Contacts of the helix formed by residues 23 - 34 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A TYR* 1.3 88.0 - - - +
24A GLU* 1.3 74.9 + - - +
25A LEU* 3.0 16.0 + - - +
26A GLU* 2.7 31.9 + - - +
27A ALA* 3.3 7.6 + - - +
102A ARG 3.6 6.1 - - - -
103A ALA* 3.4 10.1 - - + -
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Residues in contact with GLU 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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23A THR* 1.3 80.9 - - - +
25A LEU* 1.3 56.9 + - - +
27A ALA* 3.1 6.2 + - - +
28A ILE* 2.8 37.2 + - + +
49A GLU* 3.9 15.7 - - + -
54A PHE* 3.6 19.1 - - + -
102A ARG* 2.6 64.5 + - - +
103A ALA* 3.9 6.4 - - - +
194B TRP* 6.1 1.3 - - + -
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Residues in contact with LEU 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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23A THR* 3.0 11.3 + - - +
24A GLU* 1.3 77.3 - - - +
26A GLU* 1.3 81.1 + - - +
27A ALA 3.0 0.5 + - - -
28A ILE* 3.0 5.8 + - - +
29A MET* 2.8 40.5 + - + +
29B MET* 4.8 6.1 - - + -
190B LEU* 3.4 48.9 - - + +
194B TRP* 3.7 25.6 - - + -
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Residues in contact with GLU 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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20A TYR* 4.3 15.3 - - - +
21A ALA 5.1 1.8 - - - +
22A TYR* 3.8 23.3 - - + -
23A THR* 2.7 42.5 + - - +
25A LEU* 1.3 93.5 - - - +
27A ALA* 1.3 61.9 + - - +
29A MET* 3.5 19.5 + - + +
30A TYR* 3.1 21.3 + - - +
60A PHE* 3.8 8.1 - - + -
191A SER* 4.6 2.6 + - - -
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Residues in contact with ALA 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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22A TYR* 4.9 5.4 - - + -
23A THR 3.3 8.5 + - - +
24A GLU* 3.1 13.4 + - - +
25A LEU 3.0 0.4 - - - -
26A GLU* 1.3 76.7 - - - +
28A ILE* 1.3 65.9 + - - +
30A TYR* 2.9 8.0 + - - +
31A ALA* 2.9 21.4 + - - +
46A PHE 5.1 0.9 - - - -
54A PHE* 4.4 11.7 - - + -
56A CYS* 4.0 27.8 - - + -
57A LEU 5.9 1.3 + - - -
60A PHE* 4.2 11.6 - - - -
102A ARG 5.0 2.2 - - - +
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Residues in contact with ILE 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 GLU 2.8 28.4 + - - +
25A LEU 3.6 3.1 - - - +
27A ALA* 1.3 72.1 - - - +
29A MET* 1.3 64.1 + - - +
31A ALA* 3.1 2.1 + - - +
32A LEU* 2.9 28.9 + - + +
46A PHE 3.8 9.2 - - - +
47A ILE* 3.2 44.6 - - + +
49A GLU* 3.5 31.0 - - + +
54A PHE* 3.7 18.2 - - + -
186B ALA 4.9 1.1 - - - +
189B ARG* 4.6 1.1 - - - +
190B LEU* 3.9 18.2 - - + -
194B TRP* 4.4 10.8 - - + -
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Residues in contact with MET 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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25A LEU* 2.8 38.5 + - + +
26A GLU* 3.6 22.2 - - + +
28A ILE* 1.3 76.1 - - - +
30A TYR* 1.3 62.6 + - - +
32A LEU* 3.5 3.5 + - - +
33A GLY* 3.0 19.8 + - - -
187A LEU* 4.8 15.5 - - + +
188A TYR* 5.9 0.3 - - - -
190A LEU* 4.0 35.0 - - + +
191A SER* 4.3 7.5 + - - +
25B LEU* 4.7 7.2 - - + -
29B MET* 3.4 32.3 - - + +
190B LEU* 3.9 22.1 - - + +
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Residues in contact with TYR 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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26A GLU 3.1 13.0 + - - +
27A ALA 2.9 10.3 + - - +
29A MET* 1.3 77.2 - - - +
31A ALA* 1.3 67.9 + - - +
33A GLY* 3.1 3.5 + - - -
34A VAL* 2.8 42.1 + - + +
57A LEU* 4.4 11.7 - - + -
59A THR* 2.8 43.2 + - - -
60A PHE* 3.7 31.6 - + + -
62A VAL* 5.2 2.0 - - + +
63A ILE* 3.2 27.6 - - + -
188A TYR* 3.4 35.6 + + - -
191A SER* 3.7 10.0 + - - +
217A LEU 4.3 4.9 + - - -
220A PHE* 5.0 1.0 - - - -
221A GLY* 3.8 11.4 - - - -
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Residues in contact with ALA 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 ALA 2.9 11.1 + - - +
28A ILE 3.5 7.2 - - - +
30A TYR* 1.3 77.2 - - + +
32A LEU* 1.3 62.5 + - - +
34A VAL* 3.1 11.1 + - - +
35A GLY 3.2 0.7 + - - -
36A ALA* 3.1 26.1 + - + -
46A PHE* 3.5 30.5 - - + +
47A ILE* 5.1 1.6 - - + -
57A LEU* 3.8 27.8 - - + -
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Residues in contact with LEU 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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28A ILE* 2.9 24.5 + - + +
29A MET* 3.9 4.0 - - - +
31A ALA* 1.3 74.9 - - - +
33A GLY* 1.3 61.2 + - - +
34A VAL 2.9 5.4 + - - -
35A GLY* 3.0 13.3 + - - -
36A ALA 3.6 19.6 - - - +
47A ILE* 4.1 22.4 - - + -
184A GLN* 3.8 5.9 + - - -
187A LEU* 3.9 16.0 - - + +
183B ASN* 4.3 14.6 - - + +
186B ALA* 3.7 26.9 - - + +
187B LEU* 3.9 27.1 - - + -
190B LEU* 4.2 11.2 - - + -
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Residues in contact with GLY 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 MET 3.0 13.8 + - - -
30A TYR 3.5 4.7 - - - -
32A LEU* 1.3 75.1 - - - +
34A VAL* 1.3 57.0 + - - +
35A GLY 3.5 0.2 - - - -
184A GLN* 3.0 18.1 + - - -
187A LEU* 3.6 23.9 - - - +
188A TYR* 3.6 18.5 - - - +
218A CYS* 3.1 17.8 - - - -
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Residues in contact with VAL 34 (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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30A TYR* 2.8 33.1 + - + +
31A ALA 3.1 10.7 + - - +
32A LEU 2.9 0.8 - - - -
33A GLY* 1.3 79.2 - - - +
35A GLY* 1.3 49.0 + - - +
57A LEU* 3.8 24.2 - - + -
59A THR* 5.5 0.2 - - - +
188A TYR* 4.3 10.5 - - + -
218A CYS* 3.5 10.5 - - - +
221A GLY* 3.2 37.9 - - - +
222A PHE* 3.1 20.5 - - - -
225A ARG* 2.4 31.2 + - - +
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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