Contacts of the helix formed by residues 30 - 48 (chain C) in PDB entry 6O81
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 30 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ARG* 1.3 78.0 + - - +
31C SER* 1.3 62.6 + - - +
32C GLU* 4.2 6.5 + - - +
33C GLU* 2.7 48.5 + - - +
34C MET* 3.6 13.1 + - - +
172C ARG* 3.5 38.6 + - - +
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Residues in contact with SER 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ARG 4.1 0.7 + - - -
30C SER* 1.3 74.0 - - - +
32C GLU* 1.3 58.5 + - - +
34C MET* 3.3 15.7 - - - +
35C ALA* 2.9 30.3 + - - +
77C THR* 4.8 8.7 + - - +
237C LYS* 4.1 18.9 + - - +
272C PHE* 3.6 23.1 - - - -
273C LYS* 4.0 19.9 + - - -
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Residues in contact with GLU 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C SER* 3.3 6.6 - - - +
31C SER* 1.3 78.6 - - - +
33C GLU* 1.3 57.9 + - - +
35C ALA* 3.3 3.9 + - - +
36C ARG* 2.9 40.8 + - - +
144C LEU* 3.0 35.1 - - + +
145C GLU* 3.6 16.8 - - - +
147C THR* 4.1 8.5 + - - +
148C MET* 5.0 16.7 + - - +
272C PHE* 4.0 18.0 - - + -
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Residues in contact with GLU 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C PRO* 3.6 19.5 - - + -
29C ARG* 3.5 10.7 + - - +
30C SER* 2.7 42.4 + - - +
32C GLU* 1.3 78.5 - - - +
34C MET* 1.3 61.1 + - - +
36C ARG* 3.3 33.0 + - - +
37C GLU* 2.9 31.1 + - - +
172C ARG* 5.4 0.9 + - - -
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Residues in contact with MET 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C PHE* 5.1 1.8 - - + -
22C LEU* 4.0 17.0 - - + -
27C GLY 5.6 0.4 - - - +
28C PRO* 3.7 28.0 - - + +
29C ARG 5.7 0.7 - - - +
30C SER 3.7 8.5 - - - +
31C SER* 3.3 26.7 - - - +
33C GLU* 1.3 78.0 - - - +
35C ALA* 1.3 55.4 + - - +
37C GLU* 3.4 12.1 - - - +
38C THR* 2.4 38.2 + - - +
75C GLU* 3.3 39.5 - - + +
77C THR* 4.7 13.9 - - + -
78C VAL* 4.0 22.7 - - + -
237C LYS* 5.5 2.9 - - - -
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Residues in contact with ALA 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C SER 2.9 18.9 + - - +
32C GLU 3.6 5.2 - - - +
33C GLU 3.3 0.2 - - - -
34C MET* 1.3 75.0 - - - +
36C ARG* 1.3 57.9 + - - +
38C THR* 3.3 6.0 + - - -
39C LEU* 3.0 35.7 + - - +
77C THR* 4.5 10.8 - - + -
81C MET* 4.9 6.1 - - + -
144C LEU* 3.8 23.6 - - + -
272C PHE* 4.2 17.0 - - + -
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Residues in contact with ARG 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C GLU* 2.9 23.5 + - - +
33C GLU* 3.5 35.8 + - - +
34C MET 3.3 0.2 - - - -
35C ALA* 1.3 76.6 - - - +
37C GLU* 1.3 57.0 + - - +
39C LEU* 3.4 2.4 + - - +
40C GLY* 2.9 24.3 + - - -
141C LEU* 4.0 25.7 - - + +
144C LEU* 3.7 16.4 - - + -
145C GLU* 5.5 14.9 - - - +
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Residues in contact with GLU 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ARG* 4.3 16.6 + - - +
18C PHE* 3.2 31.5 - - + -
21C THR* 5.0 2.8 - - - +
27C GLY 4.2 2.3 - - - +
28C PRO* 3.3 39.3 - - - +
33C GLU* 2.9 12.1 + - - +
34C MET* 3.4 12.8 - - - +
36C ARG* 1.3 74.1 - - - +
38C THR* 1.3 62.1 + - - +
40C GLY* 3.7 1.7 - - - +
41C LEU* 2.9 28.4 + - - +
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Residues in contact with THR 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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18C PHE* 3.5 14.0 - - + -
34C MET 2.4 23.8 + - - -
35C ALA* 3.7 7.7 - - - -
36C ARG 3.3 0.2 - - - -
37C GLU* 1.3 75.2 - - - +
39C LEU* 1.3 62.2 + - - +
41C LEU* 3.3 7.6 + - + +
42C LEU* 2.9 42.4 + - + +
68C MET* 4.9 7.2 - - - -
77C THR* 6.0 0.6 - - - +
78C VAL* 3.4 48.1 - - + +
81C MET* 4.6 6.7 - - + -
82C VAL* 5.2 0.4 - - + -
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Residues in contact with LEU 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ALA 3.0 26.5 + - - +
36C ARG 3.8 3.8 - - - +
38C THR* 1.3 76.1 - - - +
40C GLY* 1.3 56.8 + - - +
42C LEU* 3.3 4.8 + - + +
43C ARG* 2.9 30.2 + - - +
81C MET* 3.7 38.8 - - + -
85C VAL* 4.1 21.1 - - + -
137C ILE* 3.8 28.4 - - + +
140C LEU* 3.9 23.6 - - + -
141C LEU* 3.8 25.4 - - + -
144C LEU* 4.6 7.2 - - + -
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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
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14C ARG* 4.3 7.4 - - - -
36C ARG 2.9 16.6 + - - -
37C GLU* 3.7 2.9 - - - -
38C THR 3.3 0.2 - - - -
39C LEU* 1.3 74.6 - - - +
41C LEU* 1.3 58.8 + - - +
43C ARG* 3.2 15.6 - - - +
44C GLN* 2.9 30.3 + - - +
141C LEU* 5.3 2.8 - - - +
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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
----------------------------------------------------------
11C LEU* 5.3 1.3 - - + +
14C ARG* 3.5 33.8 - - + +
15C ILE* 3.8 30.5 - - + +
18C PHE* 3.8 42.0 - - + -
37C GLU 2.9 17.8 + - - +
38C THR* 3.3 7.2 + - + +
40C GLY* 1.3 76.3 - - - +
42C LEU* 1.3 59.2 + - + +
44C GLN* 3.3 5.0 + - + +
45C ILE* 2.9 46.3 + - + +
68C MET* 4.6 14.4 - - + -
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Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C THR* 2.9 36.7 + - + +
39C LEU* 3.7 9.4 - - + +
40C GLY 3.3 0.2 - - - -
41C LEU* 1.3 76.4 - - + +
43C ARG* 1.3 59.9 + - - +
45C ILE* 3.2 13.5 - - + +
46C ILE* 3.0 33.6 + - - +
61C ILE* 3.8 29.8 - - + -
68C MET* 5.3 4.9 - - + -
81C MET* 4.2 7.4 - - + +
82C VAL* 4.0 26.2 - - + -
85C VAL* 3.7 38.1 - - + -
137C ILE* 4.8 3.1 - - + -
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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 LEU 2.9 15.1 + - - +
40C GLY* 3.2 20.1 - - - +
42C LEU* 1.3 75.9 - - - +
44C GLN* 1.3 57.9 + - + +
46C ILE* 3.3 10.1 + - - +
47C THR* 3.0 37.3 + - + +
134C ILE* 4.2 20.8 - - + +
137C ILE* 3.5 24.8 - - + +
138C ASN* 2.5 44.4 + - - +
141C LEU* 3.4 29.6 - - - +
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Residues in contact with GLN 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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10C GLU* 4.1 25.1 + - - +
11C LEU* 4.1 8.5 - - + +
14C ARG* 3.2 40.4 + - - +
40C GLY 2.9 17.8 + - - +
41C LEU* 3.7 7.0 - - + +
43C ARG* 1.3 79.6 - - + +
45C ILE* 1.3 59.9 + - + +
47C THR* 3.5 11.1 + - - +
48C ASP* 2.8 31.0 + - - +
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Residues in contact with ILE 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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11C LEU* 3.7 21.1 - - + -
15C ILE* 3.8 21.8 - - + -
41C LEU* 2.9 31.3 + - + +
42C LEU* 3.2 26.0 - - + +
44C GLN* 1.3 77.9 - - + +
46C ILE* 1.3 59.5 + - - +
47C THR 3.6 0.2 - - - -
48C ASP* 3.7 5.4 - - - -
49C HIS* 2.9 29.5 + - + +
60C LEU* 4.8 4.8 - - + +
61C ILE* 3.8 22.0 - - + -
64C GLU* 3.3 33.2 - - + +
68C MET* 5.8 2.7 - - + -
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Residues in contact with ILE 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 LEU* 3.0 16.4 + - + +
43C ARG* 3.3 13.2 - - - +
45C ILE* 1.3 84.9 - - + +
47C THR* 1.3 62.2 + - - +
48C ASP 3.4 1.1 - - - -
49C HIS* 4.5 0.9 - - - -
51C TRP* 3.4 22.2 - - + -
57C LEU* 4.4 32.1 - - + -
60C LEU* 6.0 1.1 - - + -
61C ILE* 4.5 9.9 - - + -
85C VAL* 5.7 5.4 - - + -
130C GLN* 3.4 16.0 + - + +
133C ILE* 3.7 31.9 - - + -
134C ILE* 3.9 18.4 - - + -
137C ILE* 3.8 18.6 - - + -
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Residues in contact with THR 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ARG* 3.0 23.6 + - + +
44C GLN* 3.5 12.5 + - - +
46C ILE* 1.3 79.8 - - - +
48C ASP* 1.3 61.5 + - - +
49C HIS 3.6 2.2 + - - +
130C GLN* 3.5 18.2 + - - +
134C ILE* 3.7 26.2 - - + -
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Residues in contact with ASP 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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8C GLY 4.4 10.0 + - - +
11C LEU* 3.3 30.9 - - - +
44C GLN* 2.8 28.9 + - - +
45C ILE 3.6 0.7 - - - +
47C THR* 1.3 76.3 - - - +
49C HIS* 1.3 67.1 + - - +
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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