Contacts of the helix formed by residues 12 - 23 (chain B) in PDB entry 2JI8
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 GLY 12 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B ASP* 1.3 68.7 - - - +
13B PHE* 1.3 65.3 + - - +
16B LEU* 3.2 24.4 + - - +
142B ILE* 4.0 12.8 - - - -
145B ILE* 3.9 9.5 - - - +
172B LEU* 3.7 15.8 - - - +
173B PHE* 2.9 19.0 + - - -
175B GLN 2.9 12.0 + - - -
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Residues in contact with PHE 13 (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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561A VAL* 3.7 27.8 - - + -
562A VAL 3.9 4.3 - - - -
563A SER* 3.7 30.5 - - - -
11B ASP* 3.3 22.8 - - - +
12B GLY* 1.3 77.1 - - - +
14B HIS* 1.3 63.2 + - - +
16B LEU* 3.4 3.1 + - - +
17B ILE* 3.1 29.4 + - + +
35B PRO 4.9 4.0 - - - -
38B ASN* 4.1 6.1 - - + -
39B LEU* 3.7 39.6 - - + +
42B MET* 3.7 18.6 - - + -
173B PHE* 3.3 53.3 + + + +
174B GLY* 5.2 0.7 - - - -
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Residues in contact with HIS 14 (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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563A SER* 4.1 1.6 - - - -
565A VAL 3.6 27.9 + - - -
10B THR* 3.3 19.8 + - - +
11B ASP* 2.8 23.5 + - - +
13B PHE* 1.3 79.2 - - - +
15B VAL* 1.3 64.8 + - - +
17B ILE* 3.5 12.6 + - + +
18B ASP* 3.0 34.5 + - - +
42B MET* 2.8 33.3 - - + +
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Residues in contact with VAL 15 (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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10B THR* 3.8 23.1 - - + -
11B ASP 3.1 17.7 + - - +
13B PHE 3.4 0.2 - - - -
14B HIS* 1.3 76.7 - - - +
16B LEU* 1.3 58.3 + - - +
18B ASP* 3.4 7.7 + - - +
19B ALA* 2.9 28.1 + - - +
142B ILE* 3.8 18.8 - - + +
145B ILE* 3.9 31.0 - - + -
146B PRO* 4.1 17.7 - - + -
177B ILE* 4.2 4.7 - - + -
182B ALA* 4.3 11.0 - - + -
186B LEU* 4.0 7.9 - - + +
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Residues in contact with LEU 16 (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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12B GLY 3.2 16.5 + - - +
13B PHE 3.5 3.6 - - - +
15B VAL* 1.3 75.9 - - - +
17B ILE* 1.3 60.3 + - - +
19B ALA* 3.3 0.9 + - - +
20B LEU* 2.8 50.1 + - + +
39B LEU* 4.0 17.0 - - + -
104B LEU* 4.9 5.4 - - + -
139B ILE* 5.6 0.2 - - + -
145B ILE* 3.7 21.2 - - + +
149B ILE* 3.9 28.5 - - + -
168B LEU* 3.9 26.9 - - + -
172B LEU* 5.5 1.6 - - + -
173B PHE* 3.8 27.4 - - + -
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Residues in contact with ILE 17 (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 PHE* 3.1 22.1 + - + +
14B HIS* 3.7 18.8 - - + +
15B VAL 3.4 0.2 - - - -
16B LEU* 1.3 78.3 - - - +
18B ASP* 1.3 62.5 + - - +
20B LEU* 3.3 3.8 + - + +
21B LYS* 2.9 48.5 + - + +
39B LEU* 4.2 13.7 - - + -
42B MET* 3.8 37.9 - - + +
43B TRP* 3.8 32.3 - - + +
46B ASP* 4.1 17.5 - - + +
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Residues in contact with ASP 18 (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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10B THR* 5.5 0.9 + - - -
14B HIS* 3.0 27.6 + - - +
15B VAL* 3.6 5.3 - - - +
17B ILE* 1.3 80.0 - - - +
19B ALA* 1.3 57.8 + - - +
21B LYS* 3.3 18.2 + - - +
22B MET* 3.0 33.2 + - + +
46B ASP* 5.5 1.0 - - - +
182B ALA* 6.1 0.7 - - - +
183B ASN* 5.9 0.7 + - - -
186B LEU* 3.7 29.1 - - + +
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Residues in contact with ALA 19 (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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15B VAL 2.9 18.1 + - - +
16B LEU 3.6 3.8 - - - +
18B ASP* 1.3 72.5 - - - +
20B LEU* 1.3 62.8 + - - +
22B MET* 3.4 3.8 + - - +
23B ASN* 2.7 35.5 + - - +
145B ILE* 3.8 19.7 - - + -
146B PRO* 4.2 11.4 - - + -
149B ILE* 4.2 12.1 - - + -
186B LEU* 3.6 16.8 - - + +
187B PHE 6.0 0.4 - - - -
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Residues in contact with LEU 20 (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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16B LEU* 2.8 38.4 + - + +
17B ILE* 3.5 5.4 - - + +
19B ALA* 1.3 77.6 - - - +
21B LYS* 1.3 62.1 + - - +
23B ASN* 3.2 9.7 + - - -
25B ILE* 3.2 43.1 + - + +
28B MET* 4.3 22.9 - - + -
39B LEU* 5.9 1.3 - - + -
43B TRP* 4.0 24.9 - - + -
75B VAL* 4.9 8.3 - - + -
102B ILE* 6.0 4.0 - - + -
104B LEU* 4.3 15.5 - - + -
149B ILE* 4.1 26.2 - - + -
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Residues in contact with LYS 21 (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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17B ILE* 2.9 31.0 + - + +
18B ASP* 3.3 15.3 + - - +
20B LEU* 1.3 76.9 - - - +
22B MET* 1.3 57.6 + - - +
24B ASP* 3.0 21.3 + - - +
25B ILE 3.6 16.2 - - - +
43B TRP* 4.2 5.2 - - + -
46B ASP* 2.9 36.1 + - - +
48B GLN* 3.7 21.9 - - - +
188B LYS* 5.3 0.9 + - - -
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Residues in contact with MET 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ASP* 3.0 18.6 + - + +
19B ALA* 3.6 8.1 - - - +
20B LEU 3.2 0.4 - - - -
21B LYS* 1.3 76.3 - - - +
23B ASN* 1.3 57.9 + - - +
24B ASP 3.2 1.1 - - - -
186B LEU* 3.9 27.8 - - + +
187B PHE* 3.5 47.3 - - - +
188B LYS* 3.2 45.0 - - + +
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Residues in contact with ASN 23 (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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19B ALA* 2.7 24.8 + - - +
20B LEU 3.2 6.9 + - - +
21B LYS 3.2 0.6 - - - -
22B MET* 1.3 80.9 - - - +
24B ASP* 1.3 68.9 + - - +
25B ILE* 3.2 16.5 + - + +
72B LYS* 5.1 1.2 - - - +
146B PRO 5.2 2.2 + - - -
149B ILE* 3.8 15.2 - - + +
150B ALA* 4.3 4.0 - - - +
153B VAL* 3.9 37.3 - - + +
187B PHE 4.5 3.6 + - - -
188B LYS* 5.3 1.6 - - - +
189B PRO* 3.2 35.7 - - - +
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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