Contacts of the helix formed by residues 34 - 56 (chain C) in PDB entry 2OB2
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C SER* 5.5 0.4 - - - -
32C ARG 4.1 2.4 + - - -
33C LEU* 1.3 73.8 - - - +
35C VAL* 1.3 65.1 + - - +
36C ASP* 3.5 7.8 + - - +
37C LEU* 2.8 36.8 + - - +
38C SER* 2.8 20.7 + - - -
117C GLN* 5.4 1.0 + - - -
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Residues in contact with VAL 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C SER* 1.3 74.1 - - - +
36C ASP* 1.3 65.7 + - + +
38C SER* 3.3 7.5 - - - -
39C LYS* 3.1 47.3 + - - +
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Residues in contact with ASP 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LYS* 5.9 0.7 + - - -
34C SER* 3.3 6.3 + - - +
35C VAL* 1.3 81.5 - - + +
37C LEU* 1.3 59.1 + - - +
39C LYS* 3.2 17.4 + - + +
40C LYS* 2.9 65.7 + - - +
117C GLN* 4.7 6.8 + - - -
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Residues in contact with LEU 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 3.6 26.4 - - + +
34C SER* 2.8 29.5 + - - +
36C ASP* 1.3 70.5 + - - +
38C SER* 1.3 60.9 + - - +
40C LYS* 4.1 3.4 - - + -
41C TYR* 2.8 30.8 + - - +
44C TRP* 3.5 35.2 - - + -
114C PRO* 4.0 9.4 - - + +
117C GLN* 3.5 29.6 - - - +
118C MET* 3.6 32.5 - - + -
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Residues in contact with SER 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C PRO* 3.5 22.2 - - - +
28C SER* 2.4 33.8 + - - -
33C LEU* 3.3 13.1 - - - +
34C SER 2.8 19.4 + - - -
35C VAL* 3.3 7.6 - - - -
37C LEU* 1.3 76.3 - - - +
39C LYS* 1.3 61.9 + - - -
41C TYR* 3.3 15.8 - - - +
42C THR* 3.4 7.7 + - - -
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Residues in contact with LYS 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LYS* 4.3 37.5 - - + +
43A GLU* 3.3 24.5 + - - -
35C VAL* 3.1 41.5 + - - +
36C ASP* 3.2 16.1 + - + +
38C SER* 1.3 74.4 - - - +
40C LYS* 1.3 59.3 + - + +
42C THR* 3.1 10.2 + - - -
43C GLU* 2.9 44.7 + - + +
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Residues in contact with LYS 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ASP* 2.9 53.3 + - - +
37C LEU* 3.6 7.4 - - + +
39C LYS* 1.3 72.2 - - + +
41C TYR* 1.3 59.3 + - - +
43C GLU* 3.1 17.1 + - - +
44C TRP* 2.8 74.2 + - + +
117C GLN* 3.9 16.0 + - - +
145C ILE* 5.9 1.6 - - + -
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Residues in contact with TYR 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LYS* 4.3 8.7 + - - +
20C ILE* 3.6 26.9 - - + -
25C LEU* 4.3 3.8 - - + +
26C PRO* 3.5 29.2 - - + -
31C GLN* 3.4 26.6 + - - -
33C LEU* 4.0 11.4 - - + -
37C LEU 2.8 18.1 + - - +
38C SER 3.3 7.2 - - - +
40C LYS* 1.3 76.0 - - - +
42C THR* 1.3 61.4 + - - +
44C TRP* 3.7 11.8 - + + +
45C HIS* 2.6 49.4 + + - -
82C THR* 3.9 14.0 - - - +
86C ASP* 5.3 1.1 - - - -
111C ARG* 5.6 8.4 - - + +
114C PRO* 3.7 28.0 - - + -
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Residues in contact with THR 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ILE* 3.5 26.6 - - + +
26C PRO* 3.6 17.2 - - - +
38C SER 3.4 9.6 + - - -
39C LYS* 3.1 11.9 + - - -
41C TYR* 1.3 77.2 - - - +
43C GLU* 1.3 58.8 + - + +
45C HIS* 3.4 3.8 + - - +
46C ARG* 3.0 51.5 + - - +
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Residues in contact with GLU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LYS* 4.5 15.2 + - - +
39C LYS* 2.9 36.6 + - - +
40C LYS* 3.1 13.4 + - - +
42C THR* 1.3 73.1 - - + +
44C TRP* 1.3 57.6 + - - +
46C ARG* 3.2 8.8 + - - +
47C SER* 2.7 37.2 + - - -
145C ILE* 3.6 28.0 - - + +
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Residues in contact with TRP 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 3.5 30.7 - - + -
40C LYS* 2.8 50.8 + - + +
41C TYR* 3.7 10.8 - + - +
43C GLU* 1.3 72.2 - - - +
45C HIS* 1.3 58.2 + + - +
47C SER* 3.5 1.0 + - - -
48C TYR* 3.0 28.1 + - - +
110C LEU* 3.6 12.3 - - + +
113C LEU* 3.6 37.2 - - + -
114C PRO* 3.7 17.7 - - + -
117C GLN* 3.9 7.4 - - + -
145C ILE* 3.7 37.4 + - + +
146C LEU* 3.8 24.6 - - + +
149C SER* 3.6 28.2 - - - -
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Residues in contact with HIS 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 5.8 3.8 - - + -
16C LYS* 3.7 25.2 + - + +
17C LEU* 3.6 27.8 - - + +
20C ILE* 3.0 29.6 - - + +
41C TYR* 2.6 59.1 + + - -
42C THR 3.7 4.9 - - - +
43C GLU 3.2 0.6 - - - -
44C TRP* 1.3 75.8 - + + +
46C ARG* 1.3 66.5 + - + +
48C TYR* 3.3 3.9 + - - +
49C LEU* 3.2 18.2 + - - +
108C SER 5.8 0.9 - - - -
110C LEU* 4.0 38.7 + - + +
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Residues in contact with ARG 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE 3.9 2.9 + - - -
21A SER* 2.7 33.7 + - - +
22A VAL 3.4 18.8 + - - -
23A GLY* 3.6 10.5 - - - -
305A LEU* 5.8 0.4 - - - +
17C LEU* 5.5 0.2 - - - -
20C ILE* 5.5 2.5 - - + -
21C SER* 5.7 5.7 + - - +
42C THR* 3.0 41.1 + - + +
43C GLU* 3.5 7.9 - - - +
45C HIS* 1.3 76.9 - - + +
47C SER* 1.3 62.7 + - - +
48C TYR 3.2 0.3 + - - -
49C LEU* 3.3 11.4 + - - +
50C ILE* 3.2 37.2 + - + +
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Residues in contact with SER 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C GLU 2.7 19.8 + - - -
44C TRP 3.8 2.9 - - - -
46C ARG* 1.3 73.6 - - - +
48C TYR* 1.3 58.8 + - - +
50C ILE* 4.0 7.3 - - - +
51C THR* 2.7 34.6 + - - -
143C SER* 2.5 29.3 + - - -
145C ILE* 3.4 19.5 - - - +
146C LEU* 4.7 1.8 - - - -
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Residues in contact with TYR 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 4.1 25.1 - - + -
44C TRP 3.0 18.6 + - - +
45C HIS* 3.6 6.7 - - - +
46C ARG 3.2 0.6 - - - -
47C SER* 1.3 75.9 - - - +
49C LEU* 1.3 53.5 + - - +
51C THR* 3.7 1.9 - - - -
52C LEU* 2.8 33.1 + - + +
108C SER* 3.3 33.7 + - - -
110C LEU* 3.6 37.2 - - + -
135C LEU* 4.9 0.9 - - - +
136C LYS* 3.5 30.1 + - + +
139C ILE* 3.4 50.8 - - + +
140C LEU* 4.4 7.9 - - + -
146C LEU* 4.1 7.8 - - + +
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Residues in contact with LEU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 6.0 0.2 - - - -
17C LEU* 3.8 25.5 - - + +
45C HIS 3.2 9.9 + - - +
46C ARG* 3.4 13.5 - - - +
48C TYR* 1.3 77.3 - - - +
50C ILE* 1.3 68.7 + - + +
52C LEU* 3.2 13.3 - - + +
53C LYS 3.0 17.5 + - - -
60C PHE* 3.6 34.8 - - + -
63C VAL* 4.0 17.9 - - + -
64C ASP* 5.2 3.8 - - - +
67C MET* 4.2 23.3 - - + -
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Residues in contact with ILE 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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22A VAL 5.2 2.7 - - - +
304A SER* 3.2 40.4 - - - +
305A LEU* 3.6 30.7 - - + +
46C ARG* 3.2 27.6 + - + +
47C SER* 4.0 6.7 - - - +
49C LEU* 1.3 85.1 - - + +
51C THR* 1.3 60.6 + - - +
53C LYS* 3.0 22.7 - - - +
54C LYS* 3.1 9.8 + - + +
60C PHE* 5.0 2.0 - - + -
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Residues in contact with THR 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C SER* 2.7 23.6 + - - -
48C TYR 3.8 3.1 - - - -
50C ILE* 1.3 76.8 - - - +
52C LEU* 1.3 65.3 + - - +
53C LYS 3.1 1.1 - - - -
54C LYS* 3.1 11.7 + - + +
55C PHE* 3.0 28.9 + - + -
139C ILE* 3.8 21.8 - - - +
142C GLU* 3.4 38.3 - - + +
143C SER* 3.8 13.9 - - - +
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Residues in contact with LEU 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C TYR* 5.0 3.6 - - + -
13C LEU* 3.9 27.6 - - + -
48C TYR* 2.8 19.6 + - + +
49C LEU* 3.2 15.0 - - + +
51C THR* 1.3 74.5 - - - +
53C LYS* 1.3 53.1 + - - +
55C PHE* 3.2 1.7 + - - +
56C SER* 2.7 37.1 + - - +
59C ALA* 4.1 20.6 - - + -
60C PHE* 4.2 9.4 - - - +
63C VAL* 3.9 18.2 - - + -
135C LEU* 3.8 24.5 - - + -
139C ILE* 3.5 28.1 - - + +
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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
----------------------------------------------------------
303A ARG 2.9 21.3 + - - -
304A SER* 3.1 20.6 + - - +
305A LEU 3.8 10.1 - - - +
306A GLN* 3.4 31.2 + - - +
307A PHE* 3.7 41.0 - - + -
49C LEU 3.0 6.5 + - - +
50C ILE 3.0 11.9 - - - +
52C LEU* 1.3 73.9 - - - +
54C LYS* 1.3 64.9 + - - +
55C PHE 3.4 0.2 + - - -
56C SER 3.5 13.0 + - - -
57C ARG 4.1 1.4 + - - -
60C PHE* 3.4 39.7 - - + +
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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 ILE* 3.1 10.9 + - + +
51C THR* 3.2 18.4 - - + +
53C LYS* 1.3 79.8 - - - +
55C PHE* 1.4 68.2 + - + +
142C GLU* 3.0 50.3 - - + +
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Residues in contact with PHE 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C THR* 3.0 30.5 + - + +
52C LEU 4.1 1.1 - - - +
54C LYS* 1.4 85.9 - - + +
56C SER* 1.3 62.1 - - - +
135C LEU* 4.0 21.1 - - + +
138C SER* 3.6 35.2 - - - -
139C ILE* 4.3 5.6 - - + -
142C GLU* 3.4 48.2 - - + -
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Residues in contact with SER 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C TYR* 5.1 0.4 + - - -
52C LEU* 2.7 23.4 + - - +
53C LYS 3.5 6.2 + - - -
55C PHE* 1.3 78.8 - - - +
57C ARG* 1.3 58.2 + - - +
58C ARG* 3.4 9.4 + - - +
59C ALA* 2.9 31.9 + - - +
60C PHE* 3.0 25.5 + - - +
135C LEU* 5.1 7.9 - - - -
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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