Contacts of the helix formed by residues 37 - 51 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B THR* 5.3 1.3 - - - -
27B LYS* 6.6 0.2 - - - -
36B ALA* 1.3 77.0 - - - +
38B HIS* 1.3 59.4 + - - +
39B SER* 4.0 7.0 - - - +
40B GLN* 2.8 27.4 + - - +
41B ILE* 3.2 11.2 + - - +
17I T 4.0 38.7 + - + +
18I T 3.7 49.3 + - + -
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Residues in contact with HIS 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR* 6.5 0.4 - - + -
23B THR* 3.7 32.1 - - + +
36B ALA 3.9 1.4 + - - -
37B LYS* 1.3 74.1 - - + +
39B SER* 1.3 61.9 + - - +
41B ILE* 4.0 5.7 - - - +
42B TYR* 3.1 53.0 + + + -
18I T 6.0 2.2 - - + -
19I A 4.4 9.0 + - - -
20I C 4.8 3.1 - - - -
21I A 5.2 0.9 - - - -
8J T 3.6 21.4 + - + +
9J G 2.8 47.8 + - - -
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Residues in contact with SER 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LYS* 3.0 2.5 + - - +
38B HIS* 1.3 86.5 + - - +
40B GLN* 1.3 60.0 + - - +
43B PRO* 3.1 22.6 - - - +
17I T 3.6 9.7 - - - +
18I T 2.5 40.1 + - - +
19I A 3.8 7.2 - - - -
10J T 3.0 32.3 - - - +
11J A 4.1 5.0 + - - -
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Residues in contact with GLN 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LYS* 5.6 0.3 + - - -
4B LEU* 3.6 24.6 - - + +
36B ALA* 4.0 14.1 - - + +
37B LYS 2.8 10.8 + - - +
39B SER* 1.3 82.6 + - - +
41B ILE* 1.3 62.3 + - - +
42B TYR 3.4 0.4 - - - -
43B PRO* 3.4 9.7 - - - +
44B GLU* 3.4 17.3 + - - +
15I A 3.8 14.3 - - - +
16I G 3.0 60.6 + - + +
17I T 3.8 16.3 + - + +
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Residues in contact with ILE 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 4.5 7.2 - - + -
8B ILE* 4.1 9.0 - - + -
19B GLY* 4.5 6.1 - - - +
22B ILE* 4.0 19.3 - - + -
23B THR* 3.5 24.2 - - - +
26B PHE* 3.8 23.1 - - + -
36B ALA* 3.5 35.9 - - + +
37B LYS 3.2 10.0 + - - +
38B HIS* 3.2 6.5 + - - +
40B GLN* 1.3 76.9 - - - +
42B TYR* 1.3 61.3 + - + +
44B GLU* 3.3 5.5 + - - +
45B LEU* 2.8 46.4 + - + +
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Residues in contact with TYR 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLY* 3.9 19.0 - - - -
20B TYR* 3.6 8.5 + - - -
23B THR* 5.2 0.6 + - - -
38B HIS* 3.1 41.8 + - + +
41B ILE* 1.3 78.4 - - + +
43B PRO* 1.3 68.6 - - + +
45B LEU* 3.3 16.3 + - + +
46B LYS* 3.2 20.3 + - - +
70B TYR* 5.8 1.1 - + - -
7J A 4.1 0.9 - - - +
8J T 2.5 79.8 + + + +
9J G 3.7 43.8 + + + +
10J T 4.7 7.4 - - + +
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Residues in contact with PRO 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B SER 3.1 27.1 - - - +
40B GLN* 3.4 8.1 - - - +
42B TYR* 1.3 94.4 - - + +
44B GLU* 1.3 55.4 + - - +
46B LYS* 3.3 11.2 + - + +
47B LYS* 3.0 24.9 + - - +
10J T 4.4 21.1 - - + +
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Residues in contact with GLU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ARG* 3.0 29.8 + - - +
4B LEU* 4.0 20.1 - - + +
5B LYS* 3.4 19.7 + - - +
8B ILE* 3.8 18.6 - - + -
40B GLN 3.4 17.7 + - - +
41B ILE 3.3 4.9 + - - +
42B TYR 3.2 0.2 - - - -
43B PRO* 1.3 77.7 - - - +
45B LEU* 1.3 54.5 + - - +
47B LYS* 3.0 17.5 + - - +
48B LEU* 2.8 39.6 + - + +
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Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 3.9 22.7 - - + -
19B GLY* 3.7 30.3 - - - -
22B ILE* 4.0 7.0 - - + -
41B ILE* 2.8 31.4 + - + +
42B TYR* 3.3 17.5 + - + +
44B GLU* 1.3 74.4 - - - +
46B LYS* 1.3 60.9 + - - +
48B LEU* 3.4 0.8 + - - -
49B THR* 2.9 29.3 + - - -
54B ILE* 3.7 25.9 - - + +
70B TYR* 3.7 37.9 - - + +
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Residues in contact with LYS 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B TYR 3.2 9.2 + - - +
43B PRO* 3.4 13.2 - - + +
44B GLU 3.2 0.2 - - - -
45B LEU* 1.3 75.7 - - - +
47B LYS* 1.3 66.5 + - - +
49B THR* 3.5 6.4 + - - -
50B ASP* 3.1 39.8 + - - +
70B TYR* 4.9 2.0 + - - -
10J T 5.4 7.2 + - - +
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Residues in contact with LYS 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ARG* 3.5 38.7 - - - +
43B PRO 3.0 13.8 + - - +
44B GLU* 3.0 21.2 + - - +
46B LYS* 1.3 77.7 - - - +
48B LEU* 1.3 58.7 + - - +
50B ASP* 3.0 8.8 + - + +
51B GLU* 2.8 50.6 + - + +
14I T 5.9 1.4 + - - -
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Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ARG* 4.2 6.5 - - - +
5B LYS* 3.7 43.1 - - + +
8B ILE* 3.6 43.5 - - + -
9B LEU* 4.3 10.8 - - + -
44B GLU* 2.8 27.4 + - + +
47B LYS* 1.3 72.4 - - - +
49B THR* 1.3 59.0 - - - +
51B GLU* 3.6 4.3 + - - +
52B GLY 3.2 2.9 + - - -
53B PHE* 2.9 42.6 + - + +
54B ILE* 3.4 23.2 + - + -
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Residues in contact with THR 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LEU 2.9 18.5 + - - -
46B LYS* 3.7 7.7 - - - -
48B LEU* 1.3 74.5 - - - +
50B ASP* 1.3 63.2 + - - +
52B GLY* 2.8 21.3 + - - -
54B ILE* 3.6 23.2 + - - +
55B THR* 5.0 2.7 - - - -
56B PHE* 4.2 23.9 - - + +
70B TYR* 3.6 18.7 + - - -
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Residues in contact with ASP 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LYS* 3.1 38.1 + - - +
47B LYS* 3.0 11.7 + - + +
49B THR* 1.3 80.1 - - - +
51B GLU* 1.3 60.3 + - + +
52B GLY* 3.5 0.7 + - - -
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Residues in contact with GLU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ARG* 2.9 34.2 + - - -
5B LYS* 4.5 0.9 + - - -
47B LYS* 2.8 49.4 + - + +
48B LEU* 3.7 2.7 + - - +
49B THR 3.1 0.2 - - - -
50B ASP* 1.3 76.5 - - + +
52B GLY* 1.3 60.5 + - - +
53B PHE* 3.5 37.4 - - + -
75B SER* 5.7 0.5 - - - -
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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