Contacts of the helix formed by residues 12 - 23 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ASP* 1.3 74.6 - - - +
13A PHE* 1.3 60.9 - - - +
15A VAL 3.9 0.2 - - - -
16A LEU* 3.1 25.5 + - - +
142A ILE* 3.5 10.5 - - - +
145A ILE* 3.7 13.7 - - - +
172A LEU* 3.6 15.6 - - - +
173A PHE* 3.2 16.2 + - - -
175A GLN 3.1 11.1 + - - -
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Residues in contact with PHE 13 (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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11A ASP* 3.2 20.7 + - - +
12A GLY* 1.3 76.1 - - - +
14A HIS* 1.3 56.9 + - - +
16A LEU* 3.7 3.9 - - - +
17A ILE* 3.0 33.5 + - + +
35A PRO 5.0 4.0 - - - -
38A ASN* 4.2 5.2 - - + -
39A LEU* 3.8 37.4 - - + +
42A MET* 3.6 25.8 - - + -
173A PHE* 3.4 61.8 + + + +
174A GLY* 4.5 2.2 - - - -
561B VAL* 3.9 16.8 - - + -
562B VAL 3.5 35.2 - - - -
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Residues in contact with HIS 14 (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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10A THR* 3.4 23.6 + - - +
11A ASP* 3.1 19.0 + - - +
13A PHE* 1.3 75.5 - - - +
15A VAL* 1.3 61.9 + - - +
16A LEU 3.2 1.1 - - - -
17A ILE* 3.7 18.8 - - + -
18A ASP* 2.8 42.8 + - - +
42A MET* 2.9 37.4 - - + +
46A ASP* 5.9 3.4 - - + -
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Residues in contact with VAL 15 (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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10A THR* 3.4 27.6 - - + +
11A ASP 3.0 22.3 + - - +
14A HIS* 1.3 75.2 - - - +
16A LEU* 1.3 58.0 + - - +
18A ASP* 3.8 5.9 - - - +
19A ALA* 2.8 31.2 + - - +
142A ILE* 4.1 10.8 - - + +
145A ILE* 3.8 30.5 - - + -
146A PRO* 4.5 13.5 - - + -
177A ILE* 4.2 8.5 - - + -
182A ALA* 4.0 17.9 - - + +
185A LEU* 6.5 1.6 - - + -
186A LEU* 4.3 6.5 - - + +
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Residues in contact with LEU 16 (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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12A GLY 3.1 19.7 + - - +
13A PHE* 3.7 4.0 - - - +
15A VAL* 1.3 74.3 - - - +
17A ILE* 1.3 59.7 + - - +
20A LEU* 2.9 45.0 + - + +
39A LEU* 4.1 21.1 - - + -
104A LEU* 4.9 3.1 - - + -
139A ILE* 5.2 0.4 - - + -
145A ILE* 3.6 27.4 - - + +
149A ILE* 3.6 27.8 - - + -
168A LEU* 3.7 38.4 - - + -
172A LEU* 5.5 0.9 - - + -
173A PHE* 4.3 8.7 - - + -
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Residues in contact with ILE 17 (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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13A PHE* 3.0 32.8 + - + +
14A HIS* 3.7 19.7 - - + +
15A VAL 3.4 0.2 - - - -
16A LEU* 1.3 75.4 - - - +
18A ASP* 1.3 64.2 + - - +
20A LEU* 3.4 1.3 + - - -
21A LYS* 3.0 46.2 + - + +
39A LEU* 4.1 13.9 - - + -
42A MET* 3.6 38.6 - - + +
43A TRP* 3.7 30.5 - - + +
46A ASP* 4.0 17.7 - - + +
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Residues in contact with ASP 18 (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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10A THR* 5.3 1.9 + - - -
14A HIS* 2.8 33.4 + - - +
15A VAL* 3.8 4.9 - - - +
17A ILE* 1.3 77.3 - - - +
19A ALA* 1.3 59.7 + - - +
21A LYS* 3.2 18.3 + - - +
22A MET* 2.8 32.3 + - + +
46A ASP* 5.1 1.9 - - - +
183A ASN* 5.7 0.2 - - - +
186A LEU* 3.8 27.8 - - + +
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Residues in contact with ALA 19 (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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15A VAL 2.8 22.1 + - - +
16A LEU 3.7 4.0 - - - +
18A ASP* 1.3 72.7 - - - +
20A LEU* 1.3 62.8 + - - +
22A MET* 3.3 3.3 + - - +
23A ASN* 3.0 31.8 + - - +
145A ILE* 3.9 18.8 - - + -
146A PRO* 4.2 12.6 - - + -
149A ILE* 4.1 13.5 - - + -
186A LEU* 3.6 17.2 - - + +
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Residues in contact with LEU 20 (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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16A LEU* 2.9 39.6 + - + +
17A ILE* 3.7 4.3 - - - +
19A ALA* 1.3 77.6 - - - +
21A LYS* 1.3 61.8 + - - +
23A ASN* 3.2 9.0 + - - -
24A ASP 3.3 0.2 + - - -
25A ILE* 3.0 42.7 + - + +
28A MET* 4.4 15.9 - - + -
39A LEU* 5.8 1.8 - - + -
43A TRP* 4.0 23.6 - - + -
75A VAL* 4.8 6.7 - - + -
102A ILE* 5.7 5.4 - - + -
104A LEU* 4.2 24.2 - - + -
149A ILE* 4.1 27.8 - - + -
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Residues in contact with LYS 21 (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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17A ILE* 3.0 31.5 + - + +
18A ASP* 3.2 15.6 + - - +
20A LEU* 1.3 75.0 - - - +
22A MET* 1.3 56.9 + - - +
24A ASP* 3.0 22.5 + - - +
25A ILE 3.6 16.6 - - - +
43A TRP* 4.1 8.5 - - + -
46A ASP* 2.5 36.6 + - - +
48A GLN* 3.9 20.0 - - + +
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Residues in contact with MET 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ASP* 2.8 17.3 + - + +
19A ALA* 3.6 9.4 - - - +
20A LEU 3.2 0.2 - - - -
21A LYS* 1.3 76.0 - - - +
23A ASN* 1.3 58.1 + - - +
24A ASP* 3.3 3.9 + - - +
186A LEU* 4.0 20.4 - - + +
187A PHE* 3.6 45.5 - - - +
188A LYS* 3.5 33.0 - - + +
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Residues in contact with ASN 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA* 3.0 22.6 + - - +
20A LEU* 3.2 8.1 + - - +
21A LYS 3.2 0.4 - - - -
22A MET* 1.3 76.9 - - - +
24A ASP* 1.3 68.2 + - - +
25A ILE* 3.4 12.2 + - + +
72A LYS* 5.0 2.3 - - - +
73A PRO* 5.9 1.0 - - - +
146A PRO 5.1 2.4 + - - -
149A ILE* 3.5 16.8 - - + +
150A ALA* 4.4 3.5 - - - +
153A VAL* 3.7 38.7 - - + +
187A PHE 4.4 6.5 + - - -
188A LYS* 4.6 6.2 + - - +
189A PRO* 3.4 35.9 - - - +
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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