Contacts of the helix formed by residues 36 - 49 (chain B) in PDB entry 1XHU
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 PRO 36 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A LYS* 6.1 4.3 - - + -
26A GLY* 6.3 2.7 - - - -
20B VAL* 5.0 19.7 - - + +
21B LYS 6.2 0.4 - - - +
23B PRO* 5.1 15.7 - - + -
32B ALA* 5.4 3.6 - - + -
33B ALA 4.9 1.6 - - - +
34B GLY* 3.0 12.1 - - - +
35B GLU* 1.3 108.6 - - + +
37B PHE* 1.3 60.1 + - - +
38B GLU 3.2 0.4 - - - -
39B LYS* 3.4 34.8 + - + +
40B LEU* 3.9 9.0 + - - +
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Residues in contact with PHE 37 (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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15B LEU* 5.0 5.1 - - + +
18B GLN* 4.2 7.6 - - + -
20B VAL* 3.6 36.1 - - + -
34B GLY 2.9 24.8 + - - +
35B GLU 2.6 5.3 + - - -
36B PRO* 1.3 72.1 - - - +
38B GLU* 1.3 62.9 + - - +
39B LYS 3.0 2.5 - - - -
40B LEU* 2.8 37.1 + - + +
41B VAL* 3.2 13.0 + - + +
128B VAL* 4.9 0.7 - - - -
130B THR* 4.4 5.4 - - + -
171B VAL* 3.9 28.3 - - + -
173B TRP* 3.9 28.9 - + + -
180B LEU* 3.9 13.5 - - + -
182B CYS* 3.8 37.5 - - + -
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Residues in contact with GLU 38 (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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27A THR* 5.9 0.7 - - - -
35B GLU* 2.6 41.2 + - + +
37B PHE* 1.3 73.4 - - - +
39B LYS* 1.3 87.9 + - + +
41B VAL* 3.1 5.9 + - - +
42B TYR* 3.1 20.3 + - - +
55B LYS* 3.5 30.4 + - - -
107B GLU* 5.1 6.7 - - - +
114B ASP* 3.7 27.9 - - + +
115B ILE* 4.6 3.9 - - + +
128B VAL* 3.8 34.9 - - + +
8F G 4.3 10.9 + - - +
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Residues in contact with LYS 39 (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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24A LYS 6.1 0.2 - - - -
25A SER 5.0 4.5 - - - -
26A GLY* 4.7 19.2 - - - -
27A THR* 4.5 9.9 + - - +
35B GLU* 3.8 13.7 + - - -
36B PRO* 3.5 27.4 - - + +
38B GLU* 1.3 94.1 + - + +
40B LEU* 1.3 63.6 + - + +
42B TYR* 2.9 9.5 + - - +
43B LYS* 2.7 35.8 + - - +
55B LYS* 5.3 0.9 - - - +
107B GLU* 5.5 3.4 + - - -
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Residues in contact with LEU 40 (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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14B ILE* 5.9 0.2 - - - +
15B LEU* 3.9 16.1 - - + +
18B GLN* 3.8 41.7 + - + +
19B LYS 5.0 1.6 - - - +
20B VAL* 4.0 24.9 - - + -
36B PRO 4.0 11.2 - - - +
37B PHE* 2.8 20.0 + - + +
39B LYS* 1.3 79.0 - - + +
41B VAL* 1.3 58.6 + - - +
43B LYS* 3.7 17.1 - - + +
44B PHE* 2.9 29.6 + - - +
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Residues in contact with VAL 41 (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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4B ILE* 5.7 0.2 - - + -
11B ILE* 5.6 2.7 - - + -
15B LEU* 3.6 23.3 - - + -
37B PHE 3.2 10.2 + - - +
38B GLU 3.1 8.4 + - - +
39B LYS 3.0 0.8 - - - -
40B LEU* 1.3 73.6 - - - +
42B TYR* 1.3 56.8 - - - +
44B PHE* 3.1 5.6 + - - +
45B LEU* 2.6 61.7 + - + +
115B ILE* 3.7 8.5 - - + -
126B LEU* 4.2 2.0 - - + -
128B VAL* 4.0 15.0 - - + -
169B LEU* 3.5 35.4 - - + -
171B VAL* 5.4 2.7 - - + -
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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
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38B GLU 3.1 7.5 + - - +
39B LYS* 2.9 9.5 + - - +
41B VAL* 1.3 77.0 - - - +
43B LYS* 1.3 57.7 + - + +
45B LEU* 3.6 1.1 - - - +
46B LYS* 2.6 65.1 + - + +
53B THR* 3.3 26.2 - - + -
54B PHE 3.7 23.8 - - - -
55B LYS* 3.7 32.1 - - + +
58B GLU* 2.3 33.8 + - - -
115B ILE* 3.4 19.7 - - + +
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Residues in contact with LYS 43 (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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18B GLN* 6.3 0.9 - - - +
39B LYS* 2.7 20.1 + - + +
40B LEU* 3.7 17.7 - - + +
42B TYR* 1.3 77.4 - - - +
44B PHE* 1.3 65.9 + - - +
46B LYS* 3.2 6.5 + - - +
47B GLU* 2.6 61.2 + - + +
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Residues in contact with PHE 44 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B ILE* 4.8 4.9 - - + -
10B ASP* 4.1 12.8 - - + -
11B ILE* 2.9 49.4 - - + -
14B ILE* 3.6 46.7 - - + -
15B LEU* 5.6 3.4 - - + -
40B LEU 2.9 19.3 + - - +
41B VAL* 3.6 3.6 - - - +
43B LYS* 1.3 77.9 - - - +
45B LEU* 1.3 74.1 + - + +
47B GLU* 3.0 19.6 + - - -
48B ASN* 3.0 56.9 + - + +
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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
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4B ILE* 3.8 16.2 - - + -
7B ILE* 5.1 0.9 - - + -
11B ILE* 3.4 33.7 - - + -
41B VAL* 2.6 30.4 + - + +
42B TYR 3.6 3.4 - - - +
44B PHE* 1.3 80.2 - - + +
46B LYS* 1.3 53.3 + - - +
48B ASN* 4.7 1.3 - - - +
49B LEU* 2.6 42.0 + - + +
53B THR* 3.0 21.2 + - + +
115B ILE* 3.6 28.5 - - + -
117B LEU* 4.0 16.2 - - + -
126B LEU* 3.7 14.1 - - + -
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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
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42B TYR* 2.6 48.0 + - + +
43B LYS* 3.4 7.4 - - - +
45B LEU* 1.3 71.3 - - - +
47B GLU* 1.3 58.9 + - + +
50B SER* 2.9 53.1 + - - +
53B THR* 2.7 39.1 + - + -
54B PHE* 4.5 3.4 - - - -
58B GLU* 2.9 23.3 + - - -
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Residues in contact with GLU 47 (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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43B LYS* 2.6 50.1 + - + +
44B PHE* 3.0 10.7 + - - +
46B LYS* 1.3 79.6 - - + +
48B ASN* 1.3 67.0 + - - +
49B LEU 3.5 0.2 + - - -
50B SER* 4.1 5.8 + - - -
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Residues in contact with ASN 48 (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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7B ILE* 4.4 13.8 - - + +
10B ASP* 5.1 7.7 + - - +
44B PHE* 3.0 53.8 + - + +
45B LEU* 4.3 1.3 - - - +
47B GLU* 1.3 84.1 - - - +
49B LEU* 1.3 75.4 + - + +
50B SER 3.8 1.1 - - - -
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Residues in contact with LEU 49 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B PHE* 3.5 30.7 - - + +
4B ILE* 4.8 0.9 - - - +
7B ILE* 3.7 23.8 - - + -
45B LEU* 2.6 26.9 + - + +
48B ASN* 1.3 86.0 - - + +
50B SER* 1.3 57.0 - - - +
51B ASP 3.3 3.1 - - - -
52B LEU* 3.1 23.7 + - + -
53B THR* 2.9 31.2 + - - +
117B LEU* 3.6 22.0 - - + -
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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