Contacts of the helix formed by residues 23 - 34 (chain J) in PDB entry 1S9C
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 THR 23 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22J TYR* 1.3 86.3 - - - +
24J GLU* 1.3 73.6 + - - +
25J LEU* 3.0 15.6 + - - +
26J GLU* 2.7 32.2 + - - +
27J ALA* 3.4 7.3 + - - +
102J ARG 3.8 5.2 - - - -
103J ALA* 3.7 10.5 - - + -
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Residues in contact with GLU 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194I TRP* 6.0 1.1 - - + -
23J THR* 1.3 81.8 - - - +
25J LEU* 1.3 51.4 + - - +
27J ALA* 3.1 7.2 + - - +
28J ILE* 2.8 41.4 + - + +
49J GLU* 3.9 17.5 - - + -
54J PHE* 3.5 24.5 - - + -
102J ARG* 2.9 56.3 + - - +
103J ALA* 4.0 7.5 - - - +
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Residues in contact with LEU 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I MET* 4.7 6.5 - - + -
190I LEU* 3.7 46.7 - - + +
194I TRP* 3.8 23.1 - - + -
23J THR* 3.0 13.7 + - - +
24J GLU* 1.3 78.7 - - - +
26J GLU* 1.3 80.3 + - - +
27J ALA 3.0 0.5 + - - -
28J ILE* 3.0 3.1 + - - +
29J MET* 2.8 40.0 + - + +
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Residues in contact with GLU 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J TYR* 3.3 27.1 - - + +
21J ALA 5.1 1.1 - - - +
22J TYR* 3.9 16.4 - - + -
23J THR* 2.7 42.4 + - - +
25J LEU* 1.3 91.6 - - - +
27J ALA* 1.3 57.1 + - - +
29J MET* 3.6 18.4 - - + +
30J TYR* 3.1 26.5 + - - +
60J PHE* 3.8 8.0 - - + -
191J SER* 4.6 2.4 + - - -
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Residues in contact with ALA 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J TYR* 5.0 4.5 - - + -
23J THR 3.4 8.7 + - - +
24J GLU* 3.1 13.6 + - - +
25J LEU 3.0 0.2 - - - -
26J GLU* 1.3 77.7 - - - +
28J ILE* 1.3 65.8 + - - +
30J TYR* 3.1 7.4 + - - +
31J ALA* 3.0 21.2 + - - +
46J PHE 5.0 0.9 - - - -
54J PHE* 4.4 11.9 - - + -
56J CYS* 4.0 28.9 - - + -
57J LEU 5.8 1.9 + - - -
60J PHE* 4.3 10.9 - - - -
102J ARG 5.1 1.6 - - - +
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Residues in contact with ILE 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186I ALA 5.1 0.7 - - - +
189I ARG* 5.5 0.2 - - - +
190I LEU* 3.9 17.9 - - + -
194I TRP* 4.1 13.9 - - + -
24J GLU 2.8 27.0 + - - +
25J LEU 3.7 2.7 - - - +
27J ALA* 1.3 68.5 - - - +
29J MET* 1.3 66.7 + - - +
31J ALA* 3.1 1.9 + - - +
32J LEU* 2.9 29.3 + - + +
46J PHE 3.8 9.9 - - - +
47J ILE* 3.2 46.7 - - + +
49J GLU* 3.6 28.0 - - + +
54J PHE* 3.7 19.1 - - + -
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Residues in contact with MET 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I LEU* 4.6 6.7 - - + -
29I MET* 3.2 34.5 - - + +
190I LEU* 3.9 22.1 - - + +
25J LEU* 2.8 30.3 + - + +
26J GLU* 3.6 29.6 - - + +
28J ILE* 1.3 77.6 - - - +
30J TYR* 1.3 62.5 + - - +
32J LEU* 3.5 3.5 + - - +
33J GLY* 3.0 20.1 + - - -
187J LEU* 4.9 12.3 - - + +
188J TYR* 5.9 0.2 - - - -
190J LEU* 4.1 34.1 - - + +
191J SER* 4.2 8.3 + - - +
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Residues in contact with TYR 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J GLU 3.1 16.1 + - - +
27J ALA 3.1 8.9 + - - +
29J MET* 1.3 76.4 - - - +
31J ALA* 1.3 60.9 + - - +
33J GLY* 3.2 3.2 + - - -
34J VAL* 2.9 47.9 + - + +
57J LEU* 4.4 11.4 - - + -
59J THR* 2.7 44.0 + - - -
60J PHE* 3.7 32.8 - + + -
62J VAL* 5.3 1.9 - - + +
63J ILE* 3.1 30.7 - - + -
188J TYR* 3.5 31.4 + + - -
191J SER* 3.6 10.3 + - - +
217J LEU 4.4 4.5 + - - -
220J PHE* 5.0 1.2 - - - -
221J GLY* 3.9 11.3 - - - -
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Residues in contact with ALA 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J ALA 3.0 10.9 + - - +
28J ILE 3.1 7.4 + - - +
30J TYR* 1.3 76.1 - - - +
32J LEU* 1.3 62.0 + - - +
34J VAL* 3.2 8.6 + - - +
35J GLY 3.2 0.5 + - - -
36J ALA* 3.0 29.3 + - + +
46J PHE* 3.5 31.2 - - + +
47J ILE* 5.1 1.3 - - + -
57J LEU* 3.8 29.4 - - + +
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Residues in contact with LEU 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183I ASN* 4.4 14.8 - - + +
186I ALA* 3.6 31.6 - - + +
187I LEU* 4.1 16.4 - - + +
190I LEU* 4.1 16.6 - - + -
28J ILE* 2.9 27.3 + - + +
29J MET* 3.8 4.0 - - - +
31J ALA* 1.3 71.8 - - - +
33J GLY* 1.3 61.3 + - - +
34J VAL 2.9 5.4 + - - -
35J GLY* 2.9 14.7 + - - -
36J ALA 3.6 19.4 - - - +
47J ILE* 4.1 21.5 - - + -
184J GLN* 3.7 5.7 + - - -
187J LEU* 3.9 15.6 - - + +
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Residues in contact with GLY 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J MET 3.0 14.8 + - - -
30J TYR 3.5 3.8 - - - -
32J LEU* 1.3 75.5 - - - +
34J VAL* 1.3 56.3 + - - +
184J GLN* 2.9 18.0 + - - -
187J LEU* 3.6 22.3 - - - +
188J TYR* 3.7 20.6 - - - +
218J CYS* 3.2 17.5 - - - -
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Residues in contact with VAL 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J TYR* 2.9 32.0 + - + +
31J ALA 3.2 10.7 + - - +
32J LEU 2.9 0.8 - - - -
33J GLY* 1.3 79.2 - - - +
35J GLY* 1.3 49.2 + - - +
57J LEU* 3.7 26.7 - - + -
59J THR* 5.5 0.2 - - - +
188J TYR* 4.2 11.4 - - + -
218J CYS* 3.5 10.5 - - - +
221J GLY* 3.2 36.8 - - - +
222J PHE* 3.2 20.0 - - - -
225J ARG* 2.5 32.4 + - - +
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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