Contacts of the helix formed by residues 23 - 34 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22L TYR* 1.3 85.1 - - - +
24L GLU* 1.3 74.3 + - - +
25L LEU* 3.0 14.9 + - - +
26L GLU* 2.6 34.1 + - - +
27L ALA* 3.3 7.6 + - - +
102L ARG 3.4 6.5 - - - -
103L ALA* 3.4 10.8 - - + -
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Residues in contact with GLU 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194K TRP* 6.1 1.1 - - + -
23L THR* 1.3 82.3 - - - +
25L LEU* 1.3 52.9 + - - +
27L ALA* 3.2 6.4 + - - +
28L ILE* 2.7 42.5 + - + +
49L GLU* 3.9 17.9 - - + -
54L PHE* 3.6 15.3 - - + -
102L ARG* 2.3 70.5 + - - +
103L ALA* 4.3 4.2 - - - +
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Residues in contact with LEU 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29K MET* 4.9 5.6 - - + -
190K LEU* 3.4 49.4 - - + +
194K TRP* 3.7 26.1 - - + -
23L THR* 3.0 12.0 + - - +
24L GLU* 1.3 77.0 - - - +
26L GLU* 1.3 81.1 + - - +
28L ILE* 3.0 6.4 + - - +
29L MET* 2.8 38.2 + - + +
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Residues in contact with GLU 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L TYR* 4.4 8.5 - - - +
21L ALA 5.1 2.0 - - - +
22L TYR* 3.9 24.7 - - + -
23L THR* 2.6 44.0 + - - -
25L LEU* 1.3 91.6 - - - +
27L ALA* 1.3 61.9 + - - +
29L MET* 3.5 17.7 + - + +
30L TYR* 3.0 21.8 + - - +
60L PHE* 3.8 11.4 - - + -
191L SER* 4.7 2.6 + - - -
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Residues in contact with ALA 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L TYR* 4.9 5.2 - - + -
23L THR 3.3 9.3 + - - +
24L GLU* 3.2 13.2 + - - +
25L LEU 3.0 0.8 - - - -
26L GLU* 1.3 76.0 - - - +
28L ILE* 1.3 66.5 + - - +
30L TYR* 3.0 7.1 + - - +
31L ALA* 2.9 21.7 + - - +
46L PHE 5.0 0.9 - - - -
54L PHE* 4.4 11.7 - - + -
56L CYS* 4.0 28.7 - - + -
57L LEU 5.7 1.4 + - - +
60L PHE* 4.2 12.4 - - - -
102L ARG 5.0 1.6 - - - +
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Residues in contact with ILE 28 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186K ALA 5.0 0.9 - - - +
189K ARG* 4.5 0.7 - - - +
190K LEU* 4.0 16.6 - - + -
194K TRP* 4.3 12.3 - - + -
24L GLU 2.7 27.9 + - - +
25L LEU 3.6 2.9 - - - +
27L ALA* 1.3 72.5 - - - +
29L MET* 1.3 63.2 + - - +
31L ALA* 3.2 2.1 + - - +
32L LEU* 2.9 29.2 + - + +
46L PHE 3.8 9.0 - - - +
47L ILE* 3.2 44.4 - - + +
49L GLU* 3.5 30.3 - - + +
54L PHE* 3.7 19.5 - - + -
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Residues in contact with MET 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25K LEU* 4.9 5.4 - - + -
29K MET* 3.3 35.0 - - + +
187K LEU* 5.6 0.2 - - + -
190K LEU* 3.8 21.5 - - + +
25L LEU* 2.8 29.9 + - + +
26L GLU* 3.5 29.6 - - + +
28L ILE* 1.3 77.7 - - - +
30L TYR* 1.3 62.4 + - - +
32L LEU* 3.5 3.1 + - - +
33L GLY* 3.0 20.4 + - - -
187L LEU* 4.9 14.4 - - + +
188L TYR* 6.0 0.3 - - - -
190L LEU* 4.1 34.3 - - + +
191L SER* 4.4 7.3 + - - +
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Residues in contact with TYR 30 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26L GLU 3.0 13.0 + - - +
27L ALA 3.0 9.9 + - - +
29L MET* 1.3 75.5 - - - +
31L ALA* 1.3 68.6 + - - +
33L GLY* 3.1 4.4 + - - -
34L VAL* 2.8 41.5 + - + +
57L LEU* 4.3 11.4 - - + -
59L THR* 2.7 43.2 + - - -
60L PHE* 3.7 32.5 - + + -
62L VAL* 5.3 1.3 - - + +
63L ILE* 3.1 30.7 - - + -
188L TYR* 3.5 33.1 + + - -
191L SER* 3.7 10.0 + - - +
217L LEU 4.3 4.3 + - - -
220L PHE* 5.0 1.4 - - - -
221L GLY* 3.8 11.8 - - - -
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Residues in contact with ALA 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L ALA 2.9 11.1 + - - +
28L ILE 3.5 7.4 - - - +
30L TYR* 1.3 77.9 - - + +
32L LEU* 1.3 62.3 + - - +
34L VAL* 3.1 9.3 + - - +
35L GLY 3.2 0.7 + - - -
36L ALA* 3.1 33.9 + - + +
46L PHE* 3.6 24.9 - - + +
47L ILE* 5.2 1.3 - - + -
57L LEU* 3.8 29.4 - - + +
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Residues in contact with LEU 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183K ASN* 4.1 20.2 - - + +
186K ALA* 3.6 33.9 - - + +
187K LEU* 3.9 20.9 - - + +
190K LEU* 4.3 8.1 - - + -
28L ILE* 2.9 27.2 + - + +
29L MET* 3.8 3.8 - - - +
31L ALA* 1.3 76.2 - - - +
33L GLY* 1.3 59.9 + - - +
34L VAL 3.0 5.4 + - - -
35L GLY* 3.1 13.5 + - - -
36L ALA 3.6 19.9 - - - +
47L ILE* 4.1 17.9 - - + -
184L GLN* 3.9 5.2 + - - -
187L LEU* 4.0 14.0 - - + +
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Residues in contact with GLY 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L MET 3.0 14.7 + - - -
30L TYR* 3.5 4.5 - - - -
32L LEU* 1.3 76.5 - - - +
34L VAL* 1.3 57.1 + - - +
184L GLN* 2.9 19.1 + - - -
187L LEU* 3.6 22.6 - - - +
188L TYR* 3.8 18.1 - - - +
218L CYS* 3.2 17.7 - - - -
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Residues in contact with VAL 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30L TYR* 2.8 34.0 + - + +
31L ALA 3.5 10.8 - - - +
32L LEU 3.0 0.8 - - - -
33L GLY* 1.3 80.2 - - - +
35L GLY* 1.3 48.5 + - - +
57L LEU* 3.7 25.6 - - + -
59L THR* 5.5 0.2 - - - +
188L TYR* 4.3 7.4 - - + -
218L CYS* 3.6 9.0 - - - +
221L GLY* 3.2 37.2 - - - +
222L PHE* 3.3 18.6 - - - -
225L ARG* 2.3 34.1 + - - -
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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