Contacts of the helix formed by residues 22 - 33 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ALA* 4.2 1.6 - - - -
19A HIS 2.7 10.3 + - - +
21A HIS* 1.3 77.4 - - - +
23A LYS* 1.3 65.2 + - - +
24A GLN 3.3 2.9 - - - -
25A MET* 3.2 36.1 + - + +
26A LEU* 3.1 21.3 + - - +
89A PHE* 3.4 30.1 - - + +
90A TRP 3.8 4.9 - - - -
91A ASP* 3.7 34.3 - - - -
92A PRO* 4.5 4.7 - - - -
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Residues in contact with LYS 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ALA* 2.7 38.7 + - + +
19A HIS* 3.1 9.4 + - - +
20A ASP* 2.6 45.2 + - - +
22A CYS* 1.3 78.4 - - - +
24A GLN* 1.3 57.2 + - - +
26A LEU* 3.4 2.0 + - + +
27A MET* 2.8 36.4 + - + +
47A THR* 3.7 19.5 - - + -
48A THR* 3.6 16.8 - - + +
51A LEU* 3.9 23.1 - - + -
201A PGA 2.8 19.0 + - - -
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Residues in contact with GLN 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ASP 4.7 1.4 + - - -
21A HIS 5.2 2.4 + - - +
22A CYS 3.3 0.8 - - - -
23A LYS* 1.3 75.7 - - - +
25A MET* 1.3 61.8 + - + +
27A MET* 3.6 6.0 - - - +
28A SER* 2.9 37.5 + - - +
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Residues in contact with MET 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A HIS 4.6 5.4 - - - +
22A CYS* 3.2 48.1 + - + +
24A GLN* 1.3 79.6 - - + +
26A LEU* 1.3 62.7 + - - +
28A SER* 3.7 5.0 - - - -
29A TRP* 3.0 24.3 + - - +
32A ARG* 5.1 0.9 + - - -
89A PHE* 4.2 16.8 - - + -
92A PRO* 6.0 1.6 - - + -
120A VAL* 4.8 17.9 - - + +
3B LEU* 5.6 9.6 - - - -
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Residues in contact with LEU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 4.3 13.9 - - + -
17A VAL 4.2 10.3 - - - +
18A ALA* 3.5 24.5 - - + -
22A CYS 3.1 9.8 + - - +
23A LYS* 3.7 6.7 - - - +
25A MET* 1.3 79.7 - - - +
27A MET* 1.3 58.9 + - + +
29A TRP* 3.1 6.8 + - + +
30A VAL* 2.8 42.1 + - + +
48A THR* 3.5 25.1 - - + -
52A ILE* 4.5 5.6 - - + -
87A ILE* 3.8 23.1 - - + -
89A PHE* 3.7 30.4 - - + -
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Residues in contact with MET 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LYS* 2.8 30.2 + - + +
24A GLN* 3.6 7.6 - - - +
25A MET 3.3 0.2 - - - -
26A LEU* 1.3 78.2 - - + +
28A SER* 1.3 63.2 + - - +
30A VAL* 3.2 6.3 + - + +
31A GLU* 2.9 23.8 + - - +
48A THR* 5.1 0.7 - - - +
51A LEU* 3.7 24.2 - - + +
52A ILE* 3.7 36.1 - - - +
55A ALA* 3.6 31.6 - - + -
56A THR* 5.1 6.1 - - + +
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Residues in contact with SER 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLN* 2.9 25.2 + - - +
25A MET* 3.7 5.5 - - - -
27A MET* 1.3 72.2 - - - +
29A TRP* 1.3 64.9 + - - +
31A GLU* 3.1 8.6 + - - +
32A ARG* 2.9 46.6 + - - -
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Residues in contact with TRP 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 4.6 6.5 - - + -
25A MET 3.0 14.1 + - - +
26A LEU* 3.4 19.5 - - + +
28A SER* 1.3 76.9 - - - +
30A VAL* 1.3 75.0 + - + +
32A ARG* 3.4 21.2 + - - +
33A HIS* 2.8 43.5 + + - -
37A LEU* 4.1 21.1 - - + -
87A ILE* 4.5 26.0 - - + -
89A PHE* 4.7 7.4 - + + -
120A VAL* 4.1 13.5 - - + -
123A ALA* 3.5 39.5 - - + +
124A ASP* 2.7 26.9 + - - -
127A ILE* 3.8 31.6 - - + -
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Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 4.3 17.9 - - + -
26A LEU* 2.8 28.9 + - + +
27A MET* 3.5 10.3 - - - +
29A TRP* 1.3 86.2 - - + +
31A GLU* 1.3 60.8 + - - +
33A HIS 3.0 3.3 + - - -
34A GLN* 2.8 27.5 + - - +
37A LEU* 4.0 16.6 - - + -
52A ILE* 3.9 20.0 - - + -
56A THR* 4.3 7.0 - - + -
58A MET* 3.4 30.3 - - + -
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Residues in contact with GLU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A MET 2.9 13.2 + - - +
28A SER* 3.5 11.0 - - - +
30A VAL* 1.3 79.9 - - - +
32A ARG* 1.3 61.3 + - + +
33A HIS 3.2 1.0 + - - -
34A GLN* 3.4 23.6 + - - +
35A PRO* 4.5 2.1 - - - +
56A THR* 4.8 8.7 - - + -
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Residues in contact with ARG 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A MET 5.1 0.6 + - - -
28A SER* 2.9 41.9 + - - +
29A TRP* 3.7 37.2 - - - +
30A VAL 3.3 0.2 - - - -
31A GLU* 1.3 76.5 - - + +
33A HIS* 1.3 73.7 + - + +
34A GLN 3.6 0.4 - - - -
35A PRO* 4.6 4.7 - - - +
120A VAL* 4.4 12.1 - - - +
124A ASP* 4.9 3.6 + - - -
139B LEU* 5.9 3.6 - - - +
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Residues in contact with HIS 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A TRP* 2.8 55.2 + + + +
30A VAL 3.0 5.7 + - - +
32A ARG* 1.3 93.0 + - + +
34A GLN* 1.3 65.7 + - - +
35A PRO* 3.3 4.5 - - - -
36A LEU* 3.2 9.1 + - + +
37A LEU* 2.9 27.2 + - + +
124A ASP* 3.6 12.6 + - - -
127A ILE* 3.9 38.2 - - + +
128A GLN* 5.4 6.7 - - + -
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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