Contacts of the helix formed by residues 37 - 51 (chain C) in PDB entry 5X11
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 37 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C THR* 4.9 2.9 - - - -
27C LYS* 5.0 17.2 - - - +
35C SER* 6.3 2.5 - - - -
36C ALA* 1.3 78.8 - - - +
38C HIS* 1.3 66.9 + - - +
39C SER* 3.1 15.3 - - - +
40C GLN* 3.1 10.3 + - + +
41C ILE* 3.1 26.6 + - - +
3N A 4.1 37.4 + - + +
4N A 3.8 24.2 + - - +
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Residues in contact with HIS 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C THR* 3.6 33.1 - - + +
27C LYS* 5.5 4.6 + - - +
37C LYS* 1.3 78.2 - - + +
39C SER* 1.3 62.0 + - - +
41C ILE* 4.3 3.1 - - - -
42C TYR* 3.1 53.1 + + + +
22M T 3.6 20.7 + - + +
23M G 2.7 47.7 + + - -
24M A 4.2 1.6 + - - -
5N T 4.5 17.5 - - + -
6N C 4.6 4.0 - - - -
7N A 5.2 0.7 - - - -
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Residues in contact with SER 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LYS* 4.2 11.3 - - - +
38C HIS* 1.3 83.2 + - - +
40C GLN* 1.3 60.8 + - - +
42C TYR* 5.4 0.4 - - - -
43C PRO* 3.3 22.2 - - - +
24M A 3.0 35.0 + - - +
25M T 4.6 5.4 - - - +
3N A 4.0 12.5 + - - -
4N A 3.4 26.0 + - - -
5N T 3.9 5.2 - - - -
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Residues in contact with GLN 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LEU* 3.8 24.8 - - + +
35C SER 5.1 1.2 - - - +
36C ALA* 4.4 12.3 - - + +
37C LYS* 3.1 12.9 + - + +
39C SER* 1.3 83.4 + - - +
41C ILE* 1.3 64.0 + - - +
42C TYR 3.5 0.2 - - - -
43C PRO* 3.3 10.8 - - - +
44C GLU* 3.3 16.5 + - - +
1N G 3.0 35.2 + - - -
2N T 3.4 43.4 + - + +
3N A 4.5 4.5 + - - +
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Residues in contact with ILE 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LEU* 4.2 11.2 - - + -
8C ILE* 4.5 5.2 - - + -
19C GLY* 4.3 9.2 - - - +
22C ILE* 3.8 18.2 - - + -
23C THR* 3.5 36.1 - - - +
26C PHE* 3.8 19.7 - - + -
36C ALA* 4.1 13.0 - - + +
37C LYS 3.1 19.4 + - - +
38C HIS* 4.0 4.9 - - - +
40C GLN* 1.3 76.8 - - - +
42C TYR* 1.3 58.8 + - + +
44C GLU* 3.1 7.9 + - - +
45C LEU* 2.8 48.3 + - + +
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Residues in contact with TYR 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C GLY* 3.7 18.6 - - - -
20C TYR* 3.5 9.7 + - - +
23C THR* 5.1 0.7 - - - -
38C HIS* 3.1 34.5 + + + +
39C SER* 5.7 0.2 - - - -
41C ILE* 1.3 75.7 - - + +
43C PRO* 1.4 68.6 - - + +
45C LEU* 3.4 16.5 + - + +
46C LYS* 3.4 19.2 + - - +
70C TYR* 6.3 0.7 - + - -
21M A 4.0 0.3 - - - +
22M T 2.6 88.0 + + + +
23M G 3.4 53.4 + + + +
24M A 5.6 1.1 - - - +
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Residues in contact with PRO 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C SER* 3.3 26.7 - - - +
40C GLN* 3.3 9.4 - - - +
42C TYR* 1.4 94.3 - - + +
44C GLU* 1.3 60.5 + - - +
46C LYS* 3.2 8.8 + - + +
47C LYS* 3.1 22.1 + - - +
23M G 5.5 0.9 - - + -
24M A 4.4 23.1 - - + +
25M T 5.7 6.5 - - + -
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Residues in contact with GLU 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ARG* 2.7 36.3 + - - -
4C LEU* 3.9 17.5 - - + +
5C LYS* 3.2 21.7 - - - +
8C ILE* 3.5 22.7 - - + -
40C GLN 3.3 16.8 + - - +
41C ILE 3.1 5.0 + - - +
43C PRO* 1.3 80.8 - - - +
45C LEU* 1.3 57.1 + - - +
47C LYS* 3.2 11.4 + - - +
48C LEU* 2.9 35.4 + - + +
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Residues in contact with LEU 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 3.8 28.5 - - + -
12C LEU* 5.4 0.2 - - + -
19C GLY* 3.7 29.4 - - - -
22C ILE* 3.8 13.7 - - + -
41C ILE* 2.8 30.1 + - + +
42C TYR* 3.7 17.5 - - + +
43C PRO 3.3 0.2 - - - -
44C GLU* 1.3 76.1 - - - +
46C LYS* 1.3 53.2 + - - +
48C LEU* 4.6 1.3 - - - -
49C THR* 2.5 33.4 + - - -
54C ILE* 3.5 10.7 - - + +
70C TYR* 3.9 41.8 - - + +
23M G 5.9 0.4 - - - +
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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 TYR 3.4 8.5 + - - +
43C PRO* 3.2 11.0 + - + +
44C GLU 3.2 0.6 - - - -
45C LEU* 1.3 77.3 - - - +
47C LYS* 1.3 58.9 + - - +
49C THR* 3.2 8.2 + - - -
50C ASP* 3.0 67.2 + - - +
56C PHE* 6.6 0.2 - - + -
68C LYS* 5.8 5.6 - - - +
70C TYR* 5.0 2.2 + - - +
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Residues in contact with LYS 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ARG* 3.5 40.7 - - - +
43C PRO 3.1 15.5 + - - +
44C GLU* 3.2 16.3 + - - +
46C LYS* 1.3 75.5 - - - +
48C LEU* 1.3 58.8 + - - +
50C ASP* 3.5 9.8 + - + +
51C GLU* 3.1 50.0 + - + +
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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
----------------------------------------------------------
5C LYS* 3.4 34.3 - - + +
8C ILE* 3.7 37.0 - - + -
9C LEU* 4.2 12.8 - - + -
44C GLU* 2.9 35.6 + - + +
45C LEU* 4.6 1.6 - - - -
47C LYS* 1.3 74.7 - - - +
49C THR* 1.3 58.6 + - - +
51C GLU* 3.5 9.2 + - - +
52C GLY 3.2 4.3 + - - -
53C PHE* 3.0 46.9 + - + +
54C ILE* 3.5 21.7 + - + -
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Residues in contact with THR 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 LEU 2.5 22.8 + - - -
46C LYS* 3.2 12.1 + - - -
48C LEU* 1.3 74.7 - - - +
50C ASP* 1.3 59.3 + - - +
51C GLU 3.0 4.0 - - - -
52C GLY* 3.1 18.0 + - - -
54C ILE* 3.3 27.8 - - - +
55C THR* 4.9 2.5 - - - -
56C PHE* 4.1 26.9 - - + -
70C TYR* 3.8 8.0 + - - -
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Residues in contact with ASP 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 LYS* 3.0 51.7 + - - +
47C LYS* 3.9 9.8 - - + +
49C THR* 1.3 76.3 - - - +
51C GLU* 1.3 59.2 + - + +
52C GLY 3.4 0.2 - - - -
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Residues in contact with GLU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ARG* 2.9 41.3 + - - -
47C LYS* 3.1 35.1 + - + +
48C LEU* 3.8 5.5 - - - +
49C THR 3.0 1.0 - - - -
50C ASP* 1.3 78.7 - - + +
52C GLY* 1.3 61.2 + - - +
53C PHE* 3.3 38.0 + - + -
75C SER* 4.9 1.7 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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