Contacts of the helix formed by residues 24 - 41 (chain G) in PDB entry 6X0A
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 24 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G ILE 3.0 10.0 + - - +
21G ALA* 3.4 4.1 + - - -
23G ASP* 1.3 91.2 - - - +
25G PRO* 1.3 70.0 - - - +
26G ARG* 3.5 9.7 + - - +
27G ALA* 3.4 26.2 + - - +
28G ALA 3.2 16.1 + - - -
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Residues in contact with PRO 25 (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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17G TRP* 3.6 23.6 - - + -
21G ALA* 3.6 23.6 - - + +
23G ASP 4.5 1.6 - - - +
24G SER* 1.3 84.2 - - - +
26G ARG* 1.3 64.0 + - + +
28G ALA* 3.3 4.6 + - + +
29G ASP* 3.2 20.2 + - - -
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Residues in contact with ARG 26 (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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24G SER* 3.2 7.7 + - - +
25G PRO* 1.3 79.1 - - + +
27G ALA* 1.3 67.1 + - - +
29G ASP* 2.9 20.9 + - + +
30G HIS* 3.1 45.6 + - + -
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Residues in contact with ALA 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G ILE* 3.8 13.6 - - + +
23G ASP* 5.2 3.8 - - - +
24G SER* 3.3 23.1 + - - +
26G ARG* 1.3 77.7 - - - +
28G ALA* 1.3 62.4 + - - +
30G HIS* 3.3 10.5 + - - +
31G PHE* 3.1 21.1 + - - +
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Residues in contact with ALA 28 (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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17G TRP* 3.3 45.3 - - + +
20G ILE* 3.5 20.3 - - + +
21G ALA 3.9 2.9 - - - +
24G SER 3.2 11.1 + - - +
25G PRO 3.3 8.7 - - - +
26G ARG 3.1 0.6 - - - -
27G ALA* 1.3 77.2 - - - +
29G ASP* 1.3 62.1 + - - +
31G PHE* 3.3 2.3 + - - +
32G LEU* 3.3 27.5 + - - +
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Residues in contact with ASP 29 (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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17G TRP* 2.8 26.9 + - - +
25G PRO 3.2 14.8 + - - +
26G ARG* 2.9 14.7 + - + +
28G ALA* 1.3 77.0 - - - +
30G HIS* 1.3 59.8 + - + +
31G PHE 3.2 0.2 + - - -
32G LEU* 3.3 2.6 + - - +
33G ASP* 2.8 41.2 + - - +
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Residues in contact with HIS 30 (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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26G ARG* 3.1 60.9 + - + +
27G ALA* 3.3 9.9 + - - +
29G ASP* 1.3 78.6 - - + +
31G PHE* 1.3 63.3 + - - +
33G ASP* 3.3 15.0 - - + +
34G ALA* 3.0 21.0 + - - +
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Residues in contact with PHE 31 (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* 3.8 24.9 - - + -
20G ILE* 3.6 30.5 - - + -
27G ALA 3.1 10.7 + - - +
28G ALA 3.7 7.0 - - - +
29G ASP 3.2 0.2 - - - -
30G HIS* 1.3 77.0 - - - +
32G LEU* 1.3 52.0 + - + +
34G ALA* 2.6 30.9 + - + +
35G ILE* 2.7 46.9 + - + +
64G ILE* 4.1 32.5 - - + -
65G GLY* 5.8 2.5 - - - -
67G TYR* 5.0 17.0 - + + -
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Residues in contact with LEU 32 (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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13G LEU* 4.0 28.7 - - + +
14G VAL* 5.8 0.2 - - - -
16G ILE* 4.2 13.7 - - + -
17G TRP* 3.3 57.7 - - + +
20G ILE* 5.3 0.4 - - + -
28G ALA 3.3 8.8 + - - +
29G ASP* 3.9 5.6 - - - +
31G PHE* 1.3 77.3 - - + +
33G ASP* 1.3 67.9 + - - +
35G ILE* 3.0 11.7 + - + +
36G ALA* 2.9 25.5 + - - +
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Residues in contact with ASP 33 (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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29G ASP* 2.8 27.1 + - - +
30G HIS* 3.3 20.2 - - + +
32G LEU* 1.3 75.5 - - - +
34G ALA* 1.3 62.6 + - - +
36G ALA* 3.4 5.7 + - - +
37G GLU* 3.0 26.6 + - - +
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Residues in contact with ALA 34 (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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30G HIS 3.0 11.3 + - - +
31G PHE* 2.6 24.6 + - + +
33G ASP* 1.3 69.0 - - - +
35G ILE* 1.3 61.9 + - - +
37G GLU* 3.6 10.7 + - - +
38G ARG* 3.2 23.0 + - - +
64G ILE* 3.9 17.9 - - + +
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Residues in contact with ILE 35 (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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13G LEU* 4.0 28.0 - - + -
16G ILE* 5.4 0.9 - - + -
31G PHE* 2.7 76.8 + - + +
32G LEU* 3.0 13.7 + - + +
34G ALA* 1.3 76.0 - - - +
36G ALA* 1.3 60.0 + - - +
38G ARG* 3.1 5.4 + - - +
39G ILE* 2.8 50.3 + - + +
64G ILE* 4.2 19.1 - - + -
69G ILE* 4.3 9.6 - - + +
83G ILE* 5.0 6.3 - - + -
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Residues in contact with ALA 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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32G LEU 2.9 15.1 + - - +
33G ASP* 3.8 5.6 - - - +
35G ILE* 1.3 77.0 - - - +
37G GLU* 1.3 53.2 + - - +
39G ILE* 2.7 14.5 + - - +
40G LEU* 2.6 49.6 + - + +
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Residues in contact with GLU 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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33G ASP 3.0 19.0 + - - +
34G ALA* 3.9 9.8 - - - +
35G ILE 3.4 0.2 - - - -
36G ALA* 1.3 76.0 - - - +
38G ARG* 1.3 59.9 + - - +
40G LEU* 3.7 12.5 + - - +
41G GLN* 3.4 32.8 + - + +
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Residues in contact with ARG 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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34G ALA 3.2 13.2 + - - +
35G ILE* 3.1 9.3 + - - +
36G ALA 3.0 0.6 - - - -
37G GLU* 1.3 77.0 - - - +
39G ILE* 1.3 64.1 + - - +
41G GLN* 3.5 31.7 + - - +
42G LEU 3.9 1.6 + - - -
62G LEU* 3.4 51.5 - - + +
63G THR* 2.9 37.0 + - - +
64G ILE* 3.9 17.6 - - + +
69G ILE* 4.3 11.0 - - + -
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Residues in contact with ILE 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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3G ILE* 3.6 20.9 - - + +
13G LEU* 5.3 5.2 - - + -
35G ILE* 2.8 37.4 + - + +
36G ALA* 2.7 16.6 + - - +
38G ARG* 1.3 70.9 - - - +
40G LEU* 1.3 59.6 + - + +
42G LEU* 2.9 30.7 + - + +
62G LEU* 5.1 0.2 - - - -
69G ILE* 3.8 32.1 - - + -
80G ILE* 3.7 37.9 - - + -
83G ILE* 5.1 4.5 - - + -
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Residues in contact with LEU 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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3G ILE* 3.8 20.4 - - + -
36G ALA* 2.6 36.1 + - + +
37G GLU* 4.1 9.0 - - - +
39G ILE* 1.3 74.1 - - + +
41G GLN* 1.3 60.6 + - - +
42G LEU 3.3 0.5 + - - -
43G ALA* 3.5 17.5 + - - +
44G ALA* 4.6 0.7 + - - +
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Residues in contact with GLN 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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37G GLU* 3.4 24.7 + - + +
38G ARG* 3.6 30.0 + - - +
39G ILE 3.1 0.8 - - - -
40G LEU* 1.3 76.5 - - - +
42G LEU* 1.3 62.6 + - - +
43G ALA 3.2 0.4 - - - -
44G ALA* 3.2 10.2 + - - +
45G PHE* 3.2 25.9 + - + +
48G SER* 5.2 2.9 + - - +
62G LEU* 6.0 0.7 - - + -
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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