Contacts of the helix formed by residues 106 - 124 (chain j) 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 j).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72j MET* 4.3 0.2 - - - -
97j TYR* 3.4 23.3 - - + +
103j GLU* 5.8 1.8 - - - +
104j PRO 3.4 5.8 - - - +
105j ILE* 1.3 98.4 - - + +
107j CYS* 1.3 66.5 + - - +
108j GLU* 4.6 2.7 - - + +
109j GLN* 3.1 29.9 + - + +
110j LEU* 3.4 1.6 + - - +
140j ASP* 3.9 21.3 - - + +
142j HIS* 4.0 18.8 - - + +
73r TYR* 3.3 21.5 - - + +
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Residues in contact with CYS 107 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72j MET* 3.6 35.4 - - - +
105j ILE 3.6 0.2 + - - -
106j PRO* 1.3 72.6 - - - +
108j GLU* 1.3 64.3 + - - +
110j LEU* 3.1 3.8 + - - +
111j VAL* 3.0 26.6 + - + +
136j TYR* 5.9 1.8 - - + -
137j ILE 5.9 0.4 - - - -
138j GLY* 3.8 7.9 - - - +
139j TRP 3.8 25.6 - - - -
140j ASP* 3.3 18.6 + - - +
146j GLN* 3.7 10.1 - - + -
148j TYR* 4.0 19.1 - - + -
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Residues in contact with GLU 108 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106j PRO* 3.3 1.7 - - + +
107j CYS* 1.3 78.3 - - - +
109j GLN* 1.3 60.0 + - + +
111j VAL* 3.3 4.8 + - - +
112j THR* 2.9 36.0 + - + +
140j ASP* 4.9 1.4 + - - -
143j TYR* 4.1 9.3 + - + -
146j GLN* 4.8 1.3 - - - +
148j TYR* 3.5 34.0 + - + +
156j TYR* 3.4 28.5 + - + +
57k ARG* 3.4 26.7 + - - +
58k THR* 4.3 14.9 - - - -
71r ASN 5.3 4.2 - - - +
73r TYR* 5.4 6.0 + - - +
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Residues in contact with GLN 109 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97j TYR* 3.2 19.1 - - - -
105j ILE* 4.0 10.9 - - + +
106j PRO* 3.1 24.4 + - + +
108j GLU* 1.3 79.3 - - + +
110j LEU* 1.3 55.3 + - - +
112j THR* 2.6 21.5 + - - -
113j ALA* 2.9 18.0 + - - +
67r TYR* 2.8 25.4 + - - -
71r ASN* 3.3 35.3 + - + +
73r TYR* 2.8 29.1 + - - +
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Residues in contact with LEU 110 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68j LEU* 4.1 23.6 - - + -
69j ASN* 5.6 0.4 - - + -
72j MET* 3.4 31.0 - - + -
90j LEU* 3.6 30.5 - - + +
93j ILE* 3.5 26.7 - - + -
94j ALA* 3.9 17.5 - - + +
105j ILE* 3.6 14.9 - - + +
106j PRO 3.4 4.5 + - - +
107j CYS 3.1 10.0 + - - +
109j GLN* 1.3 75.2 - - - +
111j VAL* 1.3 68.8 + - + +
113j ALA* 3.1 5.3 + - - +
114j LEU* 3.0 20.1 + - - +
136j TYR* 5.6 0.9 - - + -
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Residues in contact with VAL 111 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72j MET* 5.7 0.7 - - - -
107j CYS* 3.0 17.9 + - + +
108j GLU* 3.8 6.3 - - - +
110j LEU* 1.3 73.7 - - + +
112j THR* 1.3 66.4 + - - +
114j LEU* 3.2 3.1 + - - +
115j CYS* 2.9 25.5 + - - -
136j TYR* 3.5 58.3 - - + -
148j TYR* 4.2 12.8 - - + -
149j GLN 5.1 0.2 - - - +
156j TYR* 3.7 38.1 - - + -
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Residues in contact with THR 112 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108j GLU* 2.9 20.5 + - + +
109j GLN* 2.6 26.2 + - - -
111j VAL* 1.3 74.7 - - - +
113j ALA* 1.3 62.6 + - - +
115j CYS* 3.2 6.8 + - - +
116j ASP* 3.0 37.3 + - - +
156j TYR* 3.4 36.8 - - + +
81k ARG* 4.7 8.7 - - - +
85k ASN* 6.2 1.6 - - - -
71r ASN* 5.7 0.5 + - - -
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Residues in contact with ALA 113 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93j ILE* 3.7 32.6 - - + +
105j ILE* 5.7 0.2 - - + -
109j GLN 2.9 20.1 + - - +
110j LEU 3.1 5.8 + - - +
112j THR* 1.3 79.3 + - - +
114j LEU* 1.3 60.3 + - - +
116j ASP* 3.6 13.2 + - - +
117j ILE* 3.6 17.2 + - - +
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Residues in contact with LEU 114 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86j LEU* 3.9 39.9 - - + +
89j GLU* 4.8 0.9 - - + -
90j LEU* 3.5 35.7 - - + +
93j ILE* 4.1 3.5 - - + +
110j LEU 3.0 11.8 + - - +
111j VAL 3.8 6.3 - - - +
113j ALA* 1.3 74.4 - - - +
115j CYS* 1.3 65.7 + - - +
117j ILE* 3.0 35.7 + - + +
118j LYS* 3.2 14.0 + - - +
134j LEU* 3.9 17.0 - - + -
136j TYR* 3.2 25.1 - - - +
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Residues in contact with CYS 115 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111j VAL* 2.9 28.7 + - - +
112j THR* 3.7 6.7 - - - +
114j LEU* 1.3 76.5 - - - +
116j ASP* 1.3 58.6 + - - +
118j LYS* 3.3 5.8 + - - +
119j GLN* 2.9 26.7 + - - +
136j TYR* 4.9 1.8 - - - -
150j SER* 3.5 33.4 - - - -
154j GLY* 3.1 36.7 - - - +
156j TYR* 3.8 8.5 - - + -
81k ARG* 4.0 7.9 - - - +
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Residues in contact with ASP 116 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112j THR* 3.0 27.3 + - - +
113j ALA* 3.8 9.1 - - - +
114j LEU 3.2 0.2 - - - -
115j CYS* 1.3 75.3 - - - +
117j ILE* 1.3 58.3 + - + +
119j GLN* 3.6 8.5 + - - +
120j ALA* 2.9 29.6 + - - +
81k ARG* 3.4 19.6 + - - +
82k ILE* 3.4 24.7 - - + +
85k ASN* 4.3 14.9 + - - -
70r ARG* 5.0 4.9 + - - -
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Residues in contact with ILE 117 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86j LEU* 4.2 21.5 - - + -
89j GLU* 3.4 36.1 - - + +
93j ILE* 4.3 6.5 - - + -
113j ALA 3.6 15.7 - - - +
114j LEU* 3.0 17.9 + - + +
116j ASP* 1.3 75.5 - - + +
118j LYS* 1.3 67.2 + - - +
120j ALA* 3.2 7.4 + - - +
121j TYR* 3.1 35.1 + - + -
130j PHE* 4.4 9.4 - - + -
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Residues in contact with LYS 118 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86j LEU* 3.9 23.1 - - + -
114j LEU* 3.2 20.7 + - - +
115j CYS* 3.3 13.4 + - - +
117j ILE* 1.3 75.1 - - - +
119j GLN* 1.3 66.7 + - - +
121j TYR* 3.0 17.3 + - - +
122j THR* 3.1 17.2 + - - +
129j PRO* 5.3 0.9 - - - +
130j PHE* 4.2 22.0 - - + +
132j VAL 4.4 3.9 + - - +
134j LEU* 3.4 16.3 - - - +
136j TYR* 4.5 0.2 + - - -
150j SER* 2.6 32.3 + - - -
151j ASP 3.3 23.0 + - - +
152j PRO* 4.1 14.6 - - + +
154j GLY* 3.8 13.0 - - - +
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Residues in contact with GLN 119 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115j CYS 2.9 17.7 + - - +
116j ASP* 3.7 7.3 - - - +
118j LYS* 1.3 75.3 - - - +
120j ALA* 1.3 70.4 + - - +
122j THR* 2.6 37.7 + - - +
123j GLN* 3.0 39.3 + - - +
153j SER 3.8 11.2 - - - +
154j GLY* 4.0 1.2 - - - +
78k ALA* 3.6 26.5 - - + -
79k ASP* 3.5 21.0 + - - +
81k ARG* 5.1 0.7 - - - +
82k ILE* 3.4 34.4 - - + +
127k PHE* 4.7 0.2 - - - -
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Residues in contact with ALA 120 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116j ASP 2.9 14.9 + - - +
117j ILE* 3.3 13.7 - - - +
118j LYS 3.2 0.2 - - - -
119j GLN* 1.3 84.6 + - - +
121j TYR* 1.3 63.2 + - + +
123j GLN* 3.2 3.0 + - - +
124j PHE* 3.0 51.4 + - + +
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Residues in contact with TYR 121 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122i GLN* 4.6 9.2 + - + +
10j THR* 3.7 13.7 - - - +
117j ILE* 3.1 27.8 + - + +
118j LYS* 3.0 11.7 + - - +
120j ALA* 1.3 86.4 - - + +
122j THR* 1.3 60.2 + - - +
123j GLN 3.5 0.3 + - - -
124j PHE 4.0 6.9 - - - +
127j LYS* 4.0 39.1 + - + +
128j ARG 3.8 15.5 - - - -
129j PRO* 4.3 16.6 - - + +
130j PHE* 3.6 36.8 - + + -
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Residues in contact with THR 122 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9j THR 4.8 0.9 - - - +
10j THR* 3.4 17.5 - - - +
18j LEU* 4.1 9.1 - - + +
21j VAL* 3.9 20.4 - - + -
118j LYS 3.1 13.2 + - - +
119j GLN* 2.6 30.2 + - - +
121j TYR* 1.3 74.7 - - - +
123j GLN* 1.3 54.9 + - - +
129j PRO* 4.6 7.6 - - + -
152j PRO 3.7 18.8 - - - +
153j SER* 4.1 12.0 + - - +
79k ASP* 4.7 0.9 + - - -
125k ARG* 2.8 38.1 + - - -
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Residues in contact with GLN 123 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10j THR* 3.7 5.3 - - - -
119j GLN* 3.0 36.6 + - - +
120j ALA 3.2 3.5 + - - +
122j THR* 1.3 79.9 - - - +
124j PHE* 1.3 73.7 + - + +
79k ASP* 4.6 1.6 + - - -
82k ILE* 4.9 2.9 - - - +
118k TYR* 3.5 14.8 + - + -
124k ARG 3.8 0.7 - - - -
125k ARG* 2.8 67.1 + - + +
127k PHE* 2.7 47.6 - - - +
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Residues in contact with PHE 124 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10j THR* 4.0 4.9 - - - -
120j ALA* 3.0 35.5 + - + +
121j TYR* 4.0 10.0 - - - +
122j THR 3.8 0.4 - - - -
123j GLN* 1.3 102.1 - - + +
125j GLY* 1.3 63.8 + - - +
126j GLY 3.5 2.8 + - - -
127j LYS* 5.0 4.3 + - - +
118k TYR* 4.3 18.2 - + - -
123k GLY 3.1 19.5 - - - +
124k ARG* 3.9 15.3 - - + -
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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
------------------------------------------------------------
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