Contacts of the helix formed by residues 54 - 70 (chain A) in PDB entry 5JNQ
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 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A LEU* 4.0 7.0 - - - -
52A THR 3.2 1.6 - - - -
53A MET* 1.3 69.0 - - - +
55A GLY* 1.3 61.2 + - - +
56A LEU 3.1 2.9 - - - -
57A ILE* 3.2 19.9 + - - +
58A ILE* 3.6 2.6 + - - +
217A PHE* 3.4 20.8 - - - -
227A VAL* 3.8 17.9 - - - -
228A PHE 2.6 24.7 + - - -
229A MET 3.2 1.1 - - - -
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Residues in contact with GLY 55 (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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53A MET 3.2 1.0 - - - -
54A GLY* 1.3 67.2 - - - +
56A LEU* 1.4 53.5 + - - +
57A ILE 3.3 0.2 - - - -
58A ILE* 3.3 11.7 + - - +
59A LEU* 2.9 37.6 + - - +
229A MET 2.2 27.3 + - - -
232A THR* 4.0 8.1 - - - -
233A GLY* 3.6 21.6 - - - -
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 5.7 7.0 - - + -
26A PHE* 5.9 4.5 - - + -
27A LEU* 4.7 5.4 - - + -
53A MET* 3.5 36.1 - - + +
55A GLY* 1.4 73.2 - - - +
57A ILE* 1.4 53.8 - - + +
59A LEU* 4.0 8.5 - - + +
60A SER* 2.7 44.4 + - - +
91A PHE* 3.7 40.4 - - + -
232A THR* 4.0 11.6 - - + +
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Residues in contact with ILE 57 (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 SER* 3.8 13.5 - - - +
19A LEU* 3.8 21.1 - - + +
20A CYS* 3.7 42.8 - - - +
23A ILE* 3.8 46.2 - - + -
24A ILE 4.9 0.2 - - - +
27A LEU* 4.4 11.0 - - + -
54A GLY* 3.2 15.4 + - - +
56A LEU* 1.4 74.6 - - + +
58A ILE* 1.4 63.0 + - - +
60A SER* 3.7 6.1 - - - -
61A SER* 3.1 24.8 + - - -
217A PHE* 4.9 3.1 - - + -
227A VAL* 5.0 7.9 - - + -
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Residues in contact with ILE 58 (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 SER* 5.0 0.7 - - - -
54A GLY 4.0 0.9 - - - +
55A GLY* 3.3 13.4 + - - +
57A ILE* 1.4 76.0 - - - +
59A LEU* 1.4 63.2 + - + +
62A ILE* 3.2 31.4 + - + +
213A SER* 2.8 31.3 + - - +
214A LEU* 3.9 24.5 - - + -
217A PHE* 3.7 43.1 - - + -
229A MET* 3.5 32.1 - - + -
233A GLY* 5.0 3.1 - - - -
236A ALA* 6.5 0.9 - - + -
237A LEU* 4.3 12.6 - - + -
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Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLY 2.9 19.9 + - - +
56A LEU* 4.0 9.9 - - + +
58A ILE* 1.4 74.5 - - + +
60A SER* 1.4 65.2 + - - +
62A ILE* 3.1 13.0 + - + +
63A ILE* 2.9 37.5 + - + +
80A LEU* 6.3 0.2 - - + -
83A THR* 3.5 36.3 - - - +
84A VAL* 4.3 15.7 - - + +
87A GLY* 4.0 24.9 - - - -
232A THR* 4.0 19.1 - - + +
236A ALA* 3.9 9.4 - - + -
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Residues in contact with SER 60 (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 ILE* 4.9 0.9 - - - -
19A LEU* 3.8 19.7 - - - +
23A ILE* 5.3 3.9 - - - +
56A LEU* 2.7 29.9 + - - +
57A ILE* 3.7 5.1 - - - -
59A LEU* 1.4 70.3 - - - +
61A SER* 1.3 55.8 + - - +
63A ILE* 4.0 8.1 - - - +
64A ILE* 3.1 39.7 + - - +
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Residues in contact with SER 61 (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 ALA* 2.7 37.9 + - - +
15A ILE* 3.6 20.3 - - - +
16A SER* 3.5 9.4 + - - -
57A ILE 3.1 12.0 + - - -
60A SER* 1.3 76.1 - - - +
62A ILE* 1.4 62.5 + - - +
64A ILE* 4.1 1.0 - - - +
65A THR* 3.0 31.2 + - - -
213A SER* 3.4 19.1 + - - -
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Residues in contact with ILE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE* 3.2 35.9 + - + +
59A LEU* 3.1 16.9 + - + +
61A SER* 1.4 74.9 - - - +
63A ILE* 1.4 52.9 + - + +
65A THR* 3.4 2.3 + - - -
66A SER* 2.7 39.0 + - - -
80A LEU* 4.2 7.2 - - + -
83A THR* 5.1 10.8 - - + +
206A ILE* 3.8 33.0 - - + -
209A ALA* 4.2 14.3 - - + +
210A VAL* 3.7 27.8 - - + -
213A SER* 3.9 13.2 - - - +
237A LEU* 4.8 6.3 - - + -
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Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 2.9 37.9 + - + +
60A SER* 4.0 7.0 - - - +
62A ILE* 1.4 70.7 - - + +
64A ILE* 1.4 68.0 + - + +
66A SER* 3.3 6.8 + - - -
67A VAL* 3.1 33.8 + - + +
80A LEU* 4.0 16.1 - - + +
84A VAL* 3.8 33.4 - - + -
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Residues in contact with ILE 64 (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 ILE* 3.7 28.3 - - + -
19A LEU* 6.4 0.2 - - + -
60A SER* 3.1 22.4 + - - +
61A SER 4.1 3.1 - - - +
62A ILE 3.4 0.2 - - - -
63A ILE* 1.4 79.7 - - + +
65A THR* 1.4 61.2 + - - +
67A VAL* 3.4 19.9 - - + +
68A PHE* 3.3 33.1 - - + -
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Residues in contact with THR 65 (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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8A ALA* 3.4 40.8 - - + +
11A ILE* 3.5 23.9 - - + +
12A ALA* 3.5 14.1 - - - -
15A ILE* 3.6 2.6 - - - +
61A SER 3.0 17.7 + - - -
62A ILE 3.9 2.2 - - - -
64A ILE* 1.4 75.9 - - - +
66A SER* 1.3 60.7 + - - +
68A PHE* 3.2 25.1 + - - -
69A TYR* 3.2 21.4 - - + -
205A PRO 5.1 0.2 - - - +
209A ALA* 4.1 9.9 - - + -
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Residues in contact with SER 66 (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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62A ILE* 2.7 28.7 + - - -
63A ILE 3.3 6.6 + - - -
65A THR* 1.3 72.2 - - - +
67A VAL* 1.4 56.3 + - - +
69A TYR* 3.2 11.5 + - - +
70A ILE* 3.1 32.6 + - - +
76A ILE* 4.0 12.8 - - - +
80A LEU* 3.6 17.7 - - - +
205A PRO 5.8 0.7 - - - -
206A ILE* 3.8 29.4 - - - +
209A ALA* 5.0 2.2 - - - +
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Residues in contact with VAL 67 (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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63A ILE* 3.1 24.0 + - + +
64A ILE* 3.4 19.3 - - + +
65A THR 3.2 1.0 - - - -
66A SER* 1.4 75.0 - - - +
68A PHE* 1.4 75.2 - - + +
70A ILE* 3.8 19.5 + - + +
71A PRO* 3.9 13.0 - - - +
80A LEU* 5.8 1.6 - - + -
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Residues in contact with PHE 68 (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 ILE* 4.5 17.3 - - + -
64A ILE* 3.3 41.7 - - + -
65A THR* 3.2 16.5 + - + +
67A VAL* 1.4 84.9 - - + +
69A TYR* 1.3 68.5 + + + +
71A PRO* 3.7 14.0 - - - +
72A SER* 5.6 1.4 - - - -
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Residues in contact with TYR 69 (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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4A GLU* 2.7 49.3 + - + +
7A LEU* 3.9 13.5 - - - +
8A ALA* 3.4 25.1 + - + -
11A ILE* 5.2 3.7 - - + +
65A THR* 3.2 33.2 - - + -
66A SER* 3.2 6.2 + - - +
68A PHE* 1.3 86.9 - + + +
70A ILE* 1.4 55.1 + - - +
71A PRO* 3.4 2.2 - - - -
72A SER* 3.1 7.3 + - - +
73A TYR* 2.8 47.6 + + + +
76A ILE* 3.8 20.2 - - + -
205A PRO* 3.6 23.1 - - + -
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Residues in contact with ILE 70 (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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66A SER 3.1 21.5 + - - +
67A VAL* 3.8 24.7 - - + +
69A TYR* 1.4 74.0 - - - +
71A PRO* 1.4 70.4 - - + +
72A SER 3.3 0.7 + - - -
73A TYR 3.3 22.1 - - - +
74A PRO* 3.5 7.6 - - - +
76A ILE* 4.1 14.6 - - + -
77A ILE* 4.0 32.3 - - + +
80A LEU* 3.8 25.8 - - + -
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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