.0 19.1 - - + +
141D LYS* 6.3 0.2 - - - -
142D HIS* 4.1 17.9 - - + +
67d TYR* 4.2 2.5 - - - +
73d TYR* 3.3 22.2 - - - +
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Residues in contact with CYS 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D MET* 3.4 35.3 - - - +
105D ILE 3.6 0.2 + - - -
106D PRO* 1.3 73.2 - - - +
108D GLU* 1.3 63.3 + - - +
110D LEU* 3.1 4.2 + - - +
111D VAL* 3.0 27.8 + - + +
136D TYR* 6.1 0.9 - - + -
137D ILE 5.9 0.4 - - - -
138D GLY* 3.7 7.2 - - - +
139D TRP 3.7 25.1 - - - -
140D ASP* 3.4 17.9 + - - -
146D GLN* 3.6 15.7 - - + +
148D TYR* 4.1 14.4 - - + -
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Residues in contact with GLU 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D PRO* 3.4 1.5 - - + +
107D CYS* 1.3 79.2 - - - +
109D GLN* 1.3 61.0 + - + +
111D VAL* 3.4 4.8 + - - +
112D THR* 2.8 35.4 + - + +
140D ASP* 4.9 0.4 + - - -
143D TYR* 4.0 9.7 - - + -
146D GLN* 4.5 3.2 + - - +
148D TYR* 3.6 31.7 + - + +
156D TYR* 3.5 25.4 + - + +
57E ARG* 2.9 32.5 + - - +
58E THR* 4.9 8.1 - - - -
71d ASN 5.3 2.9 - - - +
73d TYR* 5.3 7.5 + - - +
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Residues in contact with GLN 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D TYR* 3.2 20.5 - - - -
105D ILE* 3.9 9.1 - - + +
106D PRO* 3.2 36.7 + - + +
108D GLU* 1.3 79.0 - - + +
110D LEU* 1.3 54.9 + - - +
112D THR* 2.7 21.9 + - - -
113D ALA* 2.9 19.4 + - - +
67d TYR* 3.0 27.5 + - - -
71d ASN* 3.1 34.3 + - - +
73d TYR* 3.4 10.5 + - - +
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Residues in contact with LEU 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D LEU* 4.1 24.2 - - + -
69D ASN* 5.4 0.7 - - + -
72D MET* 3.4 32.1 - - + -
90D LEU* 3.6 33.0 - - + +
93D ILE* 3.6 25.1 - - + -
94D ALA* 4.1 16.2 - - + +
105D ILE* 3.6 14.3 - - + +
106D PRO 3.3 5.1 + - - +
107D CYS 3.1 9.5 + - - +
109D GLN* 1.3 74.2 - - - +
111D VAL* 1.3 68.4 + - + +
113D ALA* 3.2 4.9 + - - +
114D LEU* 3.0 21.3 + - - +
136D TYR* 5.3 2.7 - - + -
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Residues in contact with VAL 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D MET* 5.8 0.7 - - - -
107D CYS* 3.0 14.9 + - + +
108D GLU* 3.7 7.9 - - - +
110D LEU* 1.3 78.1 - - + +
112D THR* 1.3 62.4 + - - +
114D LEU* 3.2 2.8 + - - +
115D CYS* 2.9 33.9 + - - -
136D TYR* 3.4 59.9 - - + -
148D TYR* 4.1 14.8 - - + -
156D TYR* 3.7 34.3 - - + -
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Residues in contact with THR 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D GLU* 2.8 25.2 + - + +
109D GLN* 2.7 26.1 + - - +
111D VAL* 1.3 73.1 - - - +
113D ALA* 1.3 62.7 + - - +
115D CYS* 3.2 6.1 + - - -
116D ASP* 3.0 38.4 + - - +
156D TYR* 3.3 34.8 - - + +
81E ARG* 4.7 7.6 - - - +
85E ASN* 6.1 2.5 - - - -
71d ASN* 5.7 0.5 + - - -
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Residues in contact with ALA 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D ILE* 3.8 30.0 - - + +
105D ILE* 5.5 0.4 - - + -
109D GLN 2.9 19.1 + - - +
110D LEU 3.2 5.1 + - - +
112D THR* 1.3 80.3 + - - +
114D LEU* 1.3 60.7 + - - +
116D ASP* 3.7 8.5 + - - +
117D ILE* 3.5 21.3 + - - +
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Residues in contact with LEU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D LEU* 3.8 38.8 - - + +
89D GLU* 4.4 13.0 - - + -
90D LEU* 3.7 31.6 - - + -
93D ILE* 4.0 5.7 - - + +
110D LEU 3.0 12.4 + - - +
111D VAL 3.8 5.8 - - - +
113D ALA* 1.3 74.8 - - - +
115D CYS* 1.3 60.6 + - - +
117D ILE* 3.0 28.4 + - + +
118D LYS* 3.1 19.9 + - - +
134D LEU* 4.0 13.7 - - + -
136D TYR* 3.3 24.7 - - - +
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Residues in contact with CYS 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D VAL* 2.9 25.8 + - - +
112D THR* 3.7 6.7 - - - +
114D LEU* 1.3 77.5 - - - +
116D ASP* 1.3 58.6 - - - +
118D LYS* 3.8 6.5 - - - +
119D GLN* 2.9 26.0 + - - +
136D TYR* 4.7 1.8 - - - -
150D SER* 3.5 33.7 - - - -
154D GLY* 3.2 34.5 - - - +
156D TYR* 3.8 18.4 - - + -
81E ARG* 3.8 7.6 - - - +
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Residues in contact with ASP 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D THR* 3.0 24.7 + - - +
113D ALA* 3.9 7.5 - - - +
114D LEU 3.2 0.2 - - - -
115D CYS* 1.3 76.7 - - - +
117D ILE* 1.3 58.7 + - + +
119D GLN* 3.8 7.5 - - - +
120D ALA* 3.0 29.6 + - - +
81E ARG* 3.0 30.0 + - - +
82E ILE* 3.7 20.5 - - + +
85E ASN* 4.2 15.8 + - - -
70d ARG* 5.0 5.5 + - - -
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Residues in contact with ILE 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D LEU* 5.5 2.0 - - + -
89D GLU* 3.6 36.1 - - + +
93D ILE* 4.6 6.3 - - + -
113D ALA 3.5 15.7 + - - +
114D LEU* 3.0 17.0 + - + +
116D ASP* 1.3 76.2 - - + +
118D LYS* 1.3 65.1 + - - +
120D ALA* 3.2 7.4 + - + +
121D TYR* 3.0 41.2 + - + -
130D PHE* 4.5 9.0 - - + -
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Residues in contact with LYS 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D LEU* 4.1 20.0 - - + -
114D LEU* 3.1 15.5 + - - +
115D CYS* 3.4 20.2 + - - +
117D ILE* 1.3 75.0 - - - +
119D GLN* 1.3 64.5 + - - +
121D TYR* 3.0 17.8 + - - +
122D THR* 3.1 17.1 + - - +
129D PRO* 5.5 0.5 - - - +
130D PHE* 4.0 23.8 - - + +
132D VAL 4.2 4.0 + - - +
134D LEU* 3.4 16.4 - - - +
150D SER* 2.7 32.7 + - - -
151D ASP 3.3 23.3 + - - +
152D PRO* 4.0 12.9 - - + +
154D GLY* 3.7 14.4 - - - +
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Residues in contact with GLN 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D CYS 2.9 17.4 + - - +
116D ASP* 3.8 6.0 - - - +
118D LYS* 1.3 76.8 - - - +
120D ALA* 1.3 72.4 + - - +
122D THR* 2.5 37.4 + - - +
123D GLN* 3.0 37.8 + - - +
153D SER 3.9 10.5 - - - +
154D GLY* 3.9 1.2 - - - +
78E ALA* 3.7 25.4 - - + -
79E ASP* 3.5 20.6 + - - +
81E ARG* 5.2 1.1 - - - +
82E ILE* 3.2 35.8 - - + +
125E ARG* 4.1 0.6 - - - +
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Residues in contact with ALA 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D ASP 3.0 16.4 + - - +
117D ILE* 3.2 9.6 + - + +
119D GLN* 1.3 87.6 + - - +
121D TYR* 1.3 64.2 - - + +
123D GLN* 3.2 4.5 + - - +
124D PHE* 3.1 46.8 + - + +
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Residues in contact with TYR 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C GLN* 3.2 32.0 + - - +
10D THR* 3.7 13.9 - - - +
117D ILE* 3.0 30.9 + - + +
118D LYS* 3.0 14.9 + - - +
120D ALA* 1.3 79.7 - - + +
122D THR* 1.3 58.8 + - - +
124D PHE 3.7 8.0 - - - +
127D LYS* 4.0 35.0 + - + +
128D ARG 3.8 16.6 - - - -
129D PRO* 4.6 10.9 - - + +
130D PHE* 3.7 31.3 - + + -
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Residues in contact with THR 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D THR 4.9 0.7 - - - +
10D THR* 3.4 21.0 - - - +
18D LEU* 4.8 3.0 - - - +
21D VAL* 3.8 27.6 - - + -
118D LYS 3.1 11.9 + - - +
119D GLN* 2.5 35.1 + - - +
121D TYR* 1.3 75.6 - - - +
123D GLN* 1.3 52.6 + - - -
129D PRO* 4.3 11.9 - - + -
152D PRO 3.7 18.8 - - - +
153D SER* 4.4 9.0 + - - -
79E ASP* 5.0 0.7 + - - -
125E ARG* 2.5 29.3 + - - -
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Residues in contact with GLN 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D THR* 3.7 4.5 - - - -
119D GLN* 3.0 35.3 + - - +
120D ALA* 3.2 4.0 + - - +
122D THR* 1.3 80.6 - - - +
124D PHE* 1.3 68.2 + - + +
79E ASP* 4.0 0.2 + - - -
82E ILE* 4.8 2.6 - - - +
118E TYR* 3.4 27.0 + - + -
123E GLY 3.6 1.9 - - - +
125E ARG* 3.3 63.7 + - - +
127E PHE* 2.8 44.5 - - - +
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Residues in contact with PHE 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D THR* 3.9 5.8 - - - -
120D ALA* 3.1 33.3 + - + +
121D TYR* 3.7 10.7 - - - +
122D THR 3.7 0.4 - - - -
123D GLN* 1.3 93.1 - - + +
125D GLY* 1.3 61.2 + - - +
126D GLY 3.6 3.1 - - - -
127D LYS* 5.6 0.7 - - - +
118E TYR* 3.6 28.5 - + - -
123E GLY* 2.9 28.7 - - - +
124E ARG* 4.0 21.5 - - + -
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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
------------------------------------------------------------
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