Contacts of the helix formed by residues 34 - 51 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20G ILE* 4.1 1.6 - - - -
24G ARG* 5.8 1.3 - - - +
31G LYS* 4.0 13.6 + - - +
32G ASP 3.3 3.7 + - - -
33G VAL* 1.3 80.4 - - - +
35G PHE* 1.3 62.9 + - - +
36G SER 3.9 0.2 + - - -
37G ALA* 3.3 11.0 + - - +
38G THR* 3.2 22.5 + - - +
21P A 2.7 45.2 + - - -
22P G 3.3 14.6 - - - -
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Residues in contact with PHE 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F VAL* 3.5 37.2 - - + -
5F ASN 5.0 1.8 - - - -
6F LEU* 4.5 1.3 - - + -
8G ILE* 4.5 1.1 - - + -
13G TYR* 3.6 36.3 - + - -
16G ILE* 3.6 36.1 - - + -
17G ASN* 3.4 27.1 - - - -
20G ILE* 3.7 12.1 - - + +
34G SER* 1.3 69.4 - - - +
36G SER* 1.3 67.5 + - - +
38G THR* 3.2 1.7 + - - -
39G ALA* 3.0 38.2 + - + +
22P G 2.8 22.1 + - - +
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Residues in contact with SER 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F ASN 3.7 11.9 - - - -
6F LEU* 3.7 13.1 - - - +
7F TYR* 2.9 33.0 + - - -
34G SER 3.4 0.2 - - - -
35G PHE* 1.3 76.7 - - - +
37G ALA* 1.3 57.8 + - - +
40G SER* 3.0 30.0 + - - -
21P A 2.7 28.3 + - - -
22P G 2.8 19.8 + - - -
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Residues in contact with ALA 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G ASP 4.3 9.2 - - - +
33G VAL* 5.2 0.2 - - - -
34G SER* 3.3 26.4 + - - +
35G PHE 3.2 0.2 - - - -
36G SER* 1.3 77.1 - - - +
38G THR* 1.3 61.5 + - + +
40G SER* 3.2 4.9 + - - -
41G MET* 2.8 30.2 + - - +
21P A 3.4 14.1 + - - +
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Residues in contact with THR 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G ILE* 3.7 8.0 - - - +
19G ILE* 5.3 11.7 - - + -
20G ILE* 3.6 29.9 - - + +
23G ARG* 5.3 4.5 - - + +
33G VAL* 4.4 22.2 - - + -
34G SER 3.2 18.7 + - - +
35G PHE 3.2 4.5 + - - -
37G ALA* 1.3 74.7 - - + +
39G ALA* 1.3 60.4 + - - +
41G MET* 3.3 19.1 + - + +
42G LEU* 3.1 34.0 + - - +
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Residues in contact with ALA 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F LEU* 3.6 26.9 - - + +
43F LEU* 3.8 9.2 - - + +
16G ILE* 4.0 23.1 - - + -
35G PHE* 3.0 22.9 + - + +
38G THR* 1.3 74.8 + - - +
40G SER* 1.3 61.2 + - - +
42G LEU* 3.2 13.4 + - - +
43G LEU* 3.0 25.8 + - - +
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Residues in contact with SER 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F LEU* 4.1 6.0 - - - +
7F TYR 4.3 6.6 + - - -
8F ILE* 3.4 33.6 - - - +
36G SER 3.0 21.7 + - - -
37G ALA* 3.6 5.2 - - - -
39G ALA* 1.3 74.2 - - - +
41G MET* 1.3 63.9 + - - +
43G LEU* 3.5 7.6 - - - +
44G GLU* 3.1 38.3 + - - +
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Residues in contact with MET 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F HIS* 4.8 5.6 - - + -
19G ILE* 5.6 3.6 - - + -
23G ARG* 3.9 25.6 - - - +
37G ALA 2.8 13.9 + - - +
38G THR* 3.4 26.7 - - + +
40G SER* 1.3 78.4 - - - +
42G LEU* 1.3 68.9 + - + +
44G GLU* 4.2 6.9 - - - +
45G LEU* 3.2 43.5 + - - +
48G ARG* 5.4 1.0 + - - -
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Residues in contact with LEU 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F LEU 3.7 1.9 - - - +
43F LEU* 3.7 25.8 - - + +
46F GLY* 3.4 28.6 - - - +
47F LEU* 3.5 25.4 - - + +
50F HIS* 4.1 20.2 - - + +
16G ILE* 4.1 12.1 - - + -
19G ILE* 4.1 12.8 - - + -
38G THR* 3.1 16.8 + - - +
39G ALA* 3.2 8.0 + - - +
41G MET* 1.3 92.8 - - + +
43G LEU* 1.3 60.9 + - - +
45G LEU* 3.4 7.8 - - + +
46G GLY 3.0 22.0 + - - -
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Residues in contact with LEU 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F LEU* 4.1 21.8 - - + -
8F ILE* 4.2 17.3 - - + -
12F ALA* 5.7 2.0 - - + -
16F ILE* 3.8 31.6 - - + -
39F ALA* 3.9 23.3 - - + +
42F LEU* 3.8 27.8 - - + +
43F LEU* 4.4 5.4 - - + +
4G VAL* 6.0 1.6 - - + -
6G LEU* 4.4 2.7 - - + -
39G ALA 3.0 11.5 + - - +
40G SER* 3.3 9.4 + - - +
42G LEU* 1.3 74.7 - - - +
44G GLU* 1.3 61.0 + - + +
46G GLY* 2.9 4.9 + - - -
47G LEU* 2.9 32.8 + - + +
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Residues in contact with GLU 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F ILE* 6.3 0.2 - - + -
9F SER* 3.6 25.1 + - - -
12F ALA* 4.4 17.4 - - + +
40G SER* 3.1 28.7 + - - +
41G MET* 4.2 5.0 - - - +
43G LEU* 1.3 77.4 - - + +
45G LEU* 1.3 61.2 + - - +
47G LEU* 3.2 12.1 + - + +
48G ARG* 3.1 44.5 + - - +
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Residues in contact with LEU 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F GLY* 3.7 17.0 - - - +
49F VAL* 3.5 42.2 - - + -
50F HIS* 4.9 10.8 - - + +
53F GLN* 5.2 6.5 - - - +
41G MET* 3.2 36.6 + - - +
42G LEU* 3.4 11.2 - - + +
43G LEU 3.1 0.2 - - - -
44G GLU* 1.3 77.1 - - - +
46G GLY* 1.3 60.6 + - - +
48G ARG* 3.6 27.0 + - - +
49G VAL* 3.3 28.4 + - + +
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Residues in contact with GLY 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F LEU* 3.5 26.2 - - - +
45F LEU* 3.8 22.9 - - - +
46F GLY* 4.0 3.5 - - - -
42G LEU 3.0 7.2 + - - -
43G LEU 2.9 8.6 + - - -
45G LEU* 1.3 74.1 - - - +
47G LEU* 1.3 58.9 + - - +
49G VAL 3.5 0.4 + - - -
50G HIS* 3.1 27.4 + - - +
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Residues in contact with LEU 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F ALA* 4.0 35.4 - - + +
15F LYS* 4.2 25.6 - - + +
16F ILE* 4.6 2.7 - - + -
19F ILE* 4.2 14.8 - - + -
42F LEU* 3.7 25.8 - - + -
43G LEU* 2.9 19.2 + - + +
44G GLU* 3.2 23.1 + - + +
46G GLY* 1.3 76.0 - - - +
48G ARG* 1.3 65.3 + - + +
50G HIS* 3.2 15.1 + - + +
51G GLU* 3.3 25.0 + - + +
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Residues in contact with ARG 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F LYS* 6.3 0.9 - - - +
41G MET 5.4 1.2 + - - -
44G GLU* 3.1 38.0 + - - +
45G LEU* 3.6 28.0 + - - +
47G LEU* 1.3 77.5 - - + +
49G VAL* 1.3 62.6 + - + +
51G GLU* 3.7 26.9 + - - +
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Residues in contact with VAL 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F LEU* 3.6 27.4 - - + -
49F VAL* 4.1 26.9 - - + -
45G LEU* 3.3 19.5 + - + +
46G GLY 3.8 1.6 - - - +
47G LEU 3.2 0.4 - - - -
48G ARG* 1.3 76.7 - - + +
50G HIS* 1.3 64.9 + - - +
51G GLU 3.1 8.0 + - - -
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Residues in contact with HIS 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F ILE* 3.8 33.4 - - + +
23F ARG* 3.6 27.9 + - - -
41F MET* 5.0 5.3 - - + +
42F LEU* 4.2 16.0 - - + +
45F LEU* 5.1 9.4 - - + +
46G GLY 3.1 14.8 + - - +
47G LEU* 3.2 12.7 + - + +
49G VAL* 1.3 78.8 - - - +
51G GLU* 1.3 64.1 + - + +
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Residues in contact with GLU 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F LYS* 3.7 29.2 + - - +
47G LEU* 3.3 22.4 + - + +
48G ARG* 3.9 21.4 - - - +
49G VAL 3.1 8.6 - - - -
50G HIS* 1.3 86.0 - - + +
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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