Contacts of the helix formed by residues 22 - 36 (chain B) in PDB entry 3URZ
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 SER 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B GLN* 1.3 79.9 - - - +
23B VAL* 1.3 63.1 + - - +
24B ASP* 3.4 15.9 + - - +
25B GLU* 3.4 20.6 + - - +
26B MSE 3.1 30.0 + - - +
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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
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21B GLN 3.9 0.2 + - - -
22B SER* 1.3 72.0 + - - +
24B ASP* 1.3 64.1 + - + +
26B MSE 3.3 7.5 + - - +
27B LEU* 2.9 39.4 + - + +
49B THR* 4.4 7.9 - - - +
52B LEU* 3.5 34.1 - - + -
53B ASN* 3.8 23.6 - - + +
56B ARG* 3.8 30.1 - - + -
57B THR* 5.8 0.9 - - - +
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Residues in contact with ASP 24 (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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22B SER* 3.3 9.8 + - - +
23B VAL* 1.3 84.9 - - + +
25B GLU* 1.3 63.0 + - + +
27B LEU* 3.4 9.6 + - - +
28B GLN* 3.3 30.3 + - - +
56B ARG* 5.4 9.9 - - - +
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Residues in contact with GLU 25 (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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21B GLN 4.9 5.6 - - - +
22B SER* 3.4 28.8 + - - +
23B VAL 3.3 0.2 - - - -
24B ASP* 1.3 77.9 - - + +
26B MSE 1.3 62.4 + - + +
28B GLN* 3.3 36.2 + - - +
29B LYS* 3.6 17.2 + - - +
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Residues in contact with MSE 26 (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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21B GLN* 4.6 12.1 - - - +
22B SER 3.1 22.1 + - - +
23B VAL* 3.3 3.6 + - - +
25B GLU* 1.3 75.5 - - + +
27B LEU* 1.3 61.8 + - - +
29B LYS* 3.2 42.4 + - - +
30B VAL* 3.4 14.0 + - - +
45B TYR* 3.7 27.7 - - + +
48B GLN* 3.2 44.9 - - + +
49B THR* 3.2 23.2 - - + +
52B LEU* 4.1 17.9 - - + -
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Residues in contact with LEU 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* 2.9 23.5 + - + +
24B ASP* 3.8 5.8 - - - +
26B MSE 1.3 73.2 - - - +
28B GLN* 1.3 65.2 + - - +
30B VAL* 3.2 12.9 + - + +
31B SER* 3.1 25.4 + - - -
46B PHE* 4.7 4.0 - - + -
49B THR* 3.8 27.1 - - + +
56B ARG* 3.9 46.0 - - + +
57B THR* 4.7 5.4 - - - +
60B TYR* 3.9 44.8 - - + -
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Residues in contact with GLN 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 ASP* 3.3 20.5 + - - +
25B GLU* 3.5 27.3 + - - +
26B MSE 3.3 0.2 - - - -
27B LEU* 1.3 77.3 - - - +
29B LYS* 1.3 56.5 + - + +
31B SER* 3.4 7.8 + - - -
32B ALA* 2.9 29.6 + - - +
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Residues in contact with LYS 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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21B GLN 5.6 3.2 - - - +
25B GLU* 3.7 17.9 - - - +
26B MSE 3.2 32.2 + - - +
28B GLN* 1.3 73.6 - - + +
30B VAL* 1.3 61.4 + - - +
32B ALA* 3.8 6.1 - - - +
33B ALA* 2.9 32.1 + - - +
45B TYR* 3.5 48.6 + - + +
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Residues in contact with VAL 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 MSE 3.6 13.7 - - - +
27B LEU* 3.2 20.1 + - + +
29B LYS* 1.3 77.2 - - - +
31B SER* 1.3 55.9 + - - +
33B ALA* 3.7 1.9 - - - +
34B ILE* 3.0 43.6 + - + +
42B ALA* 3.9 19.2 - - + +
45B TYR* 3.7 22.2 - - + +
46B PHE* 3.7 24.9 - - + +
60B TYR* 3.6 24.9 - - + +
75B LEU* 4.9 3.6 - - + -
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Residues in contact with SER 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 LEU 3.1 10.5 + - - -
28B GLN* 3.7 10.2 - - - -
29B LYS 3.3 0.2 - - - -
30B VAL* 1.3 75.7 - - - +
32B ALA* 1.3 56.8 + - - +
34B ILE* 3.3 7.0 + - - +
35B GLU* 3.0 41.0 + - - +
60B TYR* 2.7 30.3 + - - -
64B ASN* 5.0 4.5 + - - +
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Residues in contact with ALA 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 GLN 2.9 18.6 + - - +
29B LYS* 3.9 7.4 - - - +
31B SER* 1.3 75.8 - - - +
33B ALA* 1.3 63.5 + - - +
35B GLU* 3.4 8.1 + - - +
36B ALA* 3.1 24.3 + - - +
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Residues in contact with ALA 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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29B LYS 2.9 19.4 + - - +
32B ALA* 1.3 74.9 - - - +
34B ILE* 1.3 59.8 + - - +
36B ALA* 3.4 2.8 + - - -
37B GLY 3.2 3.3 + - - -
38B GLN* 2.8 54.1 + - - +
41B GLN* 3.7 20.6 - - + +
42B ALA* 3.6 20.9 - - + +
45B TYR* 4.8 0.9 - - + -
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Residues in contact with ILE 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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30B VAL* 3.0 35.6 + - + +
31B SER* 3.6 8.5 - - - +
33B ALA* 1.3 74.9 - - - +
35B GLU* 1.3 64.8 + - + +
37B GLY* 3.1 14.0 + - - -
39B ASN* 4.5 11.1 - - - +
42B ALA* 3.8 14.4 - - + -
60B TYR* 4.2 9.9 - - + +
65B VAL* 5.3 5.2 - - + -
69B SER* 6.2 1.6 - - - -
71B ILE* 4.2 35.9 - - + -
75B LEU* 4.6 7.2 - - + -
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Residues in contact with GLU 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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31B SER* 3.0 27.2 + - - +
32B ALA* 3.4 6.2 + - - +
34B ILE* 1.3 79.1 - - + +
36B ALA* 1.3 58.9 + - - +
37B GLY 3.3 0.7 + - - -
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Residues in contact with ALA 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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32B ALA 3.1 17.6 + - - +
33B ALA* 3.4 4.5 + - - +
34B ILE 3.2 0.4 - - - -
35B GLU* 1.3 75.6 - - - +
37B GLY* 1.3 61.3 + - - +
38B GLN* 4.0 20.5 + - + +
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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