Contacts of the helix formed by residues 21 - 32 (chain C) in PDB entry 3SWD
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 ALA 21 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20C GLY* 1.3 69.2 - - - -
22C LYS* 1.3 65.1 + - - +
23C ASN 4.4 1.6 - - - +
24C ALA* 3.6 11.2 - - + +
25C ALA* 2.9 25.5 + - - +
45C PRO* 4.5 0.7 - - - -
190C GLU* 4.5 10.8 - - + +
228C VAL* 3.6 2.9 - - - +
229C LEU* 2.7 40.1 + - + +
230C PRO 3.9 1.1 - - - +
231C ASP* 3.5 22.5 - - - +
232C ARG 5.2 0.2 - - - +
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Residues in contact with LYS 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C GLY 3.2 3.0 + - - -
21C ALA* 1.3 72.2 - - - +
23C ASN* 1.3 81.8 + - - +
25C ALA* 3.4 1.8 + - - +
26C LEU* 3.1 39.7 + - + +
45C PRO* 4.2 8.7 - - - -
47C LEU* 4.1 26.2 - - + -
49C ASP* 3.1 27.8 + - - -
50C VAL* 5.9 0.2 - - - -
231C ASP* 3.1 10.6 + - - +
370C LEU* 3.5 17.7 - - - -
371C ARG* 3.7 21.1 - - - +
397C ARG 3.8 5.8 - - - +
398C GLY* 3.7 21.3 - - - -
501C EPZ 2.6 25.9 + - - +
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Residues in contact with ASN 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ALA* 3.2 2.0 - - - +
22C LYS* 1.3 105.4 + - - +
24C ALA* 1.3 56.4 + - - +
26C LEU* 4.7 2.5 - - - +
27C PRO* 3.1 22.7 - - - +
95C TRP* 4.9 0.2 - - - -
190C GLU* 3.3 27.5 - - + +
231C ASP* 4.8 0.2 + - - -
233C ILE* 6.0 0.8 - - - +
305C ASP* 4.1 8.7 + - - -
371C ARG* 4.3 11.8 - - - +
501C EPZ 3.1 61.5 + - - +
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Residues in contact with ALA 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ALA* 3.1 18.6 + - + +
23C ASN* 1.3 76.2 - - - +
25C ALA* 1.3 67.6 + - - +
26C LEU 3.2 1.6 - - - -
27C PRO* 3.0 11.9 - - - +
28C ILE* 3.1 24.6 + - + +
190C GLU* 3.8 12.7 - - + +
193C ASP* 4.0 11.4 - - + +
194C THR* 5.0 0.2 - - - -
228C VAL* 3.7 17.7 - - + -
229C LEU* 3.7 13.9 - - + -
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Residues in contact with ALA 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ALA 2.9 16.3 + - - +
22C LYS 3.7 4.9 - - - +
24C ALA* 1.3 78.3 - - - +
26C LEU* 1.3 57.0 + - - +
28C ILE* 3.4 1.0 + - - +
29C LEU* 2.9 41.1 + - + +
44C VAL* 4.2 31.0 - - + -
45C PRO* 4.3 8.3 - - + -
50C VAL* 4.5 9.2 - - + -
228C VAL* 4.2 12.7 - - + +
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Residues in contact with LEU 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C LYS* 3.1 23.2 + - + +
23C ASN* 4.7 2.2 - - - +
25C ALA* 1.3 80.5 - - - +
27C PRO* 1.3 67.7 - - + +
29C LEU* 3.4 3.3 + - + +
30C PHE* 3.0 33.3 + - + -
49C ASP* 4.0 33.0 - - + +
50C VAL* 4.2 16.2 - - + -
53C SER* 3.5 22.0 - - - +
90C MET* 3.9 25.6 - - + -
92C ALA* 4.2 15.3 - - + -
95C TRP* 4.2 9.4 - - + -
501C EPZ 4.5 9.2 - - + -
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Residues in contact with PRO 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ASN 3.1 25.8 - - - +
24C ALA 3.0 17.5 - - - +
26C LEU* 1.3 85.0 - - + +
28C ILE* 1.3 58.3 + - - +
30C PHE* 3.3 4.7 + - + +
31C ALA* 2.9 29.1 + - - +
95C TRP* 3.4 32.8 - - + -
167C VAL* 4.1 23.2 - - + +
190C GLU* 5.3 1.8 - - + +
194C THR* 3.4 21.4 - - + +
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Residues in contact with ILE 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ALA* 3.1 21.7 + - + +
25C ALA* 3.6 3.6 - - - +
27C PRO* 1.3 73.8 - - - +
29C LEU* 1.3 66.3 + - - +
31C ALA* 3.0 8.3 + - - +
32C ALA* 3.0 20.7 + - - +
41C ILE* 3.5 33.2 - - + -
193C ASP* 4.1 26.7 - - - +
194C THR* 4.0 13.7 - - - +
197C PHE* 3.7 35.1 - - + -
226C TYR* 4.3 5.2 - - + -
228C VAL* 3.9 20.9 - - + -
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Residues in contact with LEU 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ALA* 2.9 34.9 + - + +
26C LEU* 3.4 5.6 + - - +
27C PRO 3.4 0.2 - - - -
28C ILE* 1.3 75.9 - - + +
30C PHE* 1.3 58.9 + - + +
32C ALA* 3.2 20.8 - - - +
33C LEU 4.2 0.3 + - - -
41C ILE* 4.4 25.6 - - + -
44C VAL* 4.9 1.3 - - + -
50C VAL* 4.1 27.1 - - + +
53C SER* 3.9 26.0 - - - -
54C MET* 4.5 9.2 - - + -
57C LEU* 3.7 24.9 - - + +
70C VAL* 4.6 10.8 - - + -
72C ILE* 3.9 22.9 - - + -
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Residues in contact with PHE 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C LEU* 3.0 28.0 + - + -
27C PRO 3.3 6.8 + - - +
28C ILE 3.2 0.6 - - - -
29C LEU* 1.3 72.9 - - - +
31C ALA* 1.3 63.5 + - - +
32C ALA 3.1 1.8 - - - -
33C LEU* 3.3 17.3 + - + +
53C SER* 3.7 32.3 - - - -
56C LEU* 3.5 36.1 - - + -
57C LEU* 4.4 17.7 - - + -
90C MET* 4.1 9.9 - - + -
92C ALA* 4.1 10.5 - - + -
93C SER* 4.1 15.0 - - - -
95C TRP* 3.8 33.2 - + + +
96C ALA* 4.0 18.2 - - + -
99C PRO* 3.4 16.7 - - + +
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Residues in contact with ALA 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C PRO 2.9 17.3 + - - +
28C ILE* 3.0 6.2 + - - +
30C PHE* 1.3 71.8 - - - +
32C ALA* 1.3 60.0 + - - +
33C LEU 3.0 2.5 - - - -
34C LEU* 2.8 32.2 + - - +
35C ALA 4.1 0.9 + - - -
99C PRO* 4.4 8.5 - - - -
171C CYS* 4.1 15.0 - - - -
194C THR* 4.7 2.5 - - + -
197C PHE* 3.9 19.4 - - + -
198C LEU* 3.9 20.2 - - + +
201C LEU* 5.0 1.0 - - - +
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Residues in contact with ALA 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ILE 3.0 9.8 + - - +
29C LEU 3.2 16.8 - - - +
31C ALA* 1.3 78.1 - - - +
33C LEU* 1.3 54.4 + - - +
34C LEU 2.9 0.2 - - - -
35C ALA* 2.8 30.4 + - - +
39C VAL* 4.2 12.6 - - + -
41C ILE* 5.4 0.2 - - + -
57C LEU* 5.5 0.4 - - + -
72C ILE* 3.7 33.0 - - + -
74C ALA* 3.6 10.7 - - - +
197C PHE* 4.1 11.9 - - + -
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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