Contacts of the helix formed by residues 33 - 54 (chain C) in PDB entry 6V3O
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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27C LYS* 4.5 7.7 - - - +
30C GLU 4.1 18.0 + - - -
31C ASP* 4.0 12.6 - - - +
32C ASP* 1.3 80.6 + - - +
34C LEU* 1.3 59.3 + - - +
35C ILE 3.3 2.9 - - - -
36C GLU* 3.1 39.6 + - + +
37C TYR* 2.9 47.2 + - + +
116C GLN* 3.2 14.8 - - - +
201C ASN* 5.4 8.5 - - - +
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Residues in contact with LEU 34 (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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32C ASP* 2.9 15.6 + - - +
33C LYS* 1.3 78.1 - - - +
35C ILE* 1.3 57.4 + - - +
37C TYR* 3.3 3.8 + - + +
38C ASP* 2.9 39.2 + - - +
109C ALA 4.9 0.2 - - - +
112C ALA* 3.8 9.9 - - + +
113C GLU* 3.7 47.1 - - + +
116C GLN* 3.7 18.8 - - + +
889C GLN* 3.7 20.4 - - + +
890C GLY* 4.6 10.3 - - - -
893C LEU* 4.0 21.1 - - + -
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Residues in contact with ILE 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ASP* 3.9 9.4 - - - +
20C LEU* 4.0 17.6 - - + +
21C ARG* 3.6 57.2 - - + +
24C VAL* 3.5 29.8 - - + +
26C GLY 5.9 1.1 - - - +
32C ASP* 4.5 2.8 + - - +
33C LYS 3.3 0.4 - - - -
34C LEU* 1.3 77.8 - - - +
36C GLU* 1.3 58.7 + - + +
38C ASP* 3.7 6.4 - - - +
39C ALA* 2.9 27.9 + - - +
889C GLN* 5.0 6.5 - - - +
893C LEU* 4.2 19.3 - - + -
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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
----------------------------------------------------------
17C ASP* 4.8 6.5 - - - +
21C ARG* 5.0 13.2 + - - +
33C LYS* 3.1 44.0 + - + +
35C ILE* 1.3 76.1 - - + +
37C TYR* 1.3 67.8 + - + +
39C ALA* 3.4 5.3 + - - +
40C LEU* 3.0 25.5 + - - +
201C ASN* 5.6 2.4 + - - -
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Residues in contact with TYR 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LYS* 2.9 30.9 + - + +
34C LEU* 3.5 8.1 - - - +
36C GLU* 1.3 73.5 - - + +
38C ASP* 1.3 70.5 + - - +
40C LEU* 3.2 7.5 + - + +
41C LEU* 3.1 26.6 + - - +
112C ALA* 3.7 29.2 - - + -
115C VAL* 3.8 25.5 - - + +
116C GLN* 4.0 23.9 + - - -
119C HIS* 6.0 1.9 - - - +
197C LEU* 3.9 25.4 + - + +
198C THR* 5.5 1.6 - - - -
201C ASN* 3.0 42.9 + - - +
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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
----------------------------------------------------------
20C LEU* 3.7 17.6 - - + +
34C LEU* 2.9 22.1 + - - +
35C ILE* 3.7 4.9 - - - +
37C TYR* 1.3 76.8 - - - +
39C ALA* 1.3 65.5 + - - +
41C LEU* 3.2 3.3 + - - +
42C VAL* 3.0 31.1 + - + +
108C LEU 6.2 0.2 - - - -
109C ALA* 3.6 28.2 - - - +
112C ALA* 3.3 22.5 - - - +
893C LEU* 3.9 28.6 - - - +
897C TYR* 4.9 5.3 + - - +
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Residues in contact with ALA 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C SER* 4.5 0.2 - - - +
16C ILE* 4.0 5.8 - - - -
17C ASP* 3.8 37.2 - - + +
20C LEU* 4.3 1.7 - - + +
35C ILE 2.9 18.8 + - - +
36C GLU 3.7 4.0 - - - +
38C ASP* 1.3 75.5 - - - +
40C LEU* 1.3 57.7 + - - +
42C VAL* 3.3 7.5 - - - +
43C ASP* 2.8 45.7 + - - +
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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 17.9 + - - +
37C TYR* 3.7 3.6 - - + +
39C ALA* 1.3 77.8 - - - +
41C LEU* 1.3 61.5 + - - +
43C ASP* 3.8 4.6 - - - +
44C ARG* 3.1 71.0 + - + +
197C LEU* 3.9 26.7 - - + -
200C LEU* 4.3 12.8 - - + -
201C ASN* 6.1 0.2 - - - +
217C LEU* 3.9 20.2 - - + -
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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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37C TYR 3.1 21.5 + - - +
38C ASP* 3.8 2.9 - - - +
40C LEU* 1.3 78.4 - - - +
42C VAL* 1.3 59.2 + - + +
44C ARG* 4.1 0.6 - - - -
45C PHE* 3.0 24.9 + - - +
108C LEU* 3.8 30.4 - - + +
111C LEU* 5.4 0.7 - - + -
112C ALA* 3.8 17.5 - - + +
193C ILE* 3.6 31.0 - - + -
197C LEU* 3.7 32.8 - - + -
217C LEU* 3.9 12.6 - - + -
221C ILE* 3.7 29.7 - - + +
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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
----------------------------------------------------------
16C ILE* 3.0 35.2 - - + -
38C ASP* 3.0 21.3 + - + +
39C ALA 3.3 3.8 - - - +
41C LEU* 1.3 76.2 - - + +
43C ASP* 1.3 64.3 + - - +
45C PHE* 3.5 6.9 - - - +
46C LEU* 2.8 35.1 + - + +
105C MET* 4.1 38.4 - - + +
108C LEU* 4.6 8.5 - - + -
109C ALA* 5.3 2.5 - - + +
897C TYR* 4.0 16.4 - - + +
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Residues in contact with ASP 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C HIS 4.6 1.7 - - - +
15C SER* 2.6 31.7 + - - -
16C ILE* 3.2 28.5 + - - +
39C ALA* 2.8 31.3 + - - +
40C LEU* 3.8 5.4 - - - +
42C VAL* 1.3 79.3 - - - +
44C ARG* 1.3 66.8 + - - +
46C LEU* 3.4 8.6 + - - +
47C ASN* 3.1 34.7 + - - +
58C ARG* 4.5 3.4 + - - +
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Residues in contact with ARG 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* 3.1 56.2 + - + +
41C LEU 4.2 2.9 - - - +
43C ASP* 1.3 80.8 - - - +
45C PHE* 1.3 65.3 + - - +
47C ASN* 3.3 18.4 + - - +
48C ILE* 2.9 29.7 + - - +
214C ASP* 2.7 42.6 + - - +
217C LEU* 5.5 4.9 - - + -
218C GLN* 4.1 26.9 - - + +
221C ILE* 4.9 7.4 - - + -
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Residues in contact with PHE 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 LEU 3.0 19.7 + - - +
42C VAL* 3.2 6.0 + - - +
44C ARG* 1.3 76.2 - - - +
46C LEU* 1.3 61.9 + - + +
48C ILE* 3.1 9.1 + - + +
49C LEU* 2.8 40.2 + - + +
101C SER* 3.8 47.3 - - - -
104C HIS* 3.8 11.2 - - + -
105C MET* 3.6 22.9 - - + -
108C LEU* 3.8 16.6 - - + -
221C ILE* 3.7 26.4 - - + +
225C PHE* 3.6 35.2 - + + -
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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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16C ILE* 4.0 24.2 - - + -
42C VAL* 2.8 22.5 + - + +
43C ASP* 3.7 5.4 - - - +
45C PHE* 1.3 78.2 - - + +
47C ASN* 1.3 58.0 + - - +
49C LEU* 3.3 13.5 + - + +
50C GLN* 2.9 24.3 + - - +
58C ARG* 3.3 39.4 - - + +
61C VAL* 4.0 26.7 - - + -
62C GLN* 3.7 26.7 - - + +
105C MET* 4.2 16.8 - - - -
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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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14C HIS* 5.4 2.3 - - - -
43C ASP* 3.1 18.9 + - - +
44C ARG* 3.6 23.1 - - + +
45C PHE 3.2 0.2 - - - -
46C LEU* 1.3 73.9 - - - +
48C ILE* 1.3 60.6 + - + +
50C GLN* 3.5 4.3 + - - +
51C ASP* 2.9 29.3 + - - +
58C ARG* 3.1 26.4 + - - +
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Residues in contact with ILE 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 ARG 2.9 22.7 + - - +
45C PHE* 3.1 8.9 + - + +
47C ASN* 1.3 75.6 - - + +
49C LEU* 1.3 57.9 + - - +
51C ASP* 3.2 9.0 + - + +
52C LEU* 2.9 31.4 + - + +
218C GLN* 3.3 40.8 - - + +
221C ILE* 3.7 24.9 - - + -
222C GLN* 3.8 40.2 - - + +
225C PHE* 5.1 11.9 - - + -
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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
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45C PHE* 2.8 21.0 + - + +
46C LEU* 3.4 16.6 - - + +
47C ASN 3.2 0.2 - - - -
48C ILE* 1.3 77.6 - - - +
50C GLN* 1.3 57.1 + - - +
52C LEU* 3.2 3.3 + - - +
53C HIS* 2.9 35.8 + - + +
54C GLY 3.8 0.7 + - - +
57C LEU* 4.5 6.0 - - + +
58C ARG* 4.2 14.6 - - - +
61C VAL* 3.9 37.9 - - + -
97C LEU* 3.7 20.0 - - + -
101C SER* 3.6 23.8 - - - +
225C PHE* 3.8 18.4 - - + -
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Residues in contact with GLN 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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14C HIS* 5.4 1.4 + - - -
46C LEU 2.9 16.0 + - - +
47C ASN* 3.8 5.3 - - - +
48C ILE 3.4 0.2 - - - -
49C LEU* 1.3 75.4 - - - +
51C ASP* 1.3 61.7 + - - +
54C GLY* 2.9 32.6 + - - -
55C PRO* 3.8 38.0 - - + +
58C ARG* 2.8 37.4 + - + +
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Residues in contact with ASP 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ASN 2.9 18.7 + - - +
48C ILE* 3.5 10.0 - - - +
50C GLN* 1.3 76.4 - - - +
52C LEU* 1.3 59.5 + - - +
54C GLY 5.2 0.2 + - - -
222C GLN* 5.1 9.0 + - - +
427D GLY 5.5 2.6 - - - +
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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
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48C ILE* 2.9 19.7 + - + +
49C LEU* 4.0 0.7 - - - +
51C ASP* 1.3 80.2 - - - +
53C HIS* 1.3 78.2 + - + +
222C GLN* 5.1 7.0 - - - +
225C PHE* 3.8 25.1 - - + -
226C ARG* 3.2 58.8 - - + +
927C LYS* 5.1 5.9 - - - +
426D CYS 5.3 2.0 - - - +
427D GLY* 5.1 9.4 - - - +
428D ASP* 5.0 0.7 - - - +
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Residues in contact with HIS 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LEU* 2.9 19.2 + - + +
52C LEU* 1.3 114.5 + - + +
54C GLY* 1.3 61.4 + - - +
57C LEU* 3.7 18.7 - - + +
97C LEU* 3.4 34.6 - - + +
225C PHE* 3.9 9.8 - + - -
226C ARG* 4.6 6.6 + - - -
925C LEU 3.8 4.0 - - - +
926C SER* 3.0 30.6 + - - +
927C LYS* 3.2 27.3 + - - +
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Residues in contact with GLY 54 (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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49C LEU 4.4 0.3 - - - +
50C GLN* 2.9 25.2 + - - -
52C LEU 3.8 0.6 - - - -
53C HIS* 1.3 80.8 - - - +
55C PRO* 1.3 75.1 - - - +
56C SER 3.4 3.1 + - - -
57C LEU* 3.5 2.6 + - - +
58C ARG 3.3 15.9 + - - -
925C LEU 5.4 0.9 - - - -
927C LYS* 5.9 1.8 - - - -
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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