Contacts of the helix formed by residues 22 - 33 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B ALA* 4.2 1.3 - - - -
19B HIS 2.8 7.7 + - - +
21B HIS* 1.3 84.4 - - - +
23B LYS* 1.3 58.2 + - - +
24B GLN 3.3 3.1 - - - -
25B MET* 3.1 25.7 + - + +
26B LEU* 2.9 26.3 + - - +
89B PHE* 3.3 38.9 - - + +
90B TRP 3.6 22.0 - - - -
91B ASP* 3.8 13.2 - - - -
92B PRO* 4.6 5.4 - - - -
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Residues in contact with LYS 23 (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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18B ALA* 2.9 32.2 + - + +
19B HIS* 3.0 8.7 + - - +
20B ASP* 2.7 42.0 + - - +
22B CYS* 1.3 77.6 - - - +
24B GLN* 1.3 57.4 + - - +
26B LEU* 3.3 2.2 + - + +
27B MET* 2.8 37.7 + - + +
47B THR* 3.7 20.9 - - + -
48B THR* 3.8 17.3 - - + +
51B LEU* 3.6 24.7 - - + -
202B PGA 2.9 24.8 + - - -
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Residues in contact with GLN 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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20B ASP 4.7 1.2 + - - -
21B HIS 5.3 1.3 - - - +
22B CYS 3.3 0.6 - - - -
23B LYS* 1.3 78.4 - - - +
25B MET* 1.3 62.7 + - - +
27B MET* 3.3 8.7 + - - +
28B SER* 3.0 26.5 + - - -
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Residues in contact with MET 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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3A LEU* 5.3 17.9 - - + -
21B HIS 5.4 3.5 + - - +
22B CYS* 3.1 27.7 + - - +
24B GLN* 1.3 80.7 - - - +
26B LEU* 1.3 59.9 + - - +
28B SER* 3.8 4.7 + - - -
29B TRP* 3.4 20.6 + - - +
89B PHE* 4.2 15.9 - - + -
119B ASN* 6.1 1.6 - - - -
120B VAL* 4.0 27.3 - - + +
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Residues in contact with LEU 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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16B LEU* 4.5 9.9 - - + -
17B VAL 4.2 6.3 - - - +
18B ALA* 3.5 19.3 - - + -
22B CYS 2.9 12.9 + - - +
23B LYS* 3.7 6.7 - - + +
25B MET* 1.3 75.7 - - - +
27B MET* 1.3 67.9 + - - +
29B TRP* 3.0 8.1 + - + +
30B VAL* 2.9 42.8 + - + +
48B THR* 3.5 32.5 - - + -
52B ILE* 4.4 7.2 - - + -
87B ILE* 4.3 18.6 - - + -
89B PHE* 3.9 28.7 - - + -
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Residues in contact with MET 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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23B LYS* 2.8 29.6 + - + +
24B GLN* 3.5 9.2 - - - +
26B LEU* 1.3 77.4 - - - +
28B SER* 1.3 63.1 + - - +
30B VAL* 3.2 6.4 + - + +
31B GLU* 3.0 36.7 + - - +
48B THR* 5.0 1.1 - - - +
51B LEU* 3.9 21.1 - - + +
52B ILE* 3.6 48.2 - - + -
55B ALA* 3.9 16.6 - - + -
56B THR* 4.8 7.9 - - + -
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Residues in contact with SER 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 GLN 3.0 13.9 + - - -
25B MET* 4.1 5.8 - - - -
27B MET* 1.3 79.8 - - - +
29B TRP* 1.3 63.0 + - - +
31B GLU* 3.4 10.9 + - - +
32B ARG* 3.0 39.5 + - - +
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Residues in contact with TRP 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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16B LEU* 4.5 9.9 - - + -
25B MET 3.4 12.3 + - - +
26B LEU* 3.0 18.9 + - + +
28B SER* 1.3 79.6 - - - +
30B VAL* 1.3 74.2 + - + +
32B ARG* 3.5 23.4 + - - +
33B HIS* 3.2 44.3 + + - +
37B LEU* 4.2 20.4 - - + -
87B ILE* 4.4 23.3 - - + -
89B PHE* 4.5 7.9 - + + -
120B VAL* 3.9 15.5 - - + -
123B ALA* 3.4 43.4 - - + +
124B ASP* 2.6 27.2 + - - -
127B ILE* 3.9 21.8 - - + -
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Residues in contact with VAL 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 LEU* 4.5 9.4 - - + -
26B LEU* 2.9 35.4 + - + +
27B MET* 3.5 9.2 - - + +
29B TRP* 1.3 82.3 - - + +
31B GLU* 1.3 60.2 + - - +
33B HIS 3.4 1.7 + - - -
34B GLN* 2.9 27.5 + - - +
37B LEU* 3.7 16.9 - - + +
42B LEU* 5.7 0.2 - - + -
52B ILE* 4.2 27.6 - - + -
56B THR* 4.6 4.7 - - + -
58B MET* 3.4 28.5 - - + -
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Residues in contact with GLU 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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27B MET* 3.0 33.7 + - + +
28B SER* 3.4 9.1 + - - +
30B VAL* 1.3 75.7 - - - +
32B ARG* 1.3 64.2 + - - +
33B HIS 3.3 0.5 + - - -
34B GLN* 3.4 23.2 + - - +
35B PRO* 4.5 2.3 - - - +
55B ALA* 4.8 12.0 - - - +
56B THR* 4.2 19.7 - - + -
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Residues in contact with ARG 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 SER* 3.0 28.5 + - - +
29B TRP* 3.6 35.5 - - - +
30B VAL 3.3 0.2 - - - -
31B GLU* 1.3 78.4 - - - +
33B HIS* 1.3 80.5 + - + +
34B GLN 3.5 0.4 + - - -
35B PRO* 4.3 6.1 - - - +
120B VAL* 4.2 13.9 - - - +
124B ASP* 4.7 6.1 + - - -
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Residues in contact with HIS 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 TRP* 3.2 48.7 + + - +
30B VAL 3.5 2.2 - - - -
31B GLU 3.2 0.2 - - - -
32B ARG* 1.3 101.0 + - + +
34B GLN* 1.3 63.7 + - - +
35B PRO* 3.3 5.2 - - - -
36B LEU* 3.0 11.1 + - + +
37B LEU* 2.9 25.3 + - + +
124B ASP* 3.0 25.9 + - + -
127B ILE* 3.9 32.1 - - + +
128B GLN* 5.5 9.0 - - + -
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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