Contacts of the helix formed by residues 31 - 49 (chain H) in PDB entry 4JCQ
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 31 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H GLU* 3.3 38.0 + - - +
30H ILE* 1.3 75.8 - - - +
32H GLN* 1.3 59.8 + - - +
33H GLU* 3.3 21.3 + - - +
34H LEU* 2.9 35.6 + - - +
35H ALA 2.9 23.9 + - - -
63H HIS* 4.0 13.5 - - + +
66H ALA* 3.4 13.5 - - - +
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Residues in contact with GLN 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H ASN* 1.3 75.7 - - - +
33H GLU* 1.3 64.8 + - - +
35H ALA* 3.4 8.7 + - + +
36H GLU* 2.9 30.4 + - - +
63H HIS* 5.4 1.0 + - - +
65H GLU* 4.4 30.0 + - + +
66H ALA* 3.8 8.0 - - + +
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Residues in contact with GLU 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H ASN* 3.3 26.6 + - - +
32H GLN* 1.3 83.9 + - - +
34H LEU* 1.3 61.6 + - - +
36H GLU* 3.4 9.7 + - - +
37H ASP* 3.1 21.7 + - - +
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Residues in contact with LEU 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H LEU 4.8 9.4 - - - +
26H ILE* 3.7 25.4 - - + -
27H TYR 5.0 10.3 - - - +
28H GLY 5.8 0.2 - - - +
29H GLU 4.0 13.5 - - - +
30H ILE* 4.1 10.5 - - + -
31H ASN* 2.9 20.5 + - - +
33H GLU* 1.3 72.6 - - - +
35H ALA* 1.3 59.8 + - - +
37H ASP* 3.2 14.2 + - + +
38H VAL* 2.8 47.9 + - + +
70H ILE* 3.6 24.2 - - + -
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Residues in contact with ALA 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H ASN 2.9 16.1 + - - +
32H GLN* 3.5 11.4 - - + +
33H GLU 3.3 0.2 - - - -
34H LEU* 1.3 78.4 - - - +
36H GLU* 1.3 54.2 + - - +
38H VAL* 3.9 0.9 - - - +
39H SER* 2.8 38.5 + - - -
66H ALA* 3.9 25.8 - - + +
69H THR* 4.5 12.6 - - + -
70H ILE* 3.8 15.5 - - + +
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Residues in contact with GLU 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H GLN 2.9 17.2 + - - +
33H GLU* 3.6 8.3 - - - +
34H LEU 3.2 0.2 - - - -
35H ALA* 1.3 74.3 - - - +
37H ASP* 1.3 60.4 + - - +
39H SER* 3.4 6.0 + - - -
40H LYS* 3.0 63.3 + - + +
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Residues in contact with ASP 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H GLU 3.1 13.7 + - - +
34H LEU* 3.6 18.8 - - + +
36H GLU* 1.3 77.4 - - - +
38H VAL* 1.3 61.6 + - - +
40H LYS* 3.4 9.4 + - - +
41H GLN* 3.1 43.5 + - - +
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Residues in contact with VAL 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H VAL* 4.4 12.6 - - + -
25H LEU 4.8 2.2 - - - +
26H ILE* 3.8 29.8 - - + -
34H LEU* 2.8 43.6 + - + +
35H ALA 4.0 2.7 - - - +
37H ASP* 1.3 67.9 - - - +
39H SER* 1.3 61.1 - - - +
41H GLN* 3.3 10.2 + - - +
42H LEU* 2.9 49.4 + - + +
55H ILE* 5.5 0.7 - - + -
70H ILE* 4.0 26.5 - - + -
73H MET* 6.2 0.2 - - + -
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Residues in contact with SER 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H ALA 2.8 25.3 + - - -
36H GLU* 3.7 6.5 - - - -
38H VAL* 1.3 77.3 - - - +
40H LYS* 1.3 56.2 + - - +
42H LEU* 3.4 5.5 + - - +
43H LEU* 3.0 41.0 + - - +
69H THR* 3.9 10.9 - - - +
70H ILE* 5.5 1.7 - - - +
73H MET* 3.7 31.9 - - - +
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Residues in contact with LYS 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H GLU* 3.0 51.3 + - + +
37H ASP* 3.7 9.4 - - - +
39H SER* 1.3 76.2 - - - +
41H GLN* 1.3 59.1 + - + +
43H LEU* 3.9 7.9 - - + +
44H LEU* 2.9 31.6 + - - +
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Residues in contact with GLN 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H THR 4.3 4.3 - - - +
24H VAL* 3.8 37.1 - - + +
25H LEU 4.7 5.9 + - - -
37H ASP* 3.1 50.4 + - - +
38H VAL* 3.7 9.2 - - - +
40H LYS* 1.3 75.5 - - + +
42H LEU* 1.3 57.1 + - - +
44H LEU* 3.4 6.8 + - - +
45H LEU* 2.9 37.8 + - + +
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Residues in contact with LEU 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H VAL* 4.2 15.5 - - + -
38H VAL* 2.9 37.2 + - + +
39H SER* 3.9 3.8 - - - +
41H GLN* 1.3 76.2 - - - +
43H LEU* 1.3 57.8 + - - +
45H LEU* 3.5 3.9 + - - +
46H GLU* 3.0 29.6 + - - +
53H ILE* 4.3 12.1 - - + -
55H ILE* 4.2 19.3 - - + -
70H ILE 4.9 0.4 - - - +
73H MET* 4.2 24.9 - - + +
74H ILE* 4.0 24.9 - - + +
77H ILE* 4.0 30.7 - - + +
81H VAL* 5.0 1.8 - - + -
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Residues in contact with LEU 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H SER* 3.0 27.9 + - - +
40H LYS* 3.9 7.0 - - + +
42H LEU* 1.3 74.7 - - - +
44H LEU* 1.3 64.5 + - - +
46H GLU* 3.5 21.7 + - - +
47H SER* 3.1 24.1 + - - -
73H MET* 3.8 26.5 - - + -
76H PHE* 5.0 8.5 - - + -
77H ILE* 4.7 1.8 - - + -
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Residues in contact with LEU 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H ILE* 3.7 27.4 - - + -
40H LYS 2.9 19.8 + - - +
41H GLN* 3.7 7.0 - - - +
43H LEU* 1.3 77.0 - - - +
45H LEU* 1.3 62.8 + - + +
47H SER* 2.7 26.6 + - - +
48H ILE* 3.3 35.9 + - + +
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Residues in contact with LEU 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H ILE* 3.5 42.4 - - + +
22H ARG* 2.8 54.6 + - - +
23H THR 4.6 1.8 - - - +
24H VAL* 3.8 26.9 - - + -
41H GLN* 2.9 22.8 + - + +
42H LEU* 4.0 1.3 - - - +
44H LEU* 1.3 76.2 - - + +
46H GLU* 1.3 64.9 + - - +
48H ILE* 3.3 4.4 + - + -
49H SER 3.2 8.1 + - - +
53H ILE* 3.8 31.2 - - + -
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Residues in contact with GLU 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H LEU 3.0 19.0 + - - +
43H LEU* 3.6 20.0 - - - +
45H LEU* 1.3 77.0 - - - +
47H SER* 1.3 61.6 + - - +
49H SER* 3.2 19.8 + - - +
50H ASN* 4.8 4.6 + - - +
53H ILE* 4.7 0.2 - - - +
76H PHE* 4.6 7.0 - - - +
77H ILE* 3.4 22.8 - - + +
78H LYS* 3.0 37.3 + - + +
79H PRO* 3.7 22.8 - - + +
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Residues in contact with SER 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43H LEU 3.1 13.0 + - - -
44H LEU* 2.7 31.7 + - - +
46H GLU* 1.3 77.2 - - - +
48H ILE* 1.3 63.4 + - - +
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Residues in contact with ILE 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H ILE* 3.7 30.3 - - + -
20H ASP* 6.1 1.1 - - - +
22H ARG* 4.1 8.3 - - - +
44H LEU* 3.3 36.0 + - + +
45H LEU* 3.7 11.7 - - + +
46H GLU 3.2 0.8 - - - -
47H SER* 1.3 83.9 + - - +
49H SER* 1.3 64.5 + - - +
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Residues in contact with SER 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H ARG* 3.3 26.3 + - - -
45H LEU 3.2 10.9 + - - +
46H GLU 3.2 16.6 + - - +
48H ILE* 1.3 85.7 - - - +
50H ASN* 1.3 61.4 + - - +
51H ASP* 3.3 26.6 + - - +
79H PRO* 3.7 4.5 - - - +
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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
------------------------------------------------------------
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