Contacts of the helix formed by residues 33 - 42 (chain B) in PDB entry 5K58
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 33 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ARG* 3.7 11.4 + - + +
32B ILE* 1.3 73.4 - - - +
34B THR* 1.3 58.5 + - - +
35B ALA* 3.2 9.3 + - - +
36B LYS* 2.6 43.6 + - + +
37B LEU* 2.9 26.4 + - - +
11T C 3.1 44.6 - - - +
12T A 3.3 13.0 - - - +
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Residues in contact with THR 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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32B ILE 3.6 1.6 + - - -
33B THR* 1.3 70.6 - - - +
35B ALA* 1.3 55.8 + - - +
37B LEU* 4.1 9.9 - - - -
38B ALA* 2.9 31.0 + - - +
45B GLU* 2.9 29.7 + - - +
48B LEU* 3.7 14.3 - - - +
49B TYR* 3.8 17.6 - - - +
55B LYS* 5.2 10.3 - - + -
12T A 3.1 44.3 + - + +
13T C 4.1 3.2 - - - +
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Residues in contact with ALA 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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33B THR* 2.9 11.8 - - - +
34B THR* 1.3 74.3 + - - +
36B LYS* 1.3 57.6 + - - +
37B LEU 3.0 3.6 - - - -
38B ALA* 2.9 20.8 + - - +
39B ALA* 2.9 13.2 + - - +
45B GLU* 3.1 19.4 + - - +
11T C 5.1 4.9 - - - +
12T A 5.8 0.6 + - - -
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Residues in contact with LYS 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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22B MET* 3.3 34.9 - - + +
27B ASP* 3.1 31.2 + - - +
31B ARG 5.7 5.4 - - - -
32B ILE* 6.4 0.7 - - - +
33B THR* 2.6 25.4 + - + +
35B ALA* 1.3 72.7 - - + +
37B LEU* 1.3 56.5 + - - +
39B ALA* 3.9 15.4 - - + +
40B SER* 3.7 8.7 + - - -
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Residues in contact with LEU 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 ILE* 4.5 10.1 - - + +
18B SER* 4.2 19.3 - - - +
19B LEU* 4.3 27.8 - - + +
22B MET* 4.0 17.7 - - - +
32B ILE* 4.1 10.5 - - + +
33B THR 2.9 17.9 + - - +
34B THR* 3.9 7.2 - - - +
36B LYS* 1.3 77.4 - - - +
38B ALA* 1.3 66.1 + - - +
39B ALA 3.1 2.3 + - - -
40B SER* 3.3 10.6 + - - -
41B VAL* 3.8 13.3 + - + +
48B LEU* 4.4 12.6 - - + -
55B LYS* 5.4 5.8 - - + -
58B MET* 3.9 28.9 - - + -
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Residues in contact with ALA 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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34B THR 2.9 20.2 + - - +
35B ALA 2.9 6.0 + - - +
37B LEU* 1.3 76.0 - - - +
39B ALA* 1.3 61.3 + - - +
41B VAL* 4.0 1.7 + - - +
42B GLY 3.4 3.1 + - - -
43B VAL* 2.9 40.4 + - - +
44B SER* 4.0 8.3 - - - -
45B GLU* 3.9 18.8 - - + -
48B LEU* 3.9 18.6 - - + +
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Residues in contact with ALA 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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35B ALA 2.9 13.4 + - - +
36B LYS* 3.9 17.5 - - + +
37B LEU 3.1 0.4 - - - -
38B ALA* 1.3 78.1 - - - +
40B SER* 1.3 66.1 + - - +
42B GLY* 3.3 12.6 + - - -
43B VAL 4.9 0.7 - - - -
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Residues in contact with SER 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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18B SER* 4.2 18.2 - - - -
22B MET* 3.9 14.7 - - - +
36B LYS 3.7 11.3 + - - -
37B LEU 3.3 9.6 + - - -
39B ALA* 1.3 77.2 - - - +
41B VAL* 1.3 67.5 + - - +
42B GLY* 3.0 2.8 + - - -
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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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11B ARG* 4.9 4.4 + - - +
14B GLU* 3.1 41.7 - - + +
15B ILE* 3.9 27.8 - - + -
18B SER* 3.3 29.6 + - - +
37B LEU* 3.8 13.6 + - + +
38B ALA 4.5 2.7 - - - +
40B SER* 1.3 74.2 - - - +
42B GLY* 1.3 60.0 + - - +
43B VAL* 4.2 16.3 - - + +
48B LEU* 5.0 7.2 - - + -
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Residues in contact with GLY 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 ALA 3.4 1.2 + - - -
39B ALA 3.3 14.5 + - - -
40B SER 3.0 4.6 + - - -
41B VAL* 1.3 77.9 - - - +
43B VAL* 1.3 67.9 + - - +
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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