Contacts of the helix formed by residues 34 - 51 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20E ILE* 4.1 2.0 - - - -
24E ARG* 5.8 1.8 - - - +
31E LYS* 4.0 13.9 + - - +
32E ASP 3.3 4.6 + - - -
33E VAL* 1.3 79.5 - - - +
35E PHE* 1.3 64.9 + - - +
36E SER 3.9 0.2 + - - -
37E ALA* 3.3 11.0 + - - +
38E THR* 3.2 22.3 + - - +
9P A 2.9 57.8 + - - -
10P G 3.4 2.5 - - - -
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Residues in contact with PHE 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E ILE* 4.5 1.1 - - + -
13E TYR* 3.6 34.8 - + - -
16E ILE* 3.6 35.9 - - + -
17E ASN* 3.4 27.4 - - - -
20E ILE* 3.7 11.7 - - + +
34E SER* 1.3 69.0 - - - +
36E SER* 1.3 66.3 + - - +
38E THR* 3.2 1.7 + - - -
39E ALA* 3.0 38.3 + - + +
4H VAL* 3.6 35.7 - - + -
5H ASN 5.1 1.6 - - - -
6H LEU* 4.5 2.0 - - + -
10P G 2.6 28.7 + - - +
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Residues in contact with SER 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E SER 3.4 0.2 - - - -
35E PHE* 1.3 79.8 - - - +
37E ALA* 1.3 57.2 + - - +
40E SER* 3.0 30.0 + - - -
5H ASN 3.8 11.4 - - - -
6H LEU* 3.7 13.5 - - - +
7H TYR* 2.9 36.1 + - - -
9P A 2.8 25.5 + - - -
10P G 3.4 14.7 + - - -
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Residues in contact with ALA 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E ASP 4.3 8.3 - - - +
33E VAL* 5.2 0.4 - - - -
34E SER* 3.3 26.6 + - - +
35E PHE 3.2 0.6 - - - -
36E SER* 1.3 77.2 - - - +
38E THR* 1.3 62.3 + - + +
40E SER* 3.2 6.2 + - - -
41E MET* 2.8 29.0 + - - +
9P A 3.5 15.0 + - - +
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Residues in contact with THR 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ILE* 3.7 8.4 - - - +
19E ILE* 5.3 9.2 - - + -
20E ILE* 3.6 29.6 - - + +
23E ARG* 5.3 7.4 - - + +
33E VAL* 4.4 21.8 - - + -
34E SER 3.2 19.0 + - - +
35E PHE 3.2 4.9 + - - -
37E ALA* 1.3 76.2 - - + +
39E ALA* 1.3 59.4 + - - +
41E MET* 3.3 18.0 + - + +
42E LEU* 3.1 34.4 + - - +
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Residues in contact with ALA 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ILE* 4.0 28.3 - - + -
35E PHE* 3.0 23.4 + - + +
38E THR* 1.3 74.6 + - - +
40E SER* 1.3 61.2 + - - +
42E LEU* 3.2 9.7 + - - +
43E LEU* 3.0 25.1 + - - +
6H LEU* 3.6 26.4 - - + +
43H LEU* 3.9 9.6 - - + +
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Residues in contact with SER 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E SER 3.0 21.7 + - - -
37E ALA* 3.6 5.6 - - - -
39E ALA* 1.3 74.2 - - - +
41E MET* 1.3 65.2 + - - +
43E LEU* 3.5 8.0 - - - +
44E GLU* 3.1 38.0 + - - +
6H LEU* 4.2 4.9 - - - +
7H TYR 4.4 6.4 + - - -
8H ILE* 3.5 32.8 - - - +
9H SER 4.9 0.2 + - - -
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Residues in contact with MET 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E ILE* 5.6 3.6 - - + -
23E ARG* 3.9 26.5 - - - +
37E ALA 2.8 13.7 + - - +
38E THR* 3.4 25.6 - - + +
39E ALA 3.2 0.2 - - - -
40E SER* 1.3 77.6 - - - +
42E LEU* 1.3 68.9 + - + +
44E GLU* 3.8 7.1 + - - +
45E LEU* 3.2 43.6 + - - +
48E ARG* 5.4 1.4 + - - -
50H HIS* 4.9 4.9 - - + -
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Residues in contact with LEU 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ILE* 4.1 11.7 - - + -
19E ILE* 4.1 12.8 - - + -
38E THR* 3.1 20.7 + - - +
39E ALA* 3.2 7.2 + - - +
41E MET* 1.3 92.3 - - + +
43E LEU* 1.3 59.3 + - - +
45E LEU* 3.4 5.5 - - + +
46E GLY 3.0 21.3 + - - -
42H LEU 3.8 2.7 - - - +
43H LEU* 3.9 21.3 - - + +
46H GLY* 3.4 31.7 - - - +
47H LEU* 3.6 29.4 - - + +
50H HIS* 4.1 21.3 - - + +
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Residues in contact with LEU 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E VAL* 6.0 1.8 - - + -
6E LEU* 4.4 2.7 - - + -
39E ALA 3.0 12.0 + - - +
40E SER* 3.3 9.6 + - - +
42E LEU* 1.3 74.7 - - - +
44E GLU* 1.3 61.1 + - + +
46E GLY* 2.9 4.7 + - - -
47E LEU* 2.9 33.0 + - + +
6H LEU* 4.2 21.5 - - + -
8H ILE* 4.3 17.0 - - + -
12H ALA* 5.7 1.8 - - + -
16H ILE* 3.9 25.1 - - + -
39H ALA* 3.9 23.8 - - + +
42H LEU* 3.7 36.3 - - + +
43H LEU* 4.4 5.8 - - + +
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Residues in contact with GLU 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E SER* 3.1 27.0 + - - +
41E MET* 4.2 5.4 - - - +
43E LEU* 1.3 76.9 - - + +
45E LEU* 1.3 61.2 + - - +
47E LEU* 3.2 12.8 + - + +
48E ARG* 3.1 44.5 + - - +
8H ILE* 6.4 0.2 - - + -
9H SER* 3.6 25.0 + - - -
12H ALA* 4.4 17.0 - - + +
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Residues in contact with LEU 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E MET* 3.2 35.7 + - - +
42E LEU* 3.4 12.8 - - + +
43E LEU 3.1 0.2 - - - -
44E GLU* 1.3 78.3 - - - +
46E GLY* 1.3 59.9 + - - +
48E ARG* 3.6 24.5 + - - +
49E VAL* 3.3 28.7 + - + +
46H GLY* 3.8 15.9 - - - +
49H VAL* 3.4 41.5 - - + -
50H HIS* 5.0 10.5 - - + +
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Residues in contact with GLY 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E LEU 3.0 8.4 + - - -
43E LEU 2.9 8.0 + - - -
45E LEU* 1.3 74.7 - - - +
47E LEU* 1.3 58.4 + - - +
49E VAL 3.9 0.2 - - - -
50E HIS* 3.1 27.4 + - - +
42H LEU* 3.5 25.6 - - - +
45H LEU* 3.7 21.6 - - - +
46H GLY* 4.0 4.4 - - - -
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Residues in contact with LEU 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E LEU* 2.9 21.6 + - + +
44E GLU* 3.2 23.5 + - + +
46E GLY* 1.3 76.0 - - - +
48E ARG* 1.3 64.7 + - + +
50E HIS* 3.2 14.9 + - + +
51E GLU* 3.3 26.2 + - + +
12H ALA* 4.1 31.6 - - + +
15H LYS* 4.4 25.6 - - + +
16H ILE* 4.7 2.2 - - + -
19H ILE* 4.2 16.2 - - + -
42H LEU* 3.7 25.1 - - + -
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Residues in contact with ARG 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E MET 5.4 0.8 + - - -
44E GLU* 3.1 39.6 + - - +
45E LEU* 4.0 27.5 + - - +
47E LEU* 1.3 77.9 - - + +
49E VAL* 1.3 63.1 + - + +
51E GLU* 3.7 26.9 + - - +
15H LYS* 6.3 0.7 - - - +
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Residues in contact with VAL 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E LEU* 3.3 19.3 + - + +
46E GLY 3.8 1.1 - - - +
47E LEU 3.2 0.4 - - - -
48E ARG* 1.3 78.0 - - + +
50E HIS* 1.3 65.2 + - - +
51E GLU 3.1 8.0 + - - -
45H LEU* 3.6 27.1 - - + -
49H VAL* 4.1 26.7 - - + -
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Residues in contact with HIS 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E GLY 3.1 14.8 + - - +
47E LEU* 3.2 12.7 + - + +
49E VAL* 1.3 76.8 - - - +
51E GLU* 1.3 63.6 + - + +
19H ILE* 3.9 31.8 - - + +
23H ARG* 3.6 28.0 + - - -
41H MET* 5.0 6.1 - - + +
42H LEU* 4.3 16.9 - - + +
45H LEU* 4.9 10.7 - - + +
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Residues in contact with GLU 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E LEU* 3.3 21.5 + - + +
48E ARG* 3.9 21.4 - - - +
49E VAL 3.1 8.5 - - - -
50E HIS* 1.3 85.2 - - + +
15H LYS* 3.9 27.9 + - - +
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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