Contacts of the helix formed by residues 40 - 63 (chain b) in PDB entry 5JPQ
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 LYS 40 (chain b).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33b ILE* 6.1 4.0 - - - -
38b ILE* 4.9 3.5 - - - +
39b GLN* 1.3 82.0 + - + +
41b PRO* 1.3 59.5 - - - +
42b GLU* 2.9 21.9 + - + +
43b ASP* 3.0 21.1 + - + +
44b TYR* 3.9 1.9 + - - +
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Residues in contact with PRO 41 (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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29b ASP* 5.5 10.3 - - + -
40b LYS* 1.3 71.5 - - - +
42b GLU* 1.4 63.7 + - - +
44b TYR* 3.1 19.9 + - + +
45b HIS* 3.2 12.1 + - - +
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Residues in contact with GLU 42 (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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40b LYS* 4.1 12.0 - - + +
41b PRO* 1.4 75.3 - - - +
43b ASP* 1.3 65.2 + - - +
45b HIS* 2.7 21.3 + - - +
46b LYS* 2.9 12.7 + - - +
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Residues in contact with ASP 43 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38b ILE* 4.8 15.0 - - + -
39b GLN* 5.4 0.9 - - + +
40b LYS* 3.0 14.6 + - - +
42b GLU* 1.3 76.7 - - - +
44b TYR* 1.3 63.1 + - - +
46b LYS* 2.9 22.6 + - - +
47b TYR* 3.1 12.5 + - - +
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Residues in contact with TYR 44 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29b ASP* 5.1 20.4 - - + +
32b VAL* 5.6 6.1 - - + -
33b ILE 6.3 0.2 - - - +
40b LYS 3.9 1.4 + - - +
41b PRO* 3.1 16.6 + - + +
42b GLU 2.9 0.2 + - - -
43b ASP* 1.3 77.5 - - - +
45b HIS* 1.3 60.9 + - - +
47b TYR* 3.1 17.6 + - - +
48b ASN* 3.2 12.1 + - - +
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Residues in contact with HIS 45 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15b LYS* 3.7 34.4 - - + +
41b PRO 3.2 8.7 + - - +
42b GLU* 2.7 15.6 + - - +
44b TYR* 1.3 68.6 - - - +
46b LYS* 1.3 57.8 + - - +
47b TYR 3.0 1.6 - - - -
48b ASN* 3.7 6.4 - - - +
49b ARG* 2.8 34.0 + - - +
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Residues in contact with LYS 46 (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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42b GLU 2.9 10.8 + - - +
43b ASP* 2.9 18.4 + - - +
45b HIS* 1.3 76.2 - - - +
47b TYR* 1.3 58.5 + - - +
49b ARG* 3.8 6.1 + - - +
50b LEU* 3.4 20.8 + - - +
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Residues in contact with TYR 47 (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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43b ASP 3.1 9.0 + - - +
44b TYR* 3.3 11.0 - - - +
45b HIS 3.0 0.6 - - - -
46b LYS* 1.3 76.4 - - - +
48b ASN* 1.3 60.8 + - - +
50b LEU* 3.0 8.6 + - - +
51b CYS* 2.9 27.7 + - - +
103b VAL* 5.4 11.2 - - + +
106b PHE* 6.1 4.6 - - + +
107b ALA* 5.3 13.2 - - + -
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Residues in contact with ASN 48 (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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44b TYR 3.2 9.8 + - - +
45b HIS* 3.2 7.2 + - - +
47b TYR* 1.3 79.9 - - - +
49b ARG* 1.3 61.1 + - - +
51b CYS* 3.3 9.2 + - - +
52b GLY* 3.0 20.3 + - - -
103b VAL* 5.4 10.0 - - + +
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Residues in contact with ARG 49 (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 LYS* 4.3 21.9 - - + +
45b HIS 2.8 22.0 + - - +
46b LYS* 4.0 7.0 - - - +
48b ASN* 1.3 72.0 - - - +
50b LEU* 1.3 60.2 + - - +
52b GLY* 3.4 9.0 + - - -
53b SER* 3.4 12.1 + - - -
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Residues in contact with LEU 50 (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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46b LYS 3.4 11.9 + - - +
47b TYR* 3.0 11.3 + - - +
49b ARG* 1.3 75.1 - - - +
51b CYS* 1.3 63.6 + - - +
52b GLY 3.0 5.1 + - - -
53b SER* 3.1 17.8 + - - -
54b LEU* 3.5 9.0 + - - +
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Residues in contact with CYS 51 (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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47b TYR 2.9 15.1 + - - +
48b ASN* 3.8 9.2 - - - +
50b LEU* 1.3 75.1 - - - +
52b GLY* 1.4 62.4 + - - +
54b LEU* 3.3 10.1 - - - +
55b ARG* 3.2 20.5 + - - +
101b VAL* 5.2 13.9 - - + +
103b VAL* 5.6 9.9 - - + -
106b PHE* 5.7 8.1 - - + -
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Residues in contact with GLY 52 (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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48b ASN 3.0 12.6 + - - -
49b ARG* 3.6 7.0 - - - -
50b LEU 3.0 1.4 - - - -
51b CYS* 1.4 73.7 - - - +
53b SER* 1.3 56.1 + - - +
54b LEU 3.0 0.9 + - - -
55b ARG* 3.1 6.2 + - - +
56b GLN* 2.8 37.4 + - - +
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Residues in contact with SER 53 (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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49b ARG 3.4 9.4 + - - -
50b LEU* 3.1 12.3 + - - -
52b GLY* 1.3 72.5 - - - +
54b LEU* 1.3 56.6 + - - +
56b GLN* 4.1 5.6 - - - +
57b PHE* 3.1 28.6 + - - +
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Residues in contact with LEU 54 (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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50b LEU 3.5 5.4 + - - +
51b CYS* 3.3 15.4 + - - +
52b GLY 3.1 0.6 - - - -
53b SER* 1.3 76.3 - - - +
55b ARG* 1.3 53.4 + - - +
57b PHE* 3.0 8.9 + - - +
58b ALA* 2.7 32.6 + - - +
97b VAL* 5.4 11.4 - - + +
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Residues in contact with ARG 55 (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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51b CYS 3.2 10.0 + - - +
52b GLY* 3.1 4.9 + - - +
54b LEU* 1.3 73.9 - - - +
56b GLN* 1.3 58.3 + - - +
57b PHE 3.0 1.6 - - - -
58b ALA* 3.3 9.2 - - - +
59b HIS* 2.7 37.4 + - - +
97b VAL 5.3 3.1 + - - +
98b GLU* 4.1 23.3 - - + +
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Residues in contact with GLN 56 (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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52b GLY 2.8 23.2 + - - +
53b SER* 4.2 5.8 - - - +
55b ARG* 1.3 71.8 - - - +
57b PHE* 1.3 56.8 + - - +
59b HIS* 4.1 5.0 - - - +
60b ARG* 3.1 27.0 + - - +
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Residues in contact with PHE 57 (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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53b SER 3.1 19.7 + - - +
54b LEU* 3.0 8.1 + - - +
56b GLN* 1.3 75.4 - - - +
58b ALA* 1.3 61.4 + - - +
60b ARG* 3.9 7.0 - - - +
61b LEU* 3.2 22.9 + - - +
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Residues in contact with ALA 58 (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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54b LEU 2.7 15.2 + - - +
55b ARG* 3.0 15.0 + - + +
57b PHE* 1.3 71.9 - - - +
59b HIS* 1.3 54.0 + - - +
61b LEU* 3.0 6.8 + - - +
62b SER* 2.8 35.6 + - - -
94b LEU* 4.9 12.2 - - + +
97b VAL* 4.0 25.1 - - + -
98b GLU* 4.8 7.6 - - + -
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Residues in contact with HIS 59 (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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55b ARG 2.7 19.1 + - - +
56b GLN* 4.1 5.8 - - - +
58b ALA* 1.3 71.7 - - - +
60b ARG* 1.3 63.0 + - - +
62b SER* 3.1 9.1 + - - -
63b LEU* 3.1 24.4 + - - +
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Residues in contact with ARG 60 (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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56b GLN 3.1 19.1 + - - +
57b PHE* 4.0 8.1 - - - +
58b ALA 3.3 0.2 - - - -
59b HIS* 1.3 79.3 - - - +
61b LEU* 1.3 58.6 + - - +
63b LEU* 3.6 16.9 - - - +
64b LEU* 4.6 2.3 + - - +
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Residues in contact with LEU 61 (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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57b PHE 3.2 17.3 + - - +
58b ALA* 3.0 6.5 + - - +
60b ARG* 1.3 75.0 - - - +
62b SER* 1.3 58.4 + - - +
63b LEU 3.1 1.8 - - - -
64b LEU* 3.0 29.8 + - - +
71b ARG* 4.3 14.3 - - + +
74b HIS* 6.0 3.6 - - + -
75b GLU* 4.9 21.1 - - + +
94b LEU* 6.1 4.3 - - + -
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Residues in contact with SER 62 (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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58b ALA 2.8 16.1 + - - -
59b HIS* 3.6 10.5 - - - -
61b LEU* 1.3 72.1 - - - +
63b LEU* 1.3 56.5 + - - +
64b LEU 2.9 18.9 + - - +
94b LEU* 6.0 6.8 - - - +
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Residues in contact with LEU 63 (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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59b HIS 3.1 10.1 + - - +
60b ARG* 3.6 17.7 - - - +
61b LEU 3.1 0.8 - - - -
62b SER* 1.3 74.7 - - - +
64b LEU* 1.3 58.1 + - - +
65b PRO 4.4 0.2 - - - -
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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