Contacts of the helix formed by residues 34 - 50 (chain C) in PDB entry 6F0X
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 LYS 34 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C GLN* 4.9 4.7 - - - +
32C THR 4.2 7.9 - - - +
33C ALA* 1.3 79.6 - - - +
35C LYS* 1.3 68.4 + - - +
36C GLU* 3.4 9.2 - - - +
37C ASP* 3.6 16.0 + - - +
38C ILE* 3.0 29.2 + - - +
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Residues in contact with LYS 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C GLN* 5.7 3.1 - - - +
34C LYS* 1.3 78.1 - - - +
36C GLU* 1.3 69.9 + - - +
38C ILE* 5.1 0.2 - - - -
39C ASN* 2.8 30.8 + - - +
99C ILE* 3.8 31.1 - - + +
201C SER* 5.0 10.5 + - - -
205C ARG* 4.2 29.5 - - - +
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Residues in contact with GLU 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LYS* 3.4 6.4 - - - +
35C LYS* 1.3 84.7 + - - +
37C ASP* 1.3 69.9 + - - +
39C ASN* 3.2 7.0 + - - +
40C LEU* 3.0 35.0 + - + +
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Residues in contact with ASP 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ALA* 5.1 1.7 - - - -
34C LYS* 3.6 20.4 + - - +
35C LYS 3.4 0.2 - - - -
36C GLU* 1.3 80.9 + - - +
38C ILE* 1.3 53.8 + - - +
40C LEU* 3.5 8.5 + - - +
41C SER* 2.7 37.5 + - - -
65C PHE* 3.4 27.0 - - + -
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Residues in contact with ILE 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C VAL* 3.7 21.8 - - + -
27C GLN* 4.4 25.6 - - + -
33C ALA* 3.6 29.2 - - + -
34C LYS 3.0 24.3 + - - +
37C ASP* 1.3 75.5 - - - +
39C ASN* 1.3 56.8 + - - +
41C SER* 4.2 2.0 - - - -
42C VAL* 2.9 37.5 + - + +
65C PHE* 4.1 9.6 - - + -
66C LEU* 4.4 9.4 - - + -
69C ASN 5.4 1.8 - - - +
70C VAL* 4.6 7.9 - - + -
99C ILE* 3.7 25.8 - - + -
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Residues in contact with ASN 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C LYS 2.8 20.3 + - - +
36C GLU* 3.5 8.9 - - - +
38C ILE* 1.3 77.9 - - - +
40C LEU* 1.3 67.4 + - + +
43C ARG* 2.8 57.2 + - - +
97C LEU* 3.8 13.2 - - - +
99C ILE* 4.4 6.0 - - + +
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Residues in contact with LEU 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C GLU* 3.0 23.2 + - + +
37C ASP* 3.9 7.9 - - - +
39C ASN* 1.3 78.6 - - + +
41C SER* 1.3 58.5 + - - +
43C ARG* 3.4 8.2 + - + +
44C LYS* 2.9 54.8 + - - +
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Residues in contact with SER 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ASP* 2.7 22.4 + - - -
38C ILE 3.7 3.6 - - - -
39C ASN 3.2 0.4 - - - -
40C LEU* 1.3 77.4 - - - +
42C VAL* 1.3 56.5 - - - +
44C LYS* 3.2 9.4 + - - +
45C LEU* 2.9 25.6 + - - +
63C GLU* 3.7 21.8 + - - +
65C PHE* 3.0 30.3 - - - -
66C LEU* 3.7 15.7 - - - -
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Residues in contact with VAL 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C VAL* 4.5 17.7 - - + -
38C ILE* 2.9 38.4 + - + +
41C SER* 1.3 68.9 - - - +
43C ARG* 1.3 67.2 + - - +
45C LEU* 3.2 7.6 + - + +
46C LEU* 3.0 29.2 + - + +
66C LEU* 3.7 22.9 - - + -
70C VAL* 5.4 0.2 - - + -
73C VAL* 4.6 19.7 - - + -
97C LEU* 3.6 33.4 - - + -
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Residues in contact with ARG 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ASN* 2.8 45.2 + - - +
40C LEU* 3.8 9.0 - - + +
42C VAL* 1.3 76.7 - - - +
44C LYS* 1.3 56.4 + - + +
46C LEU* 3.9 6.5 - - + +
47C ASN* 2.6 49.7 + - - +
95C VAL* 3.8 27.2 + - + +
96C ALA* 5.0 1.8 - - - +
97C LEU* 3.5 22.1 - - + +
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Residues in contact with LYS 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C LEU* 2.9 48.6 + - + +
41C SER* 3.2 8.0 + - - +
43C ARG* 1.3 74.8 - - + +
45C LEU* 1.3 59.8 + - - +
47C ASN* 3.8 6.3 - - - +
48C ARG* 2.8 42.6 + - - +
63C GLU* 4.8 10.3 - - - +
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Residues in contact with LEU 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C SER 2.9 13.5 + - - +
42C VAL* 3.2 16.1 + - + +
44C LYS* 1.3 75.1 - - - +
46C LEU* 1.3 67.0 + - + +
48C ARG* 3.1 20.2 + - - +
49C HIS* 3.0 55.9 + - + +
58C TRP* 4.6 20.0 - - + -
60C GLU 5.8 1.3 - - - +
61C PHE* 4.3 28.7 - - + -
62C ASP* 5.4 12.1 - - + +
63C GLU* 4.9 10.0 + - + +
66C LEU* 4.5 13.7 - - + -
73C VAL* 5.6 5.2 - - + -
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Residues in contact with LEU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C VAL* 5.1 5.2 - - + -
42C VAL* 3.0 22.3 + - + +
43C ARG* 3.9 6.5 - - + +
45C LEU* 1.3 79.1 - - + +
47C ASN* 1.3 54.7 + - - +
49C HIS* 2.6 11.8 + - + -
50C ASN* 2.3 39.8 + - - +
58C TRP* 4.3 39.0 - - + +
73C VAL* 6.2 3.6 - - + -
75C ILE* 5.6 4.0 - - + -
95C VAL* 3.6 33.7 - - + -
97C LEU* 4.0 17.7 - - + -
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Residues in contact with ASN 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ARG* 2.6 41.0 + - - +
44C LYS* 4.0 5.9 - - - +
46C LEU* 1.3 73.6 - - - +
48C ARG* 1.3 61.5 + - - +
50C ASN* 3.2 34.8 + - - +
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Residues in contact with ARG 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C LYS* 2.8 28.9 + - - +
45C LEU* 3.2 17.0 - - - +
47C ASN* 1.3 78.8 - - - +
49C HIS* 1.3 74.3 + - + +
62C ASP* 4.1 28.3 - - - +
63C GLU* 4.4 24.4 + - - +
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Residues in contact with HIS 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C LEU* 3.0 50.5 + - + +
46C LEU* 2.6 11.2 + - + +
48C ARG* 1.3 85.6 + - + +
50C ASN* 1.3 69.6 + - - +
51C ILE* 3.0 24.4 + - + +
58C TRP* 4.3 27.2 + + + +
60C GLU 5.9 1.2 + - - -
62C ASP* 4.8 12.9 + - - -
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Residues in contact with ASN 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C LEU* 2.3 28.1 + - - +
47C ASN* 3.2 36.7 + - - +
49C HIS* 1.3 72.3 - - - +
51C ILE* 1.3 58.8 + - - +
91C SER* 2.8 37.7 + - - +
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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