Contacts of the helix formed by residues 33 - 54 (chain C) in PDB entry 6ACQ
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 33 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ASP 3.4 0.4 - - - -
32C ILE* 1.3 101.6 - - + +
34C ASP* 1.3 66.7 + - - +
35C GLU* 4.0 28.9 - - + +
36C PHE* 3.3 27.2 + - + +
37C VAL* 3.3 16.1 + - - +
73C VAL* 3.6 8.5 - - - -
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Residues in contact with ASP 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LYS* 1.3 72.6 - - - +
35C GLU* 1.3 55.6 + - - +
37C VAL* 3.0 8.0 + - - +
38C ASP* 2.6 48.6 + - - +
72C THR* 5.6 1.6 - - - -
73C VAL* 3.6 20.2 - - - +
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Residues in contact with GLU 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LYS* 4.0 23.8 - - + +
34C ASP* 1.3 79.5 - - - +
36C PHE* 1.3 86.3 + - + +
38C ASP* 3.7 10.8 - - - +
39C ARG* 2.9 29.6 + - - +
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Residues in contact with PHE 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ALA* 3.6 11.2 - - + +
31C ASP* 3.4 33.2 - - - +
32C ILE* 3.6 28.0 - - + -
33C LYS* 3.3 19.5 + - + +
34C ASP 3.1 0.2 - - - -
35C GLU* 1.3 105.5 - - + +
37C VAL* 1.3 65.7 + - - +
39C ARG* 3.1 16.3 + - - +
40C GLY 3.0 19.4 + - - -
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Residues in contact with VAL 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ALA* 4.2 8.5 - - - +
29C LEU* 3.9 12.0 - - + +
31C ASP* 3.9 14.3 - - + +
33C LYS 3.3 15.9 - - - +
34C ASP* 3.0 8.5 + - - +
36C PHE* 1.3 76.6 - - - +
38C ASP* 1.3 65.2 + - - +
40C GLY* 3.2 3.5 + - - -
41C LEU* 2.9 36.7 + - + +
71C GLY* 3.7 31.0 - - - -
72C THR* 3.6 26.5 - - - +
73C VAL* 4.1 6.3 - - + -
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Residues in contact with ASP 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ASP* 2.6 34.9 + - - +
35C GLU* 3.7 8.9 - - - +
37C VAL* 1.3 73.0 - - - +
39C ARG* 1.3 52.5 + - - +
41C LEU* 3.1 15.6 + - - +
42C ASP* 2.8 47.2 + - - +
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Residues in contact with ARG 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ALA 4.6 3.8 + - - -
10C GLY* 4.2 23.2 - - - -
11C THR* 4.6 9.7 + - - +
35C GLU* 2.9 21.0 + - - +
36C PHE* 3.3 16.1 + - - +
38C ASP* 1.3 76.9 - - - +
40C GLY* 1.3 57.3 + - - +
42C ASP* 3.2 11.4 + - + +
43C PHE* 2.8 32.2 + - - +
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Residues in contact with GLY 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ALA* 3.5 13.8 + - - -
14C SER* 3.3 22.5 - - - -
29C LEU* 4.8 2.2 - - - -
36C PHE 3.0 11.7 + - - -
37C VAL 3.7 2.9 - - - -
39C ARG* 1.3 76.7 - - - +
41C LEU* 1.3 52.3 + - - +
43C PHE* 3.3 6.1 + - - +
44C ILE* 2.7 42.4 + - - +
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Residues in contact with LEU 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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29C LEU* 4.2 11.0 - - + -
37C VAL* 2.9 35.7 + - + +
38C ASP* 3.5 17.9 - - - +
40C GLY* 1.3 74.9 - - - +
42C ASP* 1.3 66.4 + - - +
44C ILE* 3.1 11.2 + - + +
45C ASN* 2.9 24.9 + - - +
66C LEU* 5.1 7.2 - - + +
69C ILE* 4.0 33.2 - - + +
71C GLY* 4.7 11.0 - - - +
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Residues in contact with ASP 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASP* 2.8 30.2 + - - +
39C ARG* 3.3 13.1 - - + +
41C LEU* 1.3 71.7 - - - +
43C PHE* 1.3 63.7 + - - +
45C ASN* 3.1 9.3 + - - +
46C LYS* 3.1 41.4 + - - +
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Residues in contact with PHE 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLY 5.6 0.4 - - - -
11C THR* 3.9 45.1 - - + -
14C SER* 3.6 22.4 - - - -
15C GLY* 4.4 8.1 - - - -
18C GLN* 5.7 0.2 - - - -
39C ARG* 2.8 20.6 + - - +
40C GLY* 3.6 5.4 - - - +
41C LEU 3.2 0.2 - - - -
42C ASP* 1.3 76.4 - - - +
44C ILE* 1.3 56.7 + - + +
46C LYS* 3.7 11.6 + - + +
47C ASN* 2.6 60.4 + - - -
142C PRO* 6.5 1.1 - - + -
144C PRO* 6.4 0.2 - - + -
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Residues in contact with ILE 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C SER* 3.3 37.5 - - - +
17C ALA* 4.3 12.3 - - + -
18C GLN* 3.4 26.2 - - + +
29C LEU* 4.7 7.4 - - + -
40C GLY 2.7 25.8 + - - +
41C LEU* 3.1 11.0 + - + +
43C PHE* 1.3 77.6 - - + +
45C ASN* 1.3 64.5 + - - +
47C ASN* 3.3 7.4 + - - +
48C LEU* 3.1 27.2 + - + +
65C ILE* 5.6 0.2 - - + -
66C LEU* 4.3 17.0 - - + -
69C ILE* 4.3 16.6 - - + -
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Residues in contact with ASN 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LEU 2.9 12.6 + - - +
42C ASP* 3.1 13.4 + - - +
44C ILE* 1.3 77.5 - - - +
46C LYS* 1.3 51.4 + - + +
48C LEU* 3.3 5.5 + - - +
49C SER* 2.7 40.7 + - - -
62C LYS* 2.6 32.0 + - - +
66C LEU* 3.8 26.0 - - + +
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Residues in contact with LYS 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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42C ASP* 3.2 30.7 - - - +
43C PHE* 3.9 9.6 - - + +
45C ASN* 1.3 74.7 - - + +
47C ASN* 1.3 67.2 + - - +
49C SER* 3.0 10.2 + - - -
50C LYS* 2.9 39.7 + - - +
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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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18C GLN* 3.7 25.6 + - - +
43C PHE* 2.6 60.7 + - - +
44C ILE 3.3 0.6 + - - +
45C ASN 3.3 0.2 - - - -
46C LYS* 1.3 78.7 - - - +
48C LEU* 1.3 62.2 + - - +
50C LYS* 3.4 19.6 + - - +
51C LEU* 3.3 25.9 + - + +
144C PRO* 5.8 4.4 - - + +
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Residues in contact with LEU 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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18C GLN* 3.6 27.6 - - + +
22C ALA* 5.8 1.3 - - + -
44C ILE* 3.1 23.5 + - + +
45C ASN 3.6 3.6 - - - +
47C ASN* 1.3 76.1 - - - +
49C SER* 1.3 58.5 + - - +
51C LEU* 2.8 36.9 + - + +
52C VAL* 3.0 14.2 + - - +
57C ILE* 4.1 6.2 - - + +
62C LYS* 3.7 33.2 - - + +
65C ILE* 3.7 41.7 - - + -
66C LEU* 3.9 17.7 - - + -
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Residues in contact with SER 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 ASN* 2.7 26.2 + - - -
46C LYS* 3.1 13.7 - - - -
48C LEU* 1.3 74.9 - - - +
50C LYS* 1.3 62.2 + - - -
52C VAL* 3.2 5.9 + - - +
53C LYS* 2.9 25.2 + - - +
62C LYS* 3.7 21.7 + - - +
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Residues in contact with LYS 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C LYS* 2.9 30.4 + - - +
47C ASN* 3.4 22.3 + - - +
49C SER* 1.3 75.0 - - - +
51C LEU* 1.3 53.9 + - + +
53C LYS* 3.1 13.2 + - + +
54C LYS* 2.6 48.8 + - + +
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Residues in contact with LEU 51 (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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18C GLN* 4.4 10.3 - - - +
47C ASN* 3.3 15.5 + - + +
48C LEU* 2.8 33.4 + - + +
50C LYS* 1.3 77.9 - - + +
52C VAL* 1.3 56.2 + - - +
54C LYS* 3.7 7.3 - - + -
55C GLY 3.3 1.6 + - - -
56C LYS* 2.6 56.1 + - + +
57C ILE* 3.1 22.4 + - + -
145C VAL* 6.5 0.9 - - + -
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Residues in contact with VAL 52 (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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48C LEU 3.0 9.4 + - - +
49C SER* 3.6 9.0 - - - +
50C LYS 3.1 0.2 - - - -
51C LEU* 1.3 74.9 - - - +
53C LYS* 1.3 61.0 + - - +
55C GLY* 2.7 24.8 + - - -
57C ILE* 3.3 34.4 - - + +
58C GLU* 3.6 1.1 - - - +
59C GLU* 3.4 47.3 - - + +
62C LYS* 4.1 7.9 - - + -
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Residues in contact with LYS 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C SER 2.9 17.0 + - - +
50C LYS* 3.5 11.4 - - + +
52C VAL* 1.3 79.1 - - - +
54C LYS* 1.3 60.8 + - + +
55C GLY* 3.2 4.0 + - - -
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Residues in contact with LYS 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LYS* 2.6 31.4 + - + +
51C LEU* 4.0 9.4 - - + +
53C LYS* 1.3 75.4 - - + +
55C GLY* 1.3 61.5 + - - +
56C LYS* 3.2 30.6 + - + +
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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) + - + + + + + -
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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