Contacts of the helix formed by residues 106 - 123 (chain B) in PDB entry 1JEQ
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 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75B GLN 5.1 1.6 + - - -
77B ILE* 4.5 0.9 - - - +
104B GLN 3.9 1.0 + - - -
105B ALA* 1.3 70.9 - - - +
107B PHE* 1.3 64.0 + - - +
108B LEU* 2.9 10.7 + - - +
109B ASP* 2.9 58.5 + - + +
110B ALA* 3.1 11.1 + - - +
141B ARG 4.0 9.6 - - - +
142B PHE* 3.3 14.0 - - - +
143B SER* 2.9 30.2 + - - -
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Residues in contact with PHE 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B CYS* 5.4 0.5 - - - -
59B PHE* 4.1 24.0 - + + -
105B ALA 3.1 6.5 + - - +
106B ASP* 1.3 72.2 + - - +
108B LEU* 1.3 94.7 + - + +
110B ALA* 3.4 5.5 + - - +
111B LEU* 3.2 20.5 + - + +
134B ILE* 5.1 7.3 - - + +
136B THR* 4.9 11.9 - - + +
138B LEU* 4.1 25.1 - - + -
140B SER 5.5 1.8 - - - +
141B ARG 4.5 1.8 + - - +
142B PHE* 3.8 41.4 - + - +
163B PHE* 4.0 24.7 - + - -
204B GLY 4.6 3.8 - - - -
207B ILE* 4.7 7.2 - - + -
208B VAL* 3.9 19.1 - - + -
211B VAL* 6.2 0.7 - - + -
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ASP* 2.9 11.0 + - - +
107B PHE* 1.3 107.6 - - + +
109B ASP* 1.3 61.7 + - - +
111B LEU* 3.2 22.6 + - + +
112B ILE* 2.9 33.3 + - - +
142B PHE* 4.2 13.2 - - + -
143B SER 3.7 22.4 - - - +
144B LYS* 4.6 0.2 - - - -
146B GLN* 5.3 2.7 - - + -
147B LEU* 3.4 35.7 - - + +
150B ILE* 4.0 18.1 - - + +
207B ILE* 4.4 5.6 - - + -
211B VAL* 5.3 4.0 - - + -
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Residues in contact with ASP 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B TYR* 3.5 39.8 + - + -
75B GLN 5.1 0.7 + - - -
77B ILE* 3.4 15.7 - - + -
106B ASP* 2.9 42.5 + - + +
108B LEU* 1.3 77.7 - - - +
110B ALA* 1.3 59.7 - - - +
112B ILE* 3.1 5.6 + - - +
113B VAL* 2.9 26.0 + - - +
143B SER* 6.1 0.5 - - - -
146B GLN* 4.5 13.7 - - - +
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Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B CYS* 3.5 9.9 - - - -
57B VAL* 4.6 0.7 - - + +
59B PHE* 3.3 47.8 - - + -
77B ILE* 3.4 15.1 - - + +
106B ASP 3.1 6.0 + - - +
107B PHE 3.4 10.3 - - - +
109B ASP* 1.3 75.8 - - - +
111B LEU* 1.3 51.8 + - - +
113B VAL* 2.9 6.0 + - - +
114B SER* 2.7 36.6 + - - -
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B CYS* 4.2 3.0 - - - -
107B PHE* 3.2 12.1 + - + +
108B LEU* 3.2 26.9 + - + +
110B ALA* 1.3 79.8 - - - +
112B ILE* 1.3 51.9 + - - +
114B SER* 2.9 7.7 + - - -
115B MET* 2.7 48.3 + - + +
132B ILE* 4.0 20.2 - - + -
134B ILE* 4.0 27.8 - - + -
150B ILE* 4.0 20.4 - - + -
154B LEU* 5.1 1.6 - - + -
161B LEU* 4.2 23.1 - - + -
163B PHE* 4.9 9.4 - - + -
211B VAL* 5.4 4.3 - - + -
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Residues in contact with ILE 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B LEU* 3.9 11.9 - - + -
74B TYR* 3.6 32.5 - - + +
108B LEU 2.9 16.6 + - - +
109B ASP* 3.5 9.2 - - - +
111B LEU* 1.3 75.9 - - - +
113B VAL* 1.3 62.2 + - - +
115B MET* 3.0 26.0 + - + +
116B ASP* 2.8 21.9 + - + +
146B GLN* 3.5 43.1 - - + +
149B ILE* 5.9 4.5 - - + -
150B ILE* 3.8 9.0 - - + -
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Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B VAL* 4.5 2.9 - - + -
66B ASN* 3.9 20.2 - - + +
67B PRO* 4.8 4.3 - - + -
68B LEU* 4.3 6.5 - - + -
74B TYR* 3.9 13.7 - - + -
77B ILE* 3.5 35.9 - - + -
79B VAL* 3.8 28.5 - - + -
109B ASP 2.9 21.7 + - - +
110B ALA 3.4 4.9 - - - +
112B ILE* 1.3 76.3 - - - +
114B SER* 1.3 62.5 + - - +
116B ASP* 3.2 9.5 + - + +
117B VAL* 3.1 21.3 + - - +
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Residues in contact with SER 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL* 3.6 20.7 - - - +
13B CYS* 3.2 35.6 - - - +
57B VAL* 3.4 19.9 - - - +
110B ALA 2.7 11.9 + - - -
111B LEU* 3.2 12.3 - - - -
113B VAL* 1.3 74.5 - - - +
115B MET* 1.3 61.1 + - - +
117B VAL* 3.2 13.2 + - - +
118B ILE* 3.4 9.9 + - - +
132B ILE* 4.1 13.7 - - - -
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Residues in contact with MET 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B LEU* 2.7 19.2 + - + +
112B ILE* 3.0 40.4 + - + +
114B SER* 1.3 73.7 - - - +
116B ASP* 1.3 57.1 + - - +
118B ILE* 3.3 3.9 + - - +
119B GLN* 3.0 40.1 + - - +
132B ILE* 3.9 20.9 - - + -
150B ILE* 3.3 40.2 - - + +
153B SER* 4.6 11.7 - - - -
154B LEU* 3.6 31.2 - - + -
159B ILE* 4.5 8.9 - - + +
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Residues in contact with ASP 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B PRO* 4.0 17.5 - - - +
68B LEU* 3.8 35.4 - - + +
112B ILE* 2.8 12.2 + - + +
113B VAL* 3.4 10.8 - - + +
114B SER 3.2 0.2 - - - -
115B MET* 1.3 74.5 - - - +
117B VAL* 1.3 67.9 + - - +
119B GLN* 3.9 14.1 + - - +
120B HIS* 3.2 30.8 + - - +
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Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL* 3.8 9.0 - - + -
55B ALA* 3.7 26.9 - - + -
57B VAL* 4.5 8.1 - - + -
67B PRO* 5.9 3.6 - - + -
79B VAL* 3.9 31.9 - - + -
82B HIS* 5.4 0.7 - - + -
83B LEU* 4.2 5.4 - - + -
113B VAL 3.1 14.8 + - - +
114B SER* 3.2 9.1 + - - +
116B ASP* 1.3 76.9 + - - +
118B ILE* 1.3 69.7 + - - +
121B GLU* 3.0 56.0 + - - +
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Residues in contact with ILE 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ALA* 4.2 10.1 - - + +
11B VAL* 3.6 17.5 - - + -
83B LEU* 5.1 2.7 - - + -
114B SER 3.4 2.1 + - - +
115B MET 3.3 7.5 + - - +
116B ASP 3.2 0.4 - - - -
117B VAL* 1.3 83.9 - - - +
119B GLN* 1.3 69.3 + - - +
122B THR* 2.8 35.0 + - + +
130B ARG* 3.8 34.5 - - + -
131B HIS 3.9 10.1 - - - +
132B ILE* 3.7 20.4 - - + -
157B CYS* 6.1 0.7 - - + -
159B ILE* 3.5 38.4 - - + -
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Residues in contact with GLN 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B MET* 3.0 31.9 + - - +
116B ASP* 3.9 14.4 + - - +
118B ILE* 1.3 82.1 - - + +
120B HIS* 1.3 62.7 + - + +
122B THR* 3.2 12.0 + - - -
123B ILE* 3.6 12.0 - - - +
153B SER* 4.2 18.7 + - - -
157B CYS* 3.0 36.9 - - + -
159B ILE* 4.5 8.3 - - + +
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Residues in contact with HIS 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ASP* 3.2 22.9 + - - +
119B GLN* 1.3 80.1 - - + +
121B GLU* 1.3 70.4 + - + +
122B THR 3.2 4.6 + - - -
123B ILE* 3.3 35.1 + - + +
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Residues in contact with GLU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B PRO* 5.8 1.2 - - - +
82B HIS* 2.9 31.0 + - - +
83B LEU* 2.7 51.8 + - + +
117B VAL* 3.0 42.1 + - - +
118B ILE 3.7 0.7 - - - -
120B HIS* 1.3 85.5 - - + +
122B THR* 1.3 60.2 + - - +
123B ILE 3.6 0.4 - - - -
124B GLY 5.3 0.7 - - - -
125B LYS* 4.0 19.6 - - - +
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Residues in contact with THR 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ALA* 4.1 5.2 - - + -
83B LEU* 3.9 11.0 - - + -
118B ILE* 2.8 38.5 + - + +
119B GLN* 3.2 9.9 + - - -
120B HIS 3.2 0.2 - - - -
121B GLU* 1.3 79.7 - - - +
123B ILE* 1.3 68.2 + - - +
124B GLY 3.4 2.2 - - - -
125B LYS* 2.9 23.0 + - - +
127B PHE* 3.5 33.4 - - + -
130B ARG* 4.8 6.8 - - + +
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Residues in contact with ILE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B GLN 3.6 9.9 - - - +
120B HIS* 3.3 40.1 + - + +
122B THR* 1.3 80.2 + - - +
124B GLY* 1.3 64.2 + - - +
125B LYS 3.2 5.2 + - - +
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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