Contacts of the helix formed by residues 19 - 33 (chain D) 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 HIS 19 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D ALA* 1.3 74.1 - - - +
20D ASP* 1.3 54.9 + - - +
21D HIS 3.2 0.9 - - - +
22D CYS 2.6 28.4 + - - -
23D LYS* 3.1 8.6 + - - +
88D PHE* 4.0 4.5 - + - -
89D PHE 3.0 7.5 + - - +
90D TRP* 3.5 19.0 - + + -
91D ASP* 3.2 38.5 + - + +
96D VAL* 3.6 34.7 - - + +
98D ASN* 4.3 2.5 + - - -
102D VAL* 3.5 33.1 - - + +
204D PGA 3.5 32.6 + - - -
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Residues in contact with ASP 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C ARG* 2.6 46.3 + - - -
19D HIS* 1.3 71.5 - - - +
21D HIS* 1.3 70.6 + - + +
22D CYS 3.1 1.4 + - - -
23D LYS* 2.9 33.2 + - - +
24D GLN 4.7 1.4 + - - -
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Residues in contact with HIS 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D HIS* 3.0 3.6 + - - +
20D ASP* 1.3 82.3 - - + +
22D CYS* 1.3 61.3 + - - +
24D GLN* 5.2 3.4 + - - +
25D MET* 5.4 1.6 + - - +
91D ASP* 3.1 31.0 + - - +
94D ASN* 3.7 23.8 + - + +
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Residues in contact with CYS 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ALA* 4.2 2.2 - - - -
19D HIS 2.6 13.1 + - - +
21D HIS* 1.3 80.3 - - - +
23D LYS* 1.3 63.4 + - - +
24D GLN 3.3 2.2 - - - -
25D MET* 3.0 15.2 + - + +
26D LEU* 2.9 21.1 + - - +
89D PHE* 3.3 38.4 - - + +
90D TRP 3.8 16.4 - - - -
91D ASP* 3.9 15.9 - - - -
92D PRO* 4.5 6.1 - - - -
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Residues in contact with LYS 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ALA* 2.8 37.0 + - + +
19D HIS* 3.1 8.3 + - - +
20D ASP* 2.9 38.7 + - - +
22D CYS* 1.3 77.8 - - - +
24D GLN* 1.3 57.2 + - - +
26D LEU* 3.1 3.0 + - - +
27D MET* 2.8 38.9 + - + +
47D THR* 3.8 17.9 - - + -
48D THR* 3.5 20.0 - - + +
51D LEU* 3.5 24.0 - - + -
204D PGA 2.8 24.8 + - - -
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Residues in contact with GLN 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D ASP 4.7 1.6 + - - -
21D HIS 5.2 3.1 - - - +
22D CYS 3.3 0.4 - - - -
23D LYS* 1.3 78.2 - - - +
25D MET* 1.3 62.0 + - - +
27D MET* 3.7 8.1 - - - +
28D SER* 3.1 25.8 + - - -
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Residues in contact with MET 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D HIS 5.4 0.6 + - - +
22D CYS* 3.0 18.7 + - + +
24D GLN* 1.3 81.2 - - - +
26D LEU* 1.3 56.5 + - - +
28D SER* 3.6 5.9 + - - -
29D TRP* 3.1 26.5 + - - +
89D PHE* 4.2 13.1 - - + -
120D VAL* 4.8 12.1 - - + +
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Residues in contact with LEU 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU* 4.3 10.3 - - + -
17D VAL 4.1 14.1 - - - +
18D ALA* 3.5 25.8 - - + -
22D CYS 2.9 12.0 + - - +
23D LYS* 3.1 6.9 + - - +
25D MET* 1.3 75.4 - - - +
27D MET* 1.3 55.7 + - + +
29D TRP* 3.1 8.1 + - + -
30D VAL* 2.8 53.8 + - + +
48D THR* 3.6 23.6 - - + -
52D ILE* 4.7 3.1 - - + -
87D ILE* 4.1 18.2 - - + -
89D PHE* 3.8 26.6 - - + -
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Residues in contact with MET 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LYS* 2.8 26.9 + - + +
24D GLN* 3.7 7.6 - - - +
26D LEU* 1.3 76.0 - - + +
28D SER* 1.3 64.2 + - - +
30D VAL* 3.2 6.8 + - - +
31D GLU* 2.9 42.3 + - - +
51D LEU* 3.3 46.2 - - + +
52D ILE* 4.0 27.6 - - - -
54D ARG 5.0 0.2 - - - +
55D ALA* 4.2 12.8 - - + -
56D THR* 6.3 1.3 - - - -
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Residues in contact with SER 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D GLN 3.1 15.6 + - - -
25D MET* 3.7 6.1 - - - -
27D MET* 1.3 80.4 - - - +
29D TRP* 1.3 63.5 + - - +
31D GLU* 3.6 6.3 + - - +
32D ARG* 3.1 34.6 + - - +
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Residues in contact with TRP 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ILE* 6.1 0.7 - - + -
16D LEU* 4.3 17.7 - - + -
25D MET 3.1 15.3 + - - +
26D LEU* 3.1 17.5 + - + +
28D SER* 1.3 77.9 + - - +
30D VAL* 1.3 73.4 + - + +
32D ARG* 3.4 23.2 + - - +
33D HIS* 3.2 36.6 + + - -
37D LEU* 4.2 20.6 - - + -
87D ILE* 4.3 18.8 - - + -
89D PHE* 4.5 7.6 - + + -
120D VAL* 4.1 12.8 - - + -
123D ALA* 3.5 38.7 - - + +
124D ASP* 2.7 30.1 + - - -
127D ILE* 3.7 30.1 - - + -
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Residues in contact with VAL 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU* 4.4 16.4 - - + -
26D LEU* 2.8 47.2 + - + +
27D MET* 3.5 7.9 - - - +
29D TRP* 1.3 82.5 - - + +
31D GLU* 1.3 54.4 + - + +
33D HIS 3.0 4.5 + - - -
34D GLN* 2.8 32.2 + - - -
37D LEU* 3.7 19.7 - - + +
42D LEU* 5.8 0.2 - - + -
52D ILE* 4.1 22.9 - - + -
56D THR* 4.6 5.8 - - + -
58D MET* 4.0 19.7 - - + -
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Residues in contact with GLU 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D MET* 2.9 34.7 + - - +
28D SER* 4.2 5.3 - - - +
30D VAL* 1.3 76.4 - - + +
32D ARG* 1.3 61.3 + - - +
33D HIS 3.2 0.9 + - - -
34D GLN* 3.4 24.3 + - - +
35D PRO* 4.4 2.8 - - - +
55D ALA* 5.0 14.7 - - - +
56D THR* 4.1 22.7 - - + -
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Residues in contact with ARG 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D SER* 3.1 32.1 + - - +
29D TRP* 3.4 34.0 - - - +
30D VAL 3.2 0.2 - - - -
31D GLU* 1.3 77.4 - - - +
33D HIS* 1.3 73.4 + - + +
34D GLN 3.6 0.2 - - - -
35D PRO* 4.6 4.7 - - - +
120D VAL* 3.7 10.7 - - - +
124D ASP* 3.0 34.4 + - - -
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Residues in contact with HIS 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D TRP* 3.2 43.8 + + - +
30D VAL 3.0 6.2 + - - +
32D ARG* 1.3 98.1 + - + +
34D GLN* 1.3 65.2 + - - +
35D PRO* 3.2 6.1 - - - -
36D LEU* 2.9 19.3 + - + +
37D LEU* 3.0 15.4 + - + +
124D ASP* 2.9 23.2 + - - -
127D ILE* 3.8 35.9 - - + +
128D GLN* 4.2 15.3 - - + -
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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