Contacts of the helix formed by residues 22 - 38 (chain F) in PDB entry 1S89
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 CYS 22 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18F ALA* 4.2 1.8 - - - -
19F HIS* 2.7 7.7 + - - +
21F HIS* 1.3 81.8 - - - +
23F LYS* 1.3 66.4 + - - +
24F GLN 3.3 2.2 - - - -
25F MET* 3.0 42.4 + - + +
26F LEU* 3.0 12.8 + - - +
89F PHE* 3.3 26.1 - - + +
90F TRP 3.5 29.4 - - - -
91F ASP* 3.9 13.9 - - - -
92F PRO* 4.8 3.6 - - - -
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Residues in contact with LYS 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F ALA* 2.9 32.0 + - + +
19F HIS* 3.0 11.1 + - - +
20F ASP* 3.1 38.1 + - - +
22F CYS* 1.3 77.0 - - - +
24F GLN* 1.3 58.3 + - - +
26F LEU* 3.2 3.6 + - - +
27F MET* 2.8 37.9 + - + +
47F THR* 3.6 20.9 - - + -
48F THR* 3.7 16.6 - - + +
51F LEU* 3.7 22.9 - - + -
206F PGA 2.8 29.2 + - - -
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Residues in contact with GLN 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F ASP 4.9 0.6 + - - -
21F HIS 5.3 3.0 - - - +
22F CYS 3.3 0.6 - - - -
23F LYS* 1.3 77.7 - - - +
25F MET* 1.3 62.3 + - + +
27F MET* 3.5 8.6 - - - +
28F SER* 3.1 29.1 + - - +
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Residues in contact with MET 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C LEU* 5.7 11.9 - - + -
21F HIS 4.2 5.4 + - - +
22F CYS* 3.0 51.9 + - + +
24F GLN* 1.3 80.8 - - + +
26F LEU* 1.3 61.9 + - - +
28F SER* 3.3 4.9 + - - -
29F TRP* 3.0 23.6 + - - +
32F ARG* 5.4 0.7 + - - -
89F PHE* 4.1 17.0 - - + -
92F PRO* 6.3 0.2 - - + -
120F VAL* 4.8 16.0 - - + +
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Residues in contact with LEU 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F LEU* 4.3 6.5 - - + -
17F VAL 4.2 12.1 - - - +
18F ALA* 3.6 32.5 - - + -
22F CYS 3.0 4.0 + - - +
23F LYS* 3.7 6.5 - - - +
25F MET* 1.3 78.3 - - - +
27F MET* 1.3 58.9 + - + +
29F TRP* 3.3 8.9 + - + +
30F VAL* 2.8 51.4 + - + +
48F THR* 3.6 25.8 - - + -
52F ILE* 4.3 8.7 - - + -
87F ILE* 4.2 25.4 - - + -
89F PHE* 3.8 16.3 - - + -
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Residues in contact with MET 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F LYS* 2.8 30.9 + - + +
24F GLN* 3.5 9.2 - - - +
26F LEU* 1.3 76.9 - - + +
28F SER* 1.3 58.1 + - - +
30F VAL* 3.2 7.3 + - - +
31F GLU* 2.8 45.1 + - + +
51F LEU* 3.7 19.7 - - + +
52F ILE* 4.0 31.0 - - - -
55F ALA* 3.5 32.1 - - + -
56F THR* 5.8 1.3 - - + -
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Residues in contact with SER 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F GLN* 3.1 15.8 + - - +
25F MET* 3.7 5.6 - - - -
27F MET* 1.3 77.0 - - - +
29F TRP* 1.3 64.6 + - - +
31F GLU* 3.0 15.6 + - - +
32F ARG* 2.8 39.7 + - - +
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Residues in contact with TRP 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F ILE* 6.3 0.2 - - + -
16F LEU* 4.5 12.6 - - + -
25F MET 3.0 11.5 + - - +
26F LEU* 3.5 17.5 - - + +
28F SER* 1.3 79.0 - - - +
30F VAL* 1.3 86.5 + - + +
32F ARG* 3.3 20.8 + - - +
33F HIS* 3.1 38.9 + + - -
37F LEU* 4.1 23.6 - - + -
87F ILE* 4.3 20.0 - - + -
89F PHE* 4.5 8.7 - + + -
120F VAL* 4.2 15.7 - - + -
123F ALA* 3.5 38.1 - - + +
124F ASP* 2.9 27.7 + - - -
127F ILE* 3.9 30.5 - - + -
132F PHE* 6.5 0.2 - + - -
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Residues in contact with VAL 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F LEU* 4.4 8.3 - - + -
26F LEU* 2.8 45.3 + - + +
27F MET* 3.4 6.7 - - - +
29F TRP* 1.3 80.7 - - + +
31F GLU* 1.3 59.5 + - - +
33F HIS 3.1 2.6 + - - -
34F GLN* 2.8 28.1 + - - -
37F LEU* 3.8 17.1 - - + +
52F ILE* 4.1 23.3 - - + -
56F THR* 4.5 5.2 - - + -
58F MET* 3.2 32.8 - - + -
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Residues in contact with GLU 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F MET* 2.8 34.8 + - + +
28F SER* 3.5 15.8 + - - +
30F VAL* 1.3 73.5 - - - +
32F ARG* 1.3 63.3 + - + +
33F HIS 3.2 0.7 + - - -
34F GLN* 3.4 21.2 + - - +
35F PRO* 4.6 1.7 - - - +
55F ALA* 4.9 14.0 - - - +
56F THR* 4.3 18.8 - - + -
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Residues in contact with ARG 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F MET 5.4 0.6 + - - -
28F SER* 2.8 25.3 + - - +
29F TRP* 3.7 31.0 - - - +
30F VAL 3.3 0.2 - - - -
31F GLU* 1.3 77.2 - - + +
33F HIS* 1.3 74.2 + - + +
34F GLN 3.6 0.4 + - - -
35F PRO* 4.6 4.7 - - - +
120F VAL* 4.4 10.9 - - - +
124F ASP* 3.4 34.4 + - - -
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Residues in contact with HIS 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F TRP* 3.1 43.8 + + - +
30F VAL 3.1 5.0 + - - +
32F ARG* 1.3 96.5 + - + +
34F GLN* 1.3 65.8 + - - +
35F PRO* 3.3 4.9 - - - -
36F LEU* 2.8 21.7 + - + +
37F LEU* 3.0 15.9 + - + -
124F ASP* 3.1 24.6 + - - -
127F ILE* 3.9 36.2 - - + +
128F GLN* 5.1 11.4 - - + -
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Residues in contact with GLN 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F VAL 2.8 12.0 + - - +
31F GLU* 3.4 17.5 + - - +
33F HIS* 1.3 75.7 - - - +
35F PRO* 1.3 72.6 - - + +
37F LEU* 3.1 6.5 + - - +
38F GLU* 2.8 54.0 + - - +
56F THR* 3.5 40.1 + - - +
58F MET* 3.7 18.6 - - + +
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Residues in contact with PRO 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F GLU 4.6 2.0 - - - +
32F ARG 4.6 4.5 - - - +
33F HIS* 3.3 6.7 - - - -
34F GLN* 1.3 97.0 - - + +
36F LEU* 1.3 59.4 + - - +
38F GLU* 3.8 13.4 + - - +
39F GLN* 3.4 24.8 + - - +
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Residues in contact with LEU 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F HIS* 2.8 14.3 + - + +
35F PRO* 1.3 79.5 - - - +
37F LEU* 1.3 66.0 + - - +
38F GLU 3.2 0.2 - - - -
39F GLN* 3.1 23.9 + - + +
40F HIS* 3.4 11.6 - - + +
127F ILE* 3.3 45.8 - - + +
132F PHE* 4.5 4.7 - - + -
133F ASN* 3.5 31.9 - - - +
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Residues in contact with LEU 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F ILE* 4.1 25.4 - - + -
16F LEU* 5.3 3.6 - - + -
29F TRP* 4.1 19.7 - - + -
30F VAL* 3.8 48.5 - - + +
33F HIS* 3.0 16.3 + - + +
34F GLN* 3.1 6.0 + - - +
36F LEU* 1.3 71.4 - - - +
38F GLU* 1.3 57.5 + - - +
39F GLN 3.0 5.4 - - - -
40F HIS* 2.9 32.0 + - - +
42F LEU* 4.1 20.2 - - + +
58F MET* 4.3 10.1 - - + -
127F ILE* 3.9 22.4 - - + -
132F PHE* 5.6 1.1 - - + -
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Residues in contact with GLU 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F ARG* 6.0 0.3 + - - -
34F GLN* 2.8 49.2 + - - +
35F PRO* 3.9 14.8 - - - +
36F LEU 3.2 0.4 - - - -
37F LEU* 1.3 75.1 - - - +
39F GLN* 1.3 68.9 + - - +
40F HIS 3.3 5.3 + - - +
42F LEU* 5.4 1.8 - - - -
56F THR 5.1 0.2 - - - +
57F GLY 6.1 0.2 - - - -
58F MET* 3.8 23.0 - - + +
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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