Contacts of the helix formed by residues 47 - 63 (chain A) in PDB entry 1J5N
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 THR 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A ASP 3.7 4.8 + - - +
46A ILE* 1.3 73.8 - - - +
48A PHE* 1.3 67.1 + - - +
49A GLY 3.1 4.5 - - - -
50A GLN* 2.9 26.0 + - - +
51A VAL* 3.0 15.0 + - - +
112B T 5.4 0.9 - - - -
113B C 3.5 38.4 - - - +
114B A 5.1 5.2 - - - +
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Residues in contact with PHE 48 (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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47A THR* 1.3 77.2 - - - +
49A GLY* 1.3 62.1 + - - +
50A GLN 2.9 0.6 + - - -
51A VAL* 4.8 2.0 - - - -
52A GLY* 2.9 37.6 + - - +
53A LYS* 3.9 4.6 + - + -
111B T 4.3 2.5 - - - -
112B T 2.5 36.1 - + - +
113B C 3.1 30.9 - - - +
118C G 5.5 0.2 - - - -
119C A 3.3 28.0 - + - -
120C A 3.0 52.7 - + - -
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Residues in contact with GLY 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A THR* 3.1 3.6 - - - -
48A PHE* 1.3 81.9 - - - +
50A GLN* 1.3 81.8 + - - +
53A LYS* 3.4 34.4 + - - +
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Residues in contact with GLN 50 (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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46A ILE* 3.3 40.4 - - + -
47A THR* 2.9 22.1 + - - +
48A PHE 2.9 0.4 - - - -
49A GLY* 1.3 116.2 + - - +
51A VAL* 1.3 57.1 + - - +
52A GLY 3.3 0.9 - - - -
54A LYS* 2.6 52.8 + - + +
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Residues in contact with VAL 51 (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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36A ARG* 4.9 3.4 - - - +
39A VAL* 3.1 32.6 - - + +
40A ARG* 3.8 23.8 - - + +
46A ILE* 3.2 32.8 - - + +
47A THR 3.0 12.4 + - - +
48A PHE* 4.8 2.0 - - - -
50A GLN* 1.3 76.6 - - - +
52A GLY* 1.3 60.4 + - - +
54A LYS* 4.6 0.7 - - - -
55A LEU* 2.8 49.6 + - + +
111B T 6.1 0.2 - - - +
112B T 4.6 21.5 - - - +
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Residues in contact with GLY 52 (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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28A TYR* 3.6 6.7 + - - -
48A PHE* 2.9 32.6 + - - -
51A VAL* 1.3 77.9 - - - +
53A LYS* 1.3 56.6 + - - -
55A LEU* 2.7 36.2 + - - +
56A GLY 3.1 4.9 + - - -
111B T 4.9 5.6 - - - -
120C A 5.6 1.1 - - - -
121C C 4.1 6.0 - - - +
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Residues in contact with LYS 53 (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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48A PHE* 3.9 6.5 + - + +
49A GLY* 3.4 31.2 + - - +
50A GLN 3.9 0.8 + - - -
52A GLY* 1.3 72.0 - - - +
54A LYS* 1.3 64.7 + - + +
55A LEU 3.2 0.5 + - - -
56A GLY* 3.2 10.9 + - - -
57A GLU* 3.2 18.2 + - - +
120C A 4.0 8.1 - - + +
121C C 3.3 48.5 + - - +
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Residues in contact with LYS 54 (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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39A VAL* 5.8 3.1 - - + -
46A ILE* 5.3 4.0 - - + -
50A GLN* 2.6 37.8 + - + +
51A VAL* 4.2 2.5 - - - +
53A LYS* 1.3 78.4 - - + +
55A LEU* 1.3 56.0 + - - +
57A GLU* 2.8 35.8 + - - +
58A LYS* 2.8 46.5 + - + +
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Residues in contact with LEU 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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28A TYR* 3.8 9.2 - - + +
31A PHE* 3.4 15.1 - - + -
32A ALA* 3.9 15.7 - - + +
35A ASN* 2.6 46.4 - - + +
36A ARG* 4.2 15.7 - - + +
39A VAL* 4.0 9.9 - - + -
51A VAL* 2.8 41.6 + - + +
52A GLY* 2.7 15.0 + - - +
54A LYS* 1.3 77.9 - - - +
56A GLY* 1.3 50.1 + - - +
58A LYS* 3.7 2.9 - - - +
59A TRP* 2.7 36.1 + - - +
111B T 5.2 9.4 - - - +
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Residues in contact with GLY 56 (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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28A TYR* 3.5 9.3 + - - -
52A GLY 3.1 7.1 + - - -
53A LYS 3.2 3.2 + - - -
55A LEU* 1.3 76.6 - - - +
57A GLU* 1.3 65.6 + - - +
59A TRP* 2.9 21.8 + - - +
60A LYS* 3.2 7.6 + - - +
121C C 3.9 4.0 - - - -
122C A 3.5 33.3 + - - +
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Residues in contact with GLU 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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53A LYS* 3.2 11.8 + - - +
54A LYS* 2.8 56.4 + - - +
56A GLY* 1.3 73.8 - - - +
58A LYS* 1.3 78.0 + - + +
60A LYS* 3.5 4.0 + - - +
61A ALA* 2.9 27.1 + - - +
122C A 4.3 8.2 + - - +
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Residues in contact with LYS 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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31A PHE* 4.5 3.8 - - + -
39A VAL* 5.2 15.1 - - + +
43A ASN* 5.6 5.9 - - - +
54A LYS* 2.8 39.2 + - - +
55A LEU* 4.0 2.9 - - - +
57A GLU* 1.3 90.1 - - + +
59A TRP* 1.3 65.7 + - - +
61A ALA* 3.3 11.9 - - + +
62A LEU* 3.0 31.3 + - + +
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Residues in contact with TRP 59 (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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27A ALA* 3.7 33.0 - - + -
28A TYR* 4.2 5.1 - + + -
31A PHE* 2.8 68.6 - + + -
55A LEU 2.7 17.2 + - - +
56A GLY* 2.9 13.7 - - - +
58A LYS* 1.3 77.0 - - - +
60A LYS* 1.3 75.9 + - + +
62A LEU* 2.7 25.2 + - + +
63A THR 4.4 1.4 + - - -
67A LYS* 3.4 40.8 - - + +
70A TYR* 3.2 28.0 - + - -
122C A 3.6 27.8 + - - -
123C A 3.3 22.2 - - - -
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Residues in contact with LYS 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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56A GLY 3.2 5.7 + - - +
57A GLU* 4.3 3.1 - - - +
59A TRP* 1.3 90.4 - - + +
61A ALA* 1.3 64.4 + - - +
62A LEU 3.2 0.2 - - - -
63A THR* 3.8 10.6 + - - +
64A PRO* 5.6 0.5 - - - +
67A LYS* 5.4 7.2 - - + +
122C A 3.0 35.4 + - - -
123C A 2.7 37.6 + - - +
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Residues in contact with ALA 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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57A GLU 2.9 19.9 + - - +
58A LYS* 3.3 16.8 - - + +
59A TRP 3.1 0.2 - - - -
60A LYS* 1.3 76.4 - - - +
62A LEU* 1.3 68.6 + - - +
63A THR* 4.0 2.8 + - - -
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Residues in contact with LEU 62 (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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31A PHE* 3.3 35.0 - - + -
58A LYS* 3.0 13.1 + - + +
59A TRP* 2.7 28.7 - - + +
60A LYS 3.2 0.2 - - - -
61A ALA* 1.3 77.7 - - - +
63A THR* 1.3 77.4 + - - +
66A GLU* 3.1 31.7 - - + +
67A LYS* 5.2 0.9 - - + -
70A TYR* 4.4 9.6 - - + +
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Residues in contact with THR 63 (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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59A TRP 4.4 1.2 + - - -
60A LYS* 3.8 10.0 + - - +
61A ALA 3.6 3.6 + - - -
62A LEU* 1.3 91.0 + - - +
64A PRO* 1.3 85.8 - - + +
65A GLU* 3.6 17.0 - - + +
66A GLU* 2.7 27.2 + - - +
67A LYS* 3.0 14.9 + - - +
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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