Contacts of the helix formed by residues 23 - 37 (chain B) in PDB entry 3S1K
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 ASN 23 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B ASN 3.9 0.8 + - - -
22B LEU* 1.3 73.5 - - - +
24B ASP* 1.3 66.4 + - - +
25B GLN* 2.9 21.5 + - - +
26B GLN* 2.8 62.0 + - - +
27B PHE* 2.8 25.1 + - - +
55B GLN* 5.3 1.6 - - - +
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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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23B ASN* 1.3 75.1 - - - +
25B GLN* 1.3 60.9 + - - +
27B PHE* 3.3 2.1 - - - +
28B HIS* 3.1 28.4 + - - +
62V ASN 3.7 16.9 - - - +
63V ASP* 3.5 33.0 - - + +
64V GLU* 4.6 2.6 + - - +
48W LYS* 2.9 33.1 + - - +
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Residues in contact with GLN 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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23B ASN* 2.9 31.5 + - - +
24B ASP* 1.3 78.2 + - - +
26B GLN* 1.3 60.6 + - + +
28B HIS* 3.5 4.3 + - - +
29B ALA* 2.9 30.7 + - - +
63V ASP* 2.6 31.4 + - - +
66V LEU* 5.7 4.2 - - + +
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Residues in contact with GLN 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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22B LEU* 3.5 16.3 - - + +
23B ASN* 2.8 50.3 + - - +
25B GLN* 1.3 70.7 - - + +
27B PHE* 1.3 66.6 + - - +
29B ALA* 3.7 5.6 - - - +
30B PHE* 3.0 35.6 + - + -
51B LEU* 3.8 19.1 - - + +
55B GLN* 2.7 40.7 + - - +
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Residues in contact with PHE 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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16B ILE* 5.0 4.2 - - + +
17B ALA* 3.4 43.7 - - + -
19B LEU 5.8 1.6 - - - -
22B LEU* 4.6 19.4 - - + +
23B ASN 2.8 18.5 + - - +
24B ASP* 3.3 9.9 - - - +
26B GLN* 1.3 78.5 - - - +
28B HIS* 1.3 68.0 + - - +
30B PHE* 3.8 2.4 - - - +
31B ILE* 3.0 46.8 + - + +
17V PHE* 4.1 10.3 - + - -
21V TYR* 4.1 21.8 - + - -
48W LYS* 3.7 35.0 - - + -
81W MET* 3.9 9.6 - - - -
89W GLN* 5.8 0.2 - - - -
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Residues in contact with HIS 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 3.1 13.2 + - - +
25B GLN* 4.0 4.5 - - - +
27B PHE* 1.3 77.5 - - - +
29B ALA* 1.3 63.4 + - - +
31B ILE* 4.6 2.5 - - - +
32B TRP* 2.7 75.4 + + + +
21V TYR* 3.2 30.8 + - - +
25V TYR* 3.1 48.1 + + - -
61V CYS 5.7 2.5 - - - +
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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 GLN 2.9 20.0 + - - +
26B GLN* 3.7 6.7 - - - +
28B HIS* 1.3 79.5 - - - +
30B PHE* 1.3 60.2 + - + +
32B TRP* 3.9 2.1 - - - +
33B SER* 2.6 35.5 + - - +
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Residues in contact with PHE 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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16B ILE* 3.8 21.0 - - + +
22B LEU* 4.5 8.3 - - + -
26B GLN* 3.0 32.0 + - + +
27B PHE 3.8 0.7 - - - +
29B ALA* 1.3 78.3 - - + +
31B ILE* 1.3 63.3 + - - +
33B SER* 3.2 5.8 + - - -
34B LEU* 3.0 23.0 + - - +
44B LEU* 3.6 42.3 - - + +
47B GLU* 3.6 34.5 - - + -
48B ALA* 3.7 27.4 - - + -
51B LEU* 3.8 28.0 - - + -
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Residues in contact with ILE 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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13B ALA* 3.6 36.6 - - + +
16B ILE* 4.3 9.2 - - + -
17B ALA* 4.2 10.8 - - + +
27B PHE* 3.0 45.2 + - + +
28B HIS* 3.9 4.0 - - - +
30B PHE* 1.3 75.0 - - - +
32B TRP* 1.3 58.6 + - - +
34B LEU* 3.2 7.9 + - + +
35B ILE* 3.0 37.6 + - + +
17V PHE* 4.3 7.4 - - + -
18V MET* 5.4 2.5 - - - -
21V TYR* 4.1 30.7 - - + -
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Residues in contact with TRP 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 HIS* 2.7 50.0 + + + +
29B ALA* 4.0 3.6 - - - +
31B ILE* 1.3 71.2 - - - +
33B SER* 1.3 58.7 + - - +
35B ILE* 3.5 20.0 + - + +
36B ASP* 3.0 36.9 + - + +
21V TYR* 4.1 8.7 - + - -
22V GLN* 3.9 31.6 - - + -
25V TYR* 3.7 42.4 - + + -
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Residues in contact with SER 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 ALA* 2.6 24.7 + - - +
30B PHE* 3.6 4.0 - - - -
32B TRP* 1.3 76.0 - - - +
34B LEU* 1.3 58.2 + - - +
36B ASP* 3.2 7.8 + - - +
37B ASP* 3.0 29.6 + - - +
40B GLN* 5.4 0.3 - - - +
44B LEU* 3.8 23.9 - - - +
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Residues in contact with LEU 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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9B HIS* 4.2 4.5 - - + +
12B TYR* 4.0 12.6 - - + -
13B ALA* 3.8 33.0 - - + +
16B ILE* 4.0 16.8 - - + -
30B PHE 3.0 12.8 + - - +
31B ILE* 3.3 12.3 - - + +
33B SER* 1.3 74.0 - - - +
35B ILE* 1.3 61.6 + - + +
37B ASP 4.5 0.4 - - - -
38B PRO* 3.0 39.2 - - + +
41B SER* 2.8 38.8 - - - +
44B LEU* 3.5 10.0 - - + +
18V MET* 4.4 14.3 - - + +
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Residues in contact with ILE 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 ILE* 3.0 32.2 + - + +
32B TRP* 3.7 30.5 - - + +
34B LEU* 1.3 75.2 - - + +
36B ASP* 1.3 64.0 + - - +
38B PRO* 3.6 10.7 - - - +
18V MET* 3.9 33.4 - - + +
21V TYR* 4.6 0.2 - - + -
22V GLN* 3.6 54.5 - - + +
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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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32B TRP* 3.0 26.5 + - - +
33B SER* 3.5 9.0 - - - +
34B LEU 3.2 0.2 - - - -
35B ILE* 1.3 80.4 - - - +
37B ASP* 1.3 63.8 + - + +
38B PRO* 3.9 2.3 - - - +
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Residues in contact with ASP 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 SER 3.0 11.2 + - - +
34B LEU* 3.3 4.2 - - - +
36B ASP* 1.3 82.4 - - + +
38B PRO* 1.3 55.2 - - - +
39B SER* 2.4 31.1 + - - -
40B GLN* 2.8 48.7 + - + +
41B SER 4.2 0.5 + - - -
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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