Contacts of the helix formed by residues 23 - 34 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22H TYR* 1.3 87.5 - - - +
24H GLU* 1.3 76.3 + - - +
25H LEU* 3.0 15.1 + - - +
26H GLU* 2.7 32.1 + - - +
27H ALA* 3.3 7.6 + - - +
102H ARG 4.0 5.2 - - - -
103H ALA* 3.8 8.5 - - + -
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Residues in contact with GLU 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194G TRP* 6.0 1.3 - - + -
23H THR* 1.3 80.6 - - - +
25H LEU* 1.3 52.9 + - - +
27H ALA* 3.1 7.0 + - - +
28H ILE* 2.8 41.0 + - + +
49H GLU* 3.9 26.9 - - + -
54H PHE* 3.6 21.5 - - + -
102H ARG* 3.1 48.3 + - - +
103H ALA* 4.1 6.0 - - - +
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Residues in contact with LEU 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G MET* 4.8 5.4 - - + -
190G LEU* 3.5 41.3 - - + +
194G TRP* 3.5 34.3 - - + -
23H THR* 3.0 12.4 + - - +
24H GLU* 1.3 78.1 - - - +
26H GLU* 1.3 79.7 + - - +
27H ALA 3.1 0.3 + - - -
28H ILE* 3.1 2.2 + - - +
29H MET* 2.9 40.8 + - + +
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Residues in contact with GLU 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H TYR* 3.9 18.8 - - - +
21H ALA 5.1 1.3 - - - +
22H TYR* 3.9 20.9 - - + -
23H THR* 2.7 43.1 + - - +
25H LEU* 1.3 94.5 - - - +
27H ALA* 1.3 60.7 + - - +
29H MET* 3.7 17.9 - - + +
30H TYR* 3.1 21.7 + - - +
60H PHE* 3.7 8.7 - - + -
191H SER* 4.7 2.4 + - - -
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Residues in contact with ALA 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H TYR* 5.0 5.2 - - + -
23H THR 3.3 8.9 + - - +
24H GLU* 3.1 13.2 + - - +
25H LEU 3.0 0.6 - - - -
26H GLU* 1.3 76.0 - - - +
28H ILE* 1.3 66.6 + - - +
30H TYR* 2.9 15.8 + - - +
31H ALA* 2.9 14.2 + - - +
46H PHE 5.0 0.9 - - - -
54H PHE* 4.4 12.6 - - + -
56H CYS* 4.0 28.0 - - + -
57H LEU 5.8 1.6 + - - +
60H PHE* 4.3 11.8 - - - -
102H ARG 5.2 1.1 - - - +
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Residues in contact with ILE 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186G ALA 5.0 0.9 - - - +
189G ARG* 5.4 0.2 - - - +
190G LEU* 3.8 17.7 - - + -
194G TRP* 4.0 14.4 - - + -
24H GLU 2.8 26.4 + - - +
25H LEU 3.7 2.7 - - - +
27H ALA* 1.3 72.2 - - - +
29H MET* 1.3 56.4 + - - +
31H ALA* 3.1 2.6 + - - +
32H LEU* 2.9 33.8 + - + +
46H PHE 3.8 9.4 - - - +
47H ILE* 3.2 45.1 - - + +
49H GLU* 3.5 31.0 - - + +
54H PHE* 3.7 19.1 - - + -
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Residues in contact with MET 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G LEU* 4.7 5.4 - - + -
29G MET* 3.3 36.3 - - + +
190G LEU* 3.7 22.8 - - + +
25H LEU* 2.9 37.7 + - + +
26H GLU* 3.7 21.5 - - + +
28H ILE* 1.3 76.1 - - - +
30H TYR* 1.3 62.6 + - - +
32H LEU* 4.0 2.7 - - - +
33H GLY* 3.1 19.4 + - - -
187H LEU* 4.8 11.6 - - + +
190H LEU* 4.0 35.7 - - + +
191H SER* 4.2 7.0 + - - +
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Residues in contact with TYR 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H GLU 3.1 12.6 + - - +
27H ALA 2.9 10.6 + - - +
29H MET* 1.3 74.7 - - - +
31H ALA* 1.3 63.8 + - - +
33H GLY* 3.1 3.4 + - - -
34H VAL* 2.8 55.9 + - + +
57H LEU* 4.3 12.3 - - + -
59H THR* 2.8 42.8 + - - -
60H PHE* 3.7 32.8 - + + -
62H VAL* 5.2 2.0 - - + +
63H ILE* 3.2 29.6 - - + -
188H TYR* 3.4 34.4 + + - -
191H SER* 3.5 10.7 + - - +
217H LEU 4.4 2.4 + - - -
220H PHE* 5.1 1.4 - - - -
221H GLY* 3.9 4.7 - - - -
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Residues in contact with ALA 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H ALA 2.9 10.3 + - - +
28H ILE 3.1 8.3 + - - +
30H TYR* 1.3 76.6 - - - +
32H LEU* 1.3 62.2 + - - +
34H VAL* 3.0 11.5 + - - +
35H GLY 3.2 0.7 + - - -
36H ALA* 3.1 30.9 + - + -
46H PHE* 3.6 25.8 - - + +
47H ILE* 5.1 1.1 - - + -
57H LEU* 3.9 28.9 - - + +
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Residues in contact with LEU 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183G ASN* 4.5 10.3 - - + +
186G ALA* 3.5 37.5 - - + +
187G LEU* 3.9 15.9 - - + +
190G LEU* 4.0 17.0 - - + -
28H ILE* 2.9 27.2 + - + +
29H MET* 4.0 3.1 - - - +
31H ALA* 1.3 70.7 - - - +
33H GLY* 1.3 61.3 + - - +
34H VAL 2.9 5.2 + - - -
35H GLY* 3.0 13.9 + - - -
36H ALA 3.6 19.9 - - - +
47H ILE* 4.1 22.0 - - + -
184H GLN* 3.8 5.4 + - - -
187H LEU* 3.8 15.3 - - + +
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Residues in contact with GLY 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H MET 3.1 12.4 + - - -
30H TYR 3.5 3.8 - - - -
32H LEU* 1.3 78.7 - - - +
34H VAL* 1.3 57.5 + - - +
35H GLY 3.5 0.2 - - - -
184H GLN* 2.9 18.3 + - - -
187H LEU* 3.5 23.9 - - - +
188H TYR* 3.7 19.6 - - - +
218H CYS* 3.2 16.3 - - - -
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Residues in contact with VAL 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H TYR* 2.8 33.5 + - + +
31H ALA 3.0 11.2 + - - +
32H LEU 2.9 0.6 - - - -
33H GLY* 1.3 79.1 - - - +
35H GLY* 1.3 48.3 + - - +
57H LEU* 3.7 25.1 - - + -
59H THR* 5.5 0.2 - - - +
188H TYR* 4.2 11.9 - - + -
218H CYS 3.6 9.9 - - - +
221H GLY* 3.2 35.7 - - - +
222H PHE* 3.2 20.5 - - - -
225H ARG* 2.4 33.2 + - - +
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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