Contacts of the helix formed by residues 36 - 59 (chain C) in PDB entry 4RVE
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 ASP 36 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C GLY* 3.4 4.0 - - - +
35C SER* 1.3 75.2 + - - +
37C THR* 1.3 60.0 + - - +
38C LYS* 2.8 66.3 + - - +
39C VAL* 3.2 18.0 + - + +
40C LEU* 2.9 22.7 + - - +
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Residues in contact with THR 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C SER 2.8 11.6 + - - +
36C ASP* 1.3 68.3 + - - +
38C LYS* 1.3 64.3 + - - +
39C VAL 3.0 2.9 - - - -
40C LEU* 3.4 9.0 - - - -
41C SER* 2.5 36.2 + - - -
93C THR* 5.2 1.6 - - - +
95C TYR* 5.1 0.2 - - + -
138C TYR* 3.5 23.3 - - - +
140C ARG* 4.7 5.8 - - - +
6F A 5.5 2.5 + - - +
7F T 3.5 30.2 + - - -
8F C 3.4 35.9 - - - +
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Residues in contact with LYS 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ASP* 2.8 34.2 + - - +
37C THR* 1.3 81.3 + - - +
39C VAL* 1.3 60.8 + - + +
41C SER* 5.0 2.1 + - - -
42C THR* 4.3 11.4 + - - -
6F A 4.0 38.9 + - + +
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Residues in contact with VAL 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ILE* 5.1 4.0 - - + -
33C LEU* 4.1 26.7 - - + -
36C ASP* 3.2 23.0 + - + +
38C LYS* 1.3 76.0 - - + +
40C LEU* 1.3 71.9 + - + +
41C SER 3.2 1.8 - - - -
42C THR* 2.8 22.3 + - + -
43C ILE* 3.0 23.9 + - + +
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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
----------------------------------------------------------
33C LEU* 4.6 3.8 - - + -
34C GLY 3.8 16.8 - - - +
35C SER* 4.0 18.2 - - - +
36C ASP 2.9 17.1 + - - +
37C THR* 3.1 9.4 + - - -
39C VAL* 1.3 83.0 - - + +
41C SER* 1.3 64.3 + - - +
43C ILE* 3.2 32.6 + - + +
44C PHE* 3.6 14.7 + - + -
93C THR* 5.6 0.4 - - - +
138C TYR* 3.9 32.3 - - + +
162C PRO* 4.4 7.4 - - + +
163C TYR* 3.8 37.5 - - + -
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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
----------------------------------------------------------
37C THR* 2.5 22.1 + - - +
38C LYS* 5.0 2.3 + - - -
40C LEU* 1.3 73.0 - - - +
42C THR* 1.3 62.4 + - - +
44C PHE* 3.3 12.6 + - - +
45C GLU* 3.5 10.8 + - - +
91C ILE* 5.1 2.3 - - - +
93C THR* 4.0 15.9 + - - +
6F A 3.1 29.0 + - - -
7F T 3.1 26.6 + - - -
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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
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38C LYS 4.3 9.1 + - - -
39C VAL* 2.8 20.5 + - + +
41C SER* 1.3 74.0 + - - +
43C ILE* 1.3 64.9 + - + +
44C PHE 3.0 0.2 - - - -
45C GLU* 2.8 35.8 + - - +
46C LEU* 3.0 28.6 + - + +
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Residues in contact with ILE 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C VAL* 4.1 21.8 - - + -
23C ILE* 5.6 1.6 - - + -
33C LEU* 3.2 35.7 - - + -
39C VAL* 3.0 24.2 + - + +
40C LEU* 3.2 17.9 + - + +
42C THR* 1.3 84.0 - - + +
44C PHE* 1.3 58.9 + - + +
45C GLU 3.5 0.2 - - - -
46C LEU* 3.8 9.0 - - + +
47C PHE* 3.5 28.1 + - + -
163C TYR* 3.9 25.8 - - + +
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Residues in contact with PHE 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C TYR* 4.8 1.1 - + + -
40C LEU* 3.6 18.3 + - + -
41C SER 3.3 7.5 + - - +
42C THR 2.8 2.0 + - - -
43C ILE* 1.3 74.2 - - + +
45C GLU* 1.3 56.2 + - - +
46C LEU 3.2 1.3 - - - -
47C PHE* 3.4 31.7 - + - +
48C SER* 2.6 31.9 + - - -
91C ILE* 4.3 3.4 - - + -
93C THR* 3.6 23.8 - - + -
136C TYR* 3.8 32.0 + + + -
138C TYR* 3.6 35.7 - + - -
163C TYR* 4.5 18.6 - + - -
166C VAL* 3.8 37.7 - - + -
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Residues in contact with GLU 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 3.5 7.2 + - - +
42C THR* 2.8 19.9 + - - +
44C PHE* 1.3 75.4 - - - +
46C LEU* 1.4 71.4 + - + +
47C PHE 3.0 5.4 + - - -
48C SER* 3.3 1.2 + - - -
49C ARG* 3.3 26.6 + - - +
65C GLU* 4.1 10.2 - - - +
74C ASP* 3.9 39.6 - - - +
75C PHE* 3.8 16.2 - - + -
91C ILE* 3.7 20.9 - - + -
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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
----------------------------------------------------------
42C THR* 3.0 32.0 + - + +
43C ILE* 3.8 10.5 - - + +
45C GLU* 1.4 87.5 - - + +
47C PHE* 1.3 63.0 + - + +
49C ARG* 3.5 30.9 - - - +
50C PRO* 3.7 12.8 - - - +
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Residues in contact with PHE 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C TYR* 3.2 55.6 - + + -
19C ASP 3.6 17.0 - - - -
20C VAL* 3.3 37.9 - - + -
43C ILE* 3.5 14.8 - - + -
44C PHE* 3.4 27.5 + + - +
46C LEU* 1.3 83.1 - - + +
48C SER* 1.3 60.4 + - - +
49C ARG 3.2 2.0 - - - -
50C PRO* 2.8 24.8 - - - +
51C ILE* 3.9 9.7 - - - +
136C TYR* 4.8 0.2 - - - -
163C TYR* 4.0 8.7 - - - -
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Residues in contact with SER 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 5.4 1.8 - - - -
44C PHE 2.6 13.9 + - - -
45C GLU 3.3 1.0 + - - -
47C PHE* 1.3 76.5 - - - +
49C ARG* 1.3 54.7 + - - +
50C PRO 3.2 0.3 - - - -
51C ILE* 3.3 10.1 + - - +
52C ILE* 2.7 48.8 + - - +
91C ILE* 3.2 27.5 - - - +
134C ILE* 5.1 6.1 - - - -
136C TYR* 2.6 26.9 + - - -
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Residues in contact with ARG 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 GLU* 3.3 15.8 + - - +
46C LEU* 3.5 36.1 - - - +
48C SER* 1.3 75.8 - - - +
50C PRO* 1.3 70.8 - - + +
52C ILE* 4.6 0.4 - - - +
53C ASN* 2.8 46.9 + - - +
65C GLU* 2.3 51.4 + - - +
75C PHE* 3.9 14.3 - - + -
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Residues in contact with PRO 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 3.7 6.5 - - - +
47C PHE* 2.8 25.1 - - - +
49C ARG* 1.3 100.6 - - + +
51C ILE* 1.3 58.0 + - + +
53C ASN* 3.7 3.2 - - + +
54C LYS* 3.0 32.4 + - - +
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Residues in contact with ILE 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LEU* 4.1 4.9 - - + +
10C ALA* 3.6 37.0 - - + +
11C LEU* 4.0 22.2 - - + -
16C GLN* 5.4 9.2 - - + -
18C TYR* 4.1 23.6 - - + +
47C PHE 3.9 15.9 - - - +
48C SER* 3.5 7.9 - - - +
50C PRO* 1.3 80.6 - - + +
52C ILE* 1.3 68.0 + - + +
53C ASN 3.1 1.1 - - - -
54C LYS* 4.4 12.1 - - - +
55C ILE* 3.2 24.1 + - + +
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Residues in contact with ILE 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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3C LEU* 5.9 0.3 - - - +
7C LEU* 4.7 14.7 - - + +
11C LEU* 5.9 0.2 - - + -
48C SER* 2.7 36.7 + - - +
49C ARG* 4.2 3.1 - - - +
51C ILE* 1.3 74.3 - - + +
53C ASN* 1.3 61.7 + - - +
55C ILE* 4.3 1.2 - - - +
56C ALA* 2.9 29.2 + - + +
63C VAL* 5.0 3.6 - - + -
75C PHE* 3.5 44.6 - - + -
77C LEU* 4.0 30.1 - - + +
89C ILE* 4.0 22.7 - - + -
91C ILE* 4.1 3.6 - - + -
134C ILE* 4.6 9.9 - - + -
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Residues in contact with ASN 53 (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 ARG* 2.8 47.4 + - - +
50C PRO* 3.7 3.6 - - + +
52C ILE* 1.3 79.9 - - - +
54C LYS* 1.3 58.5 + - - +
56C ALA* 3.3 5.8 + - - +
57C GLU* 2.8 33.6 + - - +
63C VAL* 3.8 32.2 - - - +
65C GLU* 5.0 1.2 + - - -
75C PHE* 4.7 2.8 - - - -
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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
----------------------------------------------------------
10C ALA* 4.7 9.5 - - - +
50C PRO 3.0 17.8 + - - +
51C ILE* 3.3 11.7 + - - +
53C ASN* 1.3 75.0 - - - +
55C ILE* 1.3 83.7 + - + +
57C GLU* 3.1 22.7 + - + +
58C LYS* 3.4 13.6 + - - +
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Residues in contact with ILE 55 (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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3C LEU* 4.0 15.5 - - + +
6C ASP* 3.3 33.0 - - + +
7C LEU* 4.1 11.7 - - + +
10C ALA* 3.8 30.1 - - + -
51C ILE 3.2 15.7 + - - +
52C ILE 4.4 1.3 - - - +
54C LYS* 1.3 87.7 - - + +
56C ALA* 1.3 61.6 + - - +
58C LYS* 3.3 30.3 + - - +
59C HIS* 3.0 28.5 + - + +
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Residues in contact with ALA 56 (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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3C LEU* 4.5 7.1 - - - +
52C ILE 2.9 22.2 + - - +
53C ASN 3.4 4.7 - - - +
54C LYS 3.1 0.2 - - - -
55C ILE* 1.3 77.9 - - - +
57C GLU* 1.3 61.3 + - - +
59C HIS 3.5 1.4 + - - -
60C GLY 3.5 3.6 + - - -
61C TYR* 3.2 32.0 + - + +
63C VAL* 3.8 17.7 - - + -
77C LEU* 3.3 28.5 - - + -
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Residues in contact with GLU 57 (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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57B GLU 5.7 0.5 - - - +
58B LYS 5.1 7.4 - - - +
53C ASN* 2.8 13.6 + - - +
54C LYS* 3.3 14.4 - - + +
56C ALA* 1.3 78.4 - - - +
58C LYS* 1.3 57.5 + - - +
60C GLY* 3.0 21.8 + - - -
61C TYR 4.8 4.5 - - - +
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Residues in contact with LYS 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLU* 4.9 24.1 - - + +
58B LYS* 6.4 3.1 - - + +
6C ASP* 4.4 12.7 + - - +
54C LYS* 3.4 10.4 + - - +
55C ILE* 3.3 43.1 + - - +
57C GLU* 1.3 78.6 - - - +
59C HIS* 1.3 70.1 + - + +
60C GLY 3.3 0.9 - - - -
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Residues in contact with HIS 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C SER* 4.0 9.8 + - - -
3C LEU* 3.9 22.2 - - + +
6C ASP* 2.9 29.0 + - - -
55C ILE* 3.0 34.5 + - + +
56C ALA 3.5 1.8 + - - -
57C GLU 3.2 0.8 - - - -
58C LYS* 1.3 90.7 - - + +
60C GLY* 1.3 63.3 + - - +
61C TYR* 3.6 24.5 - - + -
79C LYS* 3.2 21.2 + - - -
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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