Contacts of the helix formed by residues 53 - 66 (chain P) in PDB entry 1J0B
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 ASN 53 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52P GLY* 1.3 70.9 - - - -
54P LYS* 1.3 97.4 + - - +
55P ILE 3.1 2.2 - - - -
56P ARG* 3.1 12.1 + - - +
57P LYS* 3.4 12.2 + - - -
167P TYR* 2.9 30.8 - - + +
194P THR* 2.7 27.7 + - - +
308P THR* 3.0 34.8 + - + +
1161P 5PA 3.7 21.0 + - - +
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Residues in contact with LYS 54 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51P GLY 5.6 0.7 - - - +
52P GLY* 3.6 0.4 - - - -
53P ASN* 1.3 96.1 - - - +
55P ILE* 1.3 62.8 + - - +
56P ARG 3.1 0.3 + - - -
57P LYS* 3.2 14.6 + - + +
58P LEU* 2.9 29.2 + - + +
82P ASN* 5.2 1.6 - - + -
83P HIS* 3.4 34.5 - - + +
86P VAL* 3.7 20.9 - - + -
157P GLY* 2.7 33.9 + - - +
191P SER* 4.2 0.2 + - - -
1161P 5PA 2.8 61.5 + - - +
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Residues in contact with ILE 55 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17P LEU* 4.7 6.8 - - + +
18P ILE* 3.4 20.4 - - + +
46P THR* 3.1 42.6 - - + +
48P LEU* 3.4 52.9 - - + +
51P GLY* 4.3 4.0 + - - -
52P GLY 4.2 3.0 + - - +
53P ASN 3.1 0.8 - - - +
54P LYS* 1.3 78.6 - - - +
56P ARG* 1.3 63.0 + - - +
58P LEU* 3.9 8.1 + - + +
59P GLU* 3.8 17.3 + - - +
86P VAL* 3.1 35.4 - - + +
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Residues in contact with ARG 56 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18P ILE* 3.5 32.0 - - + +
22P THR* 3.3 15.2 + - - +
41P LYS* 4.0 5.7 - - - +
43P ASP* 2.4 45.5 + - - +
46P THR* 4.8 4.3 - - + -
53P ASN 3.1 8.8 + - - +
54P LYS 3.0 0.4 - - - -
55P ILE* 1.3 76.3 - - - +
57P LYS* 1.3 67.1 + - - +
59P GLU* 3.1 28.0 + - - +
60P TYR* 3.9 1.4 + - - -
166P GLY* 3.8 17.2 + - - +
167P TYR* 3.3 30.2 - - + +
169P ARG* 5.9 3.0 - - - +
170P ALA* 3.6 29.2 - - - +
173P GLU* 3.9 22.6 + - - -
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Residues in contact with LYS 57 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53P ASN* 3.4 20.1 + - - +
54P LYS* 3.2 21.0 + - + +
56P ARG* 1.3 76.5 - - - +
58P LEU* 1.3 52.2 + - - +
60P TYR* 2.9 8.3 + - - +
61P LEU* 2.7 46.8 + - + +
83P HIS* 6.3 0.2 - - + -
157P GLY 3.3 19.3 - - - +
158P GLY* 4.2 7.4 - - - +
159P ALA* 5.0 0.4 - - - -
163P GLY* 3.6 27.1 - - - +
164P THR* 5.0 2.9 - - - +
166P GLY* 4.5 0.7 - - - -
167P TYR* 3.4 16.1 - - + -
193P GLY* 3.5 9.2 - - - -
194P THR* 2.6 48.1 + - - +
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Residues in contact with LEU 58 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17P LEU* 5.2 3.6 - - + -
48P LEU* 6.2 0.4 - - + -
54P LYS* 2.9 32.8 + - + +
55P ILE* 3.9 10.3 - - + +
56P ARG 3.2 0.2 + - - -
57P LYS* 1.3 75.2 - - - +
59P GLU* 1.3 59.9 + - - +
61P LEU* 3.3 24.1 - - + +
62P LEU* 2.5 51.8 + - + +
83P HIS* 5.2 0.2 - - + -
86P VAL* 3.2 35.0 - - + +
87P THR* 3.9 17.7 - - + +
90P ALA* 4.2 16.6 - - + -
154P ILE* 3.9 16.6 - - + -
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Residues in contact with GLU 59 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14P ARG* 3.1 34.8 + - + -
15P VAL* 3.1 33.4 + - - +
16P GLU* 3.6 6.6 - - - -
17P LEU* 3.1 36.4 + - + +
18P ILE* 3.5 26.1 + - - +
55P ILE 3.8 8.2 + - - +
56P ARG* 3.1 17.9 + - - +
58P LEU* 1.3 79.0 - - - +
60P TYR* 1.3 63.2 + - + +
63P GLY* 3.0 18.5 + - - -
166P GLY* 5.9 0.7 - - - -
169P ARG* 4.7 5.2 - - - -
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Residues in contact with TYR 60 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9P LEU* 3.8 19.3 + - + +
12P PHE* 3.6 29.5 + - + -
13P PRO 3.9 10.7 - - - +
14P ARG* 3.1 28.9 - - + +
56P ARG 4.5 1.1 - - - -
57P LYS 2.9 7.4 + - - +
59P GLU* 1.3 83.7 - - + +
61P LEU* 1.3 67.1 + - - +
64P ASP* 3.3 12.0 + - - +
162P ILE* 3.0 51.1 - - + +
163P GLY* 4.1 2.2 - - - +
165P LEU* 3.9 25.6 - - + -
166P GLY* 4.2 16.2 - - - -
169P ARG* 2.4 38.5 + - - -
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Residues in contact with LEU 61 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57P LYS* 2.7 28.0 + - + +
58P LEU* 2.9 37.6 + - + +
60P TYR* 1.3 71.2 - - - +
62P LEU* 1.3 65.9 + - - +
64P ASP* 3.0 15.6 + - - +
65P ALA 3.0 8.8 + - - -
83P HIS* 4.7 2.2 - - + +
152P TYR* 3.3 16.6 - - + +
154P ILE* 3.7 26.0 - - + -
155P PRO* 5.7 0.4 - - + -
158P GLY* 3.5 30.3 - - - +
160P SER* 4.1 10.1 - - - -
162P ILE* 4.2 4.3 - - + -
163P GLY* 3.4 27.1 - - - +
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Residues in contact with LEU 62 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15P VAL* 4.2 4.7 - - + -
17P LEU* 4.5 11.7 - - + -
58P LEU* 2.5 48.4 + - + +
61P LEU* 1.3 74.8 - - - +
63P GLY* 1.3 51.5 + - - +
65P ALA* 2.7 12.2 + - + +
66P LEU* 2.7 35.6 + - - +
73P VAL* 4.9 5.8 - - + -
90P ALA* 4.2 20.0 - - + +
91P ALA* 4.0 27.1 - - + +
94P LEU* 3.6 31.6 - - + -
96P LEU* 4.9 6.7 - - + -
154P ILE* 4.7 9.4 - - + -
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Residues in contact with GLY 63 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13P PRO* 3.6 25.3 - - - +
14P ARG 4.7 0.2 - - - -
15P VAL* 3.6 15.8 - - - +
59P GLU 3.0 19.4 + - - -
62P LEU* 1.3 76.5 - - - +
64P ASP* 1.3 55.6 + - - +
66P LEU* 3.6 7.2 + - - +
67P SER* 2.9 25.3 + - - -
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Residues in contact with ASP 64 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13P PRO* 4.1 6.7 + - + +
60P TYR 3.3 13.7 + - - +
61P LEU 3.0 11.8 + - - +
63P GLY* 1.3 73.0 - - - +
65P ALA* 1.3 61.9 + - - +
67P SER* 2.9 29.5 + - - -
68P LYS* 2.6 48.1 + - - +
152P TYR* 2.6 26.4 + - - +
162P ILE* 4.1 19.0 - - + +
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Residues in contact with ALA 65 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61P LEU 3.0 4.8 + - - -
62P LEU* 2.7 21.1 + - + +
64P ASP* 1.3 67.2 - - - +
66P LEU* 1.3 62.2 + - - +
67P SER 2.9 5.4 + - - -
68P LYS* 3.2 3.9 + - - -
69P GLY 3.1 16.6 + - - -
70P ALA* 3.1 15.9 + - + +
73P VAL* 5.7 0.2 - - + -
96P LEU* 4.7 13.0 - - + -
152P TYR* 3.3 47.8 - - + -
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Residues in contact with LEU 66 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15P VAL* 3.6 29.8 - - + -
62P LEU 2.7 17.9 + - - +
63P GLY* 3.7 7.2 - - - +
65P ALA* 1.3 72.1 - - - +
67P SER* 1.3 63.3 + - - +
69P GLY* 3.6 9.4 + - - +
70P ALA 4.9 3.4 - - - +
94P LEU* 3.8 20.9 - - + +
96P LEU* 4.1 32.3 - - + -
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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
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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