Contacts of the helix formed by residues 22 - 36 (chain B) in PDB entry 2XWU
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 THR 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B ASP* 3.3 17.5 + - + +
21B PHE* 1.3 78.4 - - - +
23B VAL* 1.3 56.8 + - - +
24B GLU* 3.4 18.2 + - - +
25B ASN* 3.1 25.3 + - - +
26B VAL* 2.7 35.3 + - - +
60B HIS* 6.5 0.7 - - - -
61B PHE* 4.4 3.6 - - - -
64B GLN* 5.7 0.2 - - - -
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Residues in contact with VAL 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B THR* 1.3 72.4 - - - +
24B GLU* 1.3 70.7 + - - +
26B VAL* 4.2 3.3 - - - +
27B GLU* 2.8 38.9 + - - +
61B PHE* 3.7 17.4 - - + +
64B GLN* 2.8 58.9 + - + +
65B LEU* 4.6 10.2 - - + +
67B GLN* 6.2 0.7 - - - +
70B LYS* 3.7 31.4 - - - +
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Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B THR* 3.4 19.1 - - - +
23B VAL* 1.3 90.2 + - + +
25B ASN* 1.3 61.5 + - - +
27B GLU* 3.8 7.3 - - - +
28B LYS* 3.1 25.8 + - - +
64B GLN* 5.8 1.2 + - - -
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Residues in contact with ASN 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 4.6 7.4 - - - +
20B ASP* 3.2 30.4 + - - +
22B THR* 3.1 18.7 + - - +
24B GLU* 1.3 77.4 - - - +
26B VAL* 1.3 66.0 + - - +
27B GLU 3.1 1.3 - - - -
28B LYS* 3.1 9.3 + - - +
29B ALA* 3.1 22.7 + - - +
48B TRP* 3.7 12.9 - - + -
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Residues in contact with VAL 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B PHE* 4.3 1.3 - - + -
22B THR 2.7 28.9 + - - +
23B VAL* 4.2 2.5 - - - +
25B ASN* 1.3 73.1 - - - +
27B GLU* 1.3 58.0 + - - +
29B ALA* 3.4 3.5 + - - +
30B LEU* 3.1 26.3 + - + +
48B TRP* 3.5 23.6 - - + -
49B LEU* 3.9 4.7 - - + +
52B ALA* 4.2 4.5 - - + -
61B PHE* 3.7 36.3 - - + -
65B LEU* 3.8 8.3 - - + -
77B PHE* 3.5 35.4 - - + -
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Residues in contact with GLU 27 (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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23B VAL* 2.8 24.8 + - - +
24B GLU* 3.8 6.2 - - - +
26B VAL* 1.3 77.0 - - - +
28B LYS* 1.3 62.8 + - - +
30B LEU* 3.5 10.6 + - - +
31B HIS* 2.9 46.0 + - + +
65B LEU* 4.5 7.2 - - + +
70B LYS* 3.1 44.4 + - - +
74B ILE* 3.9 17.0 - - + +
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Residues in contact with LYS 28 (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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24B GLU 3.1 18.1 + - - +
25B ASN* 3.1 12.0 + - - +
27B GLU* 1.3 78.0 - - - +
29B ALA* 1.3 63.6 + - - +
31B HIS* 3.2 10.5 + - - +
32B GLN* 3.2 19.9 + - - +
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Residues in contact with ALA 29 (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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25B ASN 3.1 6.3 + - - +
26B VAL 3.7 2.5 - - - +
27B GLU 3.3 0.2 - - - -
28B LYS* 1.3 75.5 - - - +
30B LEU* 1.3 64.4 + - - +
32B GLN* 3.3 6.8 + - - -
33B LEU* 3.1 20.3 + - - +
45B ALA* 3.6 18.8 - - + +
48B TRP* 3.5 39.7 - - + -
49B LEU* 3.9 10.7 - - + +
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Residues in contact with LEU 30 (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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26B VAL 3.1 21.4 + - - +
27B GLU* 3.8 5.6 - - - +
28B LYS 3.3 0.4 - - - -
29B ALA* 1.3 74.8 - - - +
31B HIS* 1.3 65.1 + - - +
32B GLN 3.2 0.2 + - - -
33B LEU* 3.3 2.0 + - + +
34B TYR* 2.8 62.3 + - + +
49B LEU* 3.4 26.2 - - + -
65B LEU* 4.3 5.8 - - + -
74B ILE* 3.5 37.2 - - + +
77B PHE* 3.7 35.9 - - + -
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Residues in contact with HIS 31 (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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27B GLU* 2.9 32.4 + - + +
28B LYS* 3.2 13.0 + - - +
30B LEU* 1.3 80.2 - - - +
32B GLN* 1.3 53.9 + - - +
35B TYR* 2.7 63.9 + + + +
36B ASP 3.8 0.5 + - - -
71B VAL* 5.8 0.8 - - - +
74B ILE* 3.3 31.1 - - + +
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Residues in contact with GLN 32 (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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28B LYS 3.2 9.6 + - - +
29B ALA* 3.6 10.5 - - - +
30B LEU 3.2 0.4 - - - -
31B HIS* 1.3 77.5 - - - +
33B LEU* 1.3 60.7 + - - +
36B ASP* 2.7 47.9 + - + +
41B ASN* 5.6 5.6 - - + -
42B LYS* 4.1 3.3 - - - +
45B ALA* 4.3 9.6 - - + -
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Residues in contact with LEU 33 (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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125A ILE 5.0 2.2 - - - +
126A GLN 5.5 2.5 - - - +
128A PRO* 3.8 20.4 - - + -
134A TYR* 3.4 23.0 - - + +
29B ALA 3.1 16.2 + - - +
30B LEU* 3.8 5.2 - - + +
32B GLN* 1.3 75.5 - - - +
34B TYR* 1.3 62.2 + - + +
42B LYS* 2.6 67.5 + - + +
45B ALA* 3.8 9.3 - - + +
46B GLN* 4.4 19.1 - - + -
49B LEU* 4.1 19.3 - - + -
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Residues in contact with TYR 34 (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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125A ILE* 3.6 27.2 + - + +
134A TYR* 3.4 27.8 - - - -
135A THR* 3.9 9.5 - - - -
138A CYS* 3.8 28.6 - - + +
30B LEU* 2.8 55.2 + - + +
33B LEU* 1.3 84.5 - - + +
35B TYR* 1.3 89.0 + + + +
42B LYS* 3.4 10.3 + - - -
73B GLU* 3.3 45.6 + - + -
74B ILE* 4.0 5.4 - - + -
76B TYR* 5.0 1.2 - - - -
77B PHE* 4.6 5.5 + - - +
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Residues in contact with TYR 35 (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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135A THR* 3.8 9.1 - - - +
138A CYS* 3.9 22.2 - - + -
139A GLN* 4.0 32.1 - - + +
31B HIS* 2.7 63.5 + + + +
34B TYR* 1.3 100.4 - + + +
36B ASP* 1.3 62.6 + - - +
37B PRO* 3.1 14.6 - - - +
42B LYS* 4.2 0.9 - - - -
71B VAL* 4.0 13.2 - - - +
73B GLU* 3.8 18.5 + - - +
74B ILE* 5.1 1.0 - - + +
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Residues in contact with ASP 36 (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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31B HIS 3.8 1.2 + - - -
32B GLN* 2.7 37.2 + - + +
35B TYR* 1.3 71.1 - - - +
37B PRO* 1.4 60.6 - - - +
38B ASN* 3.2 12.3 + - - +
41B ASN* 3.0 38.3 + - + +
42B LYS* 2.8 35.3 + - - +
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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