Contacts of the helix formed by residues 110 - 125 (chain A) in PDB entry 2JG1
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 ASP 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A LYS* 3.4 30.8 + - - -
108A GLU* 3.8 2.9 + - - +
109A ILE* 1.3 75.5 - - - +
111A ASN* 1.3 66.3 + - - +
112A GLN* 3.1 11.1 + - - +
113A GLU* 2.8 43.3 + - - +
114A ALA* 3.0 27.5 + - - +
140A GLY 5.6 1.1 - - - -
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Residues in contact with ASN 111 (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 ASP* 1.3 80.3 - - - +
112A GLN* 1.3 70.2 + - - +
114A ALA* 3.4 7.2 + - - +
115A ALA* 3.0 30.2 + - - +
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Residues in contact with GLN 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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81A TYR* 3.9 3.3 + - - -
84A LYS* 5.0 9.7 + - - -
110A ASP* 3.1 10.3 + - - +
111A ASN* 1.3 89.9 + - - +
113A GLU* 1.3 59.8 + - + +
115A ALA* 3.5 4.8 + - - +
116A GLY* 2.8 26.2 + - - -
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Residues in contact with GLU 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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58A PHE* 3.9 1.0 - - - -
81A TYR* 3.7 26.6 - - + +
82A ASN 4.6 0.6 - - - +
83A ILE* 3.3 19.9 - - + +
84A LYS* 2.7 43.5 + - - +
85A GLY 5.3 0.9 + - - -
108A GLU 4.1 3.3 - - - +
109A ILE* 3.7 18.7 - - + -
110A ASP* 2.8 42.7 + - - +
112A GLN* 1.3 75.8 - - + +
114A ALA* 1.3 59.6 + - - +
117A PHE* 2.9 31.9 + - - +
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Residues in contact with ALA 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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58A PHE* 4.7 0.4 - - - -
109A ILE* 3.7 6.6 - - - +
110A ASP 3.0 17.0 + - - +
111A ASN* 3.7 8.5 - - - +
113A GLU* 1.3 78.3 - - - +
115A ALA* 1.3 60.8 + - - +
118A ILE* 3.4 11.8 + - - +
140A GLY 5.7 1.1 - - - +
141A LEU* 3.8 23.1 - - + -
142A ASN 6.1 0.7 - - - +
145A TYR* 2.6 34.8 + - + -
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Residues in contact with ALA 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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111A ASN 3.0 17.9 + - - +
112A GLN* 3.8 6.1 - - - +
114A ALA* 1.3 74.7 - - - +
116A GLY* 1.3 64.3 + - - +
118A ILE* 3.3 9.6 + - - +
119A LYS* 3.2 27.9 + - + +
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Residues in contact with GLY 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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81A TYR* 3.5 29.7 - - - -
112A GLN 2.8 15.7 + - - -
113A GLU 3.3 0.4 + - - -
115A ALA* 1.3 73.6 - - - +
117A PHE* 1.3 57.1 + - - +
119A LYS* 3.2 7.9 + - - +
120A HIS* 2.9 28.2 + - - +
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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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5A LEU* 4.0 20.0 - - + -
7A LEU* 4.0 16.4 - - + -
56A SER* 3.6 21.3 - - - -
57A GLY* 3.9 12.6 - - - -
58A PHE* 3.6 15.9 - + + -
81A TYR* 3.8 26.8 - - + -
113A GLU 2.9 15.1 + - - +
115A ALA 3.3 0.2 - - - -
116A GLY* 1.3 72.9 - - - +
118A ILE* 1.3 58.7 - - + +
120A HIS* 3.2 9.4 + + - +
121A PHE* 2.7 47.6 + + + +
145A TYR* 3.3 29.2 - + - +
149A ILE* 4.1 22.7 - - + -
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Residues in contact with ILE 118 (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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114A ALA 3.4 13.6 + - - +
115A ALA* 3.3 11.5 + - - +
117A PHE* 1.3 76.4 - - + +
119A LYS* 1.3 61.0 + - + +
121A PHE* 3.4 6.3 + - + +
122A GLU* 2.9 34.4 + - - +
145A TYR* 3.6 21.5 - - + +
148A GLN* 4.2 24.9 - - + +
149A ILE* 3.9 30.7 - - + +
152A ARG* 3.5 38.1 - - + +
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Residues in contact with LYS 119 (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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115A ALA* 3.2 17.0 + - + +
116A GLY* 3.6 9.2 - - - +
117A PHE 3.2 0.4 - - - -
118A ILE* 1.3 77.5 - - + +
120A HIS* 1.3 63.0 + - - +
122A GLU* 3.3 26.7 + - - +
123A GLN* 3.1 39.6 + - - +
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Residues in contact with HIS 120 (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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56A SER* 4.1 9.0 - - - -
79A ALA* 2.8 32.6 + - + -
80A PHE 4.3 3.5 + - - -
81A TYR* 4.2 26.5 - + + -
116A GLY 2.9 14.2 + - - +
117A PHE* 3.4 16.4 - + - +
119A LYS* 1.3 75.9 - - - +
121A PHE* 1.3 62.2 + - - +
123A GLN* 3.3 18.2 + - - +
124A MSE 3.1 55.8 + - + +
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Residues in contact with PHE 121 (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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3A LEU* 3.5 28.3 - - + -
5A LEU* 3.8 19.5 - - + -
117A PHE* 2.7 45.8 + + + +
118A ILE* 3.5 8.3 - - + +
120A HIS* 1.3 71.3 - - - +
122A GLU* 1.3 67.7 + - - +
124A MSE 3.1 15.5 + - - +
125A MSE 3.4 30.6 + - + +
131A VAL* 4.1 6.5 - - + -
149A ILE* 3.5 25.4 - - + -
152A ARG* 4.0 17.3 - - + -
153A CYS* 3.4 34.5 - - - -
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Residues in contact with GLU 122 (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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118A ILE* 2.9 21.9 + - - +
119A LYS* 3.3 34.3 + - - +
121A PHE* 1.3 76.4 - - - +
123A GLN* 1.3 62.8 + - + +
125A MSE 3.1 27.3 + - - +
126A GLU 4.6 0.9 + - - -
152A ARG* 2.8 45.2 + - + -
156A LYS* 5.7 2.8 - - - -
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Residues in contact with GLN 123 (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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119A LYS* 3.1 28.8 + - - +
120A HIS* 3.6 19.0 + - - +
121A PHE 3.3 0.2 - - - -
122A GLU* 1.3 76.0 - - + +
124A MSE 1.3 61.5 + - + +
125A MSE 3.3 0.4 + - - -
126A GLU* 3.9 13.7 - - - +
127A LYS* 3.7 18.4 - - - -
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Residues in contact with MSE 124 (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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3A LEU* 4.2 26.9 - - + -
54A LEU* 3.7 26.2 - - + -
56A SER* 4.7 3.1 - - - -
79A ALA* 3.2 33.9 - - + +
120A HIS* 3.1 40.6 - - + +
121A PHE* 3.1 11.2 + - - +
123A GLN* 1.3 76.3 - - + +
125A MSE 1.3 65.8 + - - +
126A GLU 3.3 1.6 - - - -
127A LYS* 3.1 34.7 + - + +
128A VAL* 3.4 17.7 - - + +
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Residues in contact with MSE 125 (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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3A LEU* 3.9 11.0 - - + -
121A PHE* 3.4 48.8 + - + +
122A GLU* 3.1 22.9 + - - +
124A MSE 1.3 80.7 - - - +
126A GLU* 1.3 59.7 + - - +
128A VAL* 3.4 36.1 - - + +
131A VAL* 4.2 1.8 - - + -
152A ARG* 4.1 14.4 - - + +
153A CYS* 4.1 17.3 - - - -
156A LYS* 3.9 26.7 - - + +
158A VAL* 4.1 25.6 - - - +
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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