Contacts of the helix formed by residues 34 - 52 (chain H) in PDB entry 4QPQ
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 SER 34 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H ILE* 3.9 1.7 - - - +
24H ARG* 5.8 1.3 - - - +
31H LYS* 4.0 14.1 + - - +
32H ASP 3.3 3.4 + - - -
33H VAL* 1.3 80.0 - - - +
35H PHE* 1.3 63.9 + - - +
37H ALA* 3.3 10.7 + - - +
38H THR* 3.2 22.5 + - - +
14Q C 2.5 49.4 + - - -
15Q G 3.4 12.6 - - - -
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Residues in contact with PHE 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E VAL* 3.5 37.0 - - + -
5E ASN 4.9 1.8 - - - -
6E LEU* 4.5 1.3 - - + -
8H ILE* 4.5 0.9 - - + -
13H TYR* 3.6 35.2 - + - -
16H ILE* 3.6 35.7 - - + -
17H ASN* 3.4 27.4 - - - -
20H ILE* 3.7 12.6 - - + +
34H SER* 1.3 69.4 - - - +
36H SER* 1.3 66.9 + - - +
38H THR* 3.2 1.9 + - - -
39H ALA* 3.0 38.1 + - + +
15Q G 2.7 24.2 + - - +
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Residues in contact with SER 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E ASN 3.7 11.4 - - - -
6E LEU* 3.8 13.0 - - - +
7E TYR* 2.9 34.1 + - - -
34H SER 3.4 0.4 - - - -
35H PHE* 1.3 75.0 - - - +
37H ALA* 1.3 56.1 + - - +
40H SER* 3.0 30.7 + - - -
14Q C 2.7 29.3 + - - -
15Q G 2.9 19.6 + - - -
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Residues in contact with ALA 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H ASP 4.3 9.2 - - - +
33H VAL* 5.2 0.4 - - - -
34H SER* 3.3 27.2 + - - +
35H PHE 3.2 0.6 - - - -
36H SER* 1.3 77.1 - - - +
38H THR* 1.3 63.1 + - + +
40H SER* 3.2 5.1 + - - -
41H MET* 2.8 29.6 + - - +
14Q C 3.3 13.9 + - - +
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Residues in contact with THR 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H ILE* 3.7 9.1 - - - +
19H ILE* 5.2 11.9 - - + -
20H ILE* 3.6 29.1 - - + +
23H ARG* 5.3 4.7 - - + +
33H VAL* 4.4 22.4 - - + -
34H SER 3.2 19.2 + - - +
35H PHE 3.2 4.7 + - - -
37H ALA* 1.3 76.0 - - + +
39H ALA* 1.3 59.6 + - - +
41H MET* 3.3 18.1 + - + +
42H LEU* 3.1 34.6 + - - +
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Residues in contact with ALA 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E VAL* 5.4 0.2 - - + -
6E LEU* 3.5 26.4 - - + +
43E LEU* 3.9 8.7 - - + +
16H ILE* 3.9 24.0 - - + -
35H PHE* 3.0 23.6 + - + +
38H THR* 1.3 75.2 + - - +
40H SER* 1.3 61.8 + - - +
42H LEU* 3.2 13.4 + - - +
43H LEU* 3.0 25.3 + - - +
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Residues in contact with SER 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E LEU* 4.1 6.6 - - - +
7E TYR 4.2 7.7 + - - -
8E ILE* 3.4 33.5 - - - +
36H SER 3.0 20.6 + - - -
37H ALA* 3.6 5.2 - - - -
39H ALA* 1.3 74.3 - - - +
41H MET* 1.3 63.8 + - - +
43H LEU* 3.5 7.6 - - - +
44H GLU* 3.1 38.0 + - - +
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Residues in contact with MET 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E HIS* 5.0 4.9 - - + -
19H ILE* 5.6 3.8 - - + -
23H ARG* 3.9 26.0 - - - +
37H ALA 2.8 14.3 + - - +
38H THR* 3.4 26.5 - - + +
40H SER* 1.3 78.8 - - - +
42H LEU* 1.3 68.6 + - + +
44H GLU* 4.1 7.0 - - - +
45H LEU* 3.2 44.2 + - - +
48H ARG* 5.4 1.4 + - - -
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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
----------------------------------------------------------
42E LEU 3.8 1.9 - - - +
43E LEU* 3.7 26.2 - - + +
46E GLY* 3.5 27.9 - - - +
47E LEU* 3.7 26.5 - - + -
50E HIS* 4.3 19.5 - - + +
16H ILE* 4.1 11.7 - - + -
19H ILE* 4.1 13.7 - - + -
38H THR* 3.1 20.9 + - - +
39H ALA* 3.2 7.8 + - - +
41H MET* 1.3 92.7 - - + +
43H LEU* 1.3 60.8 + - - +
45H LEU* 3.4 8.2 - - + +
46H GLY 3.0 21.7 + - - -
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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
----------------------------------------------------------
6E LEU* 4.0 22.2 - - + -
8E ILE* 4.2 17.7 - - + -
12E ALA* 5.7 1.6 - - + -
16E ILE* 3.7 32.3 - - + -
39E ALA* 3.9 22.4 - - + +
42E LEU* 3.9 22.0 - - + +
43E LEU* 4.4 11.2 - - + +
4H VAL* 6.0 2.0 - - + -
6H LEU* 4.4 3.1 - - + -
39H ALA 3.0 11.7 + - - +
40H SER* 3.5 9.4 - - - +
42H LEU* 1.3 74.5 - - - +
44H GLU* 1.3 60.5 + - + +
46H GLY* 2.9 4.5 + - - -
47H LEU* 2.9 32.9 + - + +
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Residues in contact with GLU 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E ILE* 6.2 0.2 - - + -
9E SER* 3.5 25.4 + - - -
12E ALA* 4.3 19.1 - - + +
40H SER* 3.1 27.3 + - - +
41H MET* 4.2 5.9 - - - +
43H LEU* 1.3 77.1 - - + +
45H LEU* 1.3 61.4 + - - +
47H LEU* 3.2 12.9 + - + +
48H ARG* 3.1 45.2 + - - +
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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
----------------------------------------------------------
46E GLY* 3.7 21.5 - - - +
49E VAL* 3.6 34.3 - - + -
50E HIS* 4.9 11.7 - - + +
41H MET* 3.2 36.2 + - - +
42H LEU* 3.4 11.9 - - + +
43H LEU 3.1 0.2 - - - -
44H GLU* 1.3 79.4 - - - +
46H GLY* 1.3 59.0 + - - +
48H ARG* 3.6 25.8 + - - +
49H VAL* 3.3 29.2 + - + +
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Residues in contact with GLY 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E LEU* 3.4 30.9 - - - +
45E LEU* 3.8 18.6 - - - +
46E GLY* 4.0 3.8 - - - -
42H LEU 3.0 7.5 + - - -
43H LEU 2.9 4.9 + - - -
45H LEU* 1.3 74.4 - - - +
47H LEU* 1.3 59.2 + - - +
49H VAL* 3.5 2.5 + - - +
50H HIS* 3.1 27.0 + - - +
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Residues in contact with LEU 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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12E ALA* 3.9 36.6 - - + +
15E LYS* 4.3 25.8 - - + +
16E ILE* 4.5 3.1 - - + -
19E ILE* 4.2 15.3 - - + -
42E LEU* 3.6 25.8 - - + -
43H LEU* 2.9 19.6 + - + +
44H GLU* 3.2 21.9 + - + +
46H GLY* 1.3 76.4 - - - +
48H ARG* 1.3 65.6 + - + +
50H HIS* 3.2 14.9 + - + +
51H GLU* 3.3 24.6 + - + +
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Residues in contact with ARG 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E LYS* 6.3 1.6 - - - +
41H MET 5.4 1.2 + - - -
44H GLU* 3.1 37.9 + - - +
45H LEU* 4.0 28.0 + - - +
46H GLY 3.4 0.2 - - - -
47H LEU* 1.3 77.0 - - + +
49H VAL* 1.3 62.7 + - + +
51H GLU* 3.7 16.6 + - - +
52H ALA* 3.5 18.2 + - - +
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Residues in contact with VAL 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E LEU* 3.4 27.6 - - + -
49E VAL* 4.1 27.6 - - + -
45H LEU* 3.3 19.2 + - + +
46H GLY 3.8 1.6 - - - +
47H LEU 3.2 0.6 - - - -
48H ARG* 1.3 76.5 - - + +
50H HIS* 1.3 64.4 + - - +
51H GLU 3.1 1.6 - - - -
52H ALA* 3.1 24.7 + - + +
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Residues in contact with HIS 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E ILE* 3.7 33.4 - - + +
23E ARG* 3.6 28.1 + - - -
41E MET* 4.9 6.2 - - + +
42E LEU* 4.1 17.3 - - + +
45E LEU* 4.9 10.0 - - + +
46H GLY 3.1 15.6 + - - +
47H LEU* 3.2 12.1 + - + +
49H VAL* 1.3 77.0 - - - +
51H GLU* 1.3 64.3 + - + +
52H ALA 4.7 1.9 - - - -
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Residues in contact with GLU 51 (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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15E LYS* 3.7 30.3 + - - +
47H LEU* 3.3 21.6 - - + +
48H ARG* 3.9 16.4 - - - +
49H VAL 3.1 0.4 - - - -
50H HIS* 1.3 80.9 - - + +
52H ALA* 1.3 67.4 + - - +
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Residues in contact with ALA 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H ARG 3.5 10.3 + - - +
49H VAL* 3.1 21.0 + - + +
50H HIS 4.7 1.6 - - - -
51H GLU* 1.3 84.6 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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