Contacts of the helix formed by residues 32 - 47 (chain B) in PDB entry 3SF4
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 ASP 32 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B LEU* 2.7 49.5 - - + +
30B SER* 3.3 8.8 + - - +
31B GLY* 1.3 75.0 - - - +
33B CYS* 1.3 59.3 + - - +
34B ARG* 3.5 12.6 + - - +
35B ALA* 2.8 39.3 + - - +
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Residues in contact with CYS 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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28B CYS* 3.7 42.0 - - - -
31B GLY 3.6 3.7 + - - -
32B ASP* 1.3 71.2 - - - +
34B ARG* 1.3 68.6 + - - +
35B ALA 3.0 2.5 - - - -
36B GLY 3.4 0.2 - - - -
37B VAL* 2.7 29.3 + - - +
64B ALA* 4.2 13.9 - - + +
67B TYR* 3.6 32.1 - - + -
68B LEU* 4.0 19.6 - - + +
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Residues in contact with ARG 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ASP* 3.5 9.8 + - - +
33B CYS* 1.3 79.5 - - - +
35B ALA* 1.3 59.3 + - + +
37B VAL* 3.8 10.2 - - - +
38B SER* 3.6 9.9 + - - -
68B LEU* 3.6 42.8 + - + +
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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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27B LEU* 3.6 13.9 - - + +
32B ASP* 2.8 25.6 + - - +
33B CYS 3.0 0.2 - - - -
34B ARG* 1.3 76.8 - - + +
36B GLY* 1.3 58.5 + - - +
37B VAL 3.0 2.5 - - - -
38B SER* 2.7 37.5 + - - +
39B PHE 3.2 4.0 + - - -
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Residues in contact with GLY 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLY* 3.6 11.9 - - - -
27B LEU* 3.3 28.3 - - - +
28B CYS* 4.1 6.7 - - - -
33B CYS 2.8 8.7 + - - -
35B ALA* 1.3 79.3 - - - +
37B VAL* 1.3 60.5 + - - +
39B PHE* 3.3 6.1 + - - +
40B PHE* 3.0 30.6 + - - -
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Residues in contact with VAL 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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33B CYS 2.7 22.4 + - - +
34B ARG* 3.8 7.2 - - - +
36B GLY* 1.3 73.9 - - - +
38B SER* 1.3 54.9 - - - +
40B PHE* 2.9 11.4 + - + +
41B GLU* 2.6 52.4 + - + +
61B LEU* 5.2 2.7 - - + +
64B ALA* 4.0 22.7 - - + -
65B TYR* 3.2 43.1 - - + +
68B LEU* 4.2 13.7 - - + -
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Residues in contact with SER 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ARG 3.6 10.9 + - - -
35B ALA* 2.7 19.9 + - - -
37B VAL* 1.3 77.7 - - - +
39B PHE* 1.3 60.3 + - - -
40B PHE 3.1 0.9 + - - -
41B GLU* 3.2 11.1 + - - +
42B ALA* 3.1 23.6 + - - +
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Residues in contact with PHE 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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20B LEU* 3.2 36.0 - - - +
21B ALA* 3.9 3.4 - - - -
23B GLU* 4.5 4.7 - - + -
24B GLY* 3.4 34.1 - - - +
27B LEU* 4.3 8.1 - - + -
35B ALA 3.2 5.7 + - - +
36B GLY 3.5 1.3 - - - +
38B SER* 1.3 79.6 - - - +
40B PHE* 1.3 59.3 + - - +
42B ALA* 4.0 3.3 + - - -
43B ALA* 3.4 1.9 + - - +
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Residues in contact with PHE 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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21B ALA* 3.6 30.1 - - + -
24B GLY 3.5 17.0 - - - -
25B GLU* 3.5 23.8 - - + -
28B CYS* 4.1 13.7 - - - -
36B GLY 3.0 22.7 + - - -
37B VAL* 2.9 10.8 + - + +
39B PHE* 1.3 75.6 - - - +
41B GLU* 1.3 66.3 + - - +
42B ALA 3.0 2.0 - - - -
43B ALA* 2.7 16.5 + - - +
44B VAL* 3.0 17.0 + - + +
57B ILE* 4.0 19.1 - - + -
60B GLN* 3.9 29.6 - - + -
61B LEU* 4.3 24.2 - - + -
64B ALA* 5.5 0.9 - - + -
77B TYR* 6.5 0.2 - - + -
52E ILE* 4.1 12.1 - - + -
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Residues in contact with GLU 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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37B VAL* 2.6 41.4 + - + +
38B SER* 3.4 9.9 - - - +
40B PHE* 1.3 71.6 - - - +
42B ALA* 1.3 60.3 + - - +
44B VAL* 3.4 11.4 - - - +
45B GLN* 3.2 17.3 + - - +
61B LEU* 5.9 0.5 - - - +
65B TYR* 2.9 22.1 + - - +
77B TYR* 2.9 32.8 + - - -
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Residues in contact with ALA 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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20B LEU* 4.0 11.2 - - + -
38B SER 3.1 13.7 + - - +
39B PHE* 4.0 6.7 - - - +
40B PHE 3.0 0.6 - - - -
41B GLU* 1.3 74.4 - - - +
43B ALA* 1.3 59.9 + - - +
44B VAL 2.9 2.0 - - - -
45B GLN* 2.6 30.0 + - + +
46B VAL* 2.7 17.5 + - + +
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Residues in contact with ALA 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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20B LEU* 3.2 24.0 - - + +
21B ALA* 3.3 34.5 - - + -
39B PHE 3.4 1.7 + - - +
40B PHE* 2.7 16.7 + - - +
42B ALA* 1.3 74.1 - - - +
44B VAL* 1.3 55.3 + - - +
46B VAL* 3.9 1.4 - - - +
47B GLY* 2.9 28.6 + - - +
48B THR* 5.5 1.2 - - - +
54B LEU* 6.0 1.0 - - - +
57B ILE* 4.3 12.3 - - + -
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Residues in contact with VAL 44 (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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40B PHE* 3.3 15.0 - - + +
41B GLU* 3.4 10.5 - - - +
42B ALA 2.9 0.6 - - - -
43B ALA* 1.3 76.0 - - - +
45B GLN* 1.3 66.6 + - - +
46B VAL 3.2 0.2 - - - -
47B GLY* 3.3 12.6 + - - +
54B LEU* 6.2 3.8 - - + -
57B ILE* 4.2 18.2 - - + -
58B TYR* 4.8 23.3 - - + +
61B LEU* 6.1 0.7 - - + -
77B TYR* 5.0 15.3 - - + -
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Residues in contact with GLN 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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41B GLU 3.2 10.6 + - - +
42B ALA* 2.6 18.8 + - + +
44B VAL* 1.3 76.7 - - - +
46B VAL* 1.3 63.2 + - + +
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Residues in contact with VAL 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 3.2 33.9 - - + -
42B ALA* 2.7 18.3 + - + +
43B ALA 3.9 2.5 - - - +
45B GLN* 1.3 76.5 - - + +
47B GLY* 1.3 68.1 + - - +
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Residues in contact with GLY 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 ALA 2.9 17.4 + - - +
44B VAL* 3.3 11.5 + - - -
46B VAL* 1.3 90.8 - - - +
48B THR* 1.3 70.8 + - - +
54B LEU* 5.7 3.4 - - - -
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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