Contacts of the helix formed by residues 21 - 34 (chain O) in PDB entry 3SDI
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 LEU 21 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13O THR* 3.8 14.1 - - + -
14O THR 3.2 32.8 - - - +
15O PHE* 3.7 34.8 - - + +
19O GLY 3.9 0.6 + - - +
20O LYS* 1.3 75.1 - - - +
22O GLY* 1.3 65.4 + - - +
23O GLN 3.4 2.5 - - - -
24O ILE* 3.2 41.1 + - + +
25O ASP* 3.2 16.4 + - - +
30P SER* 5.6 0.4 - - - +
81P LEU* 4.0 24.0 - - + -
130P ARG* 3.9 21.8 - - - +
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Residues in contact with GLY 22 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13O THR* 5.0 0.4 - - - +
14O THR 4.0 7.3 + - - +
16O SER* 5.6 2.9 + - - +
20O LYS* 3.7 6.3 + - - +
21O LEU* 1.3 70.4 - - - +
23O GLN* 1.3 57.7 + - - +
25O ASP* 3.1 11.4 + - - +
26O TYR* 2.9 49.3 + - - -
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Residues in contact with GLN 23 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12O LEU* 3.5 25.3 + - + +
13O THR* 3.3 23.1 - - + +
21O LEU 3.4 0.6 - - - -
22O GLY* 1.3 74.2 - - - +
24O ILE* 1.3 58.0 + - - +
26O TYR* 3.9 11.7 - - - -
27O ALA* 2.9 28.6 + - - +
130O ARG* 4.6 0.6 - - - +
131O PRO* 3.7 15.7 - - + +
14U ILE* 3.5 28.2 - - + +
15U PHE* 3.0 59.7 + - - +
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Residues in contact with ILE 24 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13O THR* 3.9 4.9 - - + -
21O LEU* 3.2 41.9 + - + +
23O GLN* 1.3 74.0 - - - +
25O ASP* 1.3 64.6 + - - +
27O ALA* 3.4 7.8 + - - +
28O LEU* 2.9 38.7 + - + +
124O THR* 3.6 36.6 - - + +
131O PRO* 4.3 8.1 - - + -
153O PRO* 4.4 5.1 - - + +
154O SER* 4.0 35.2 - - - +
81P LEU* 5.7 2.7 - - + -
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Residues in contact with ASP 25 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20O LYS* 3.4 44.0 + - - +
21O LEU 3.2 10.5 + - - +
22O GLY* 3.1 10.4 + - - +
24O ILE* 1.3 78.7 - - - +
26O TYR* 1.3 65.8 + - + +
28O LEU* 3.0 18.0 + - - +
29O THR* 2.9 29.8 + - - -
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Residues in contact with TYR 26 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22O GLY* 2.9 35.5 + - - +
23O GLN* 4.0 13.2 - - - +
25O ASP* 1.3 82.7 - - + +
27O ALA* 1.3 56.8 + - - +
29O THR* 3.2 11.3 + - - -
30O ALA 2.9 23.6 + - - -
15U PHE* 3.6 31.4 - - + -
16U SER 3.6 17.9 - - - +
17U PRO* 3.6 43.7 - - + +
19U GLY* 3.5 9.5 - - - -
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Residues in contact with ALA 27 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23O GLN 2.9 18.1 + - - +
24O ILE* 3.4 7.9 - - - +
26O TYR* 1.3 73.6 - - - +
28O LEU* 1.3 58.9 + - - +
30O ALA* 3.1 5.3 + - - +
31O VAL* 2.9 31.6 + - - +
131O PRO* 4.3 3.6 - - + -
132O PHE 3.8 8.3 - - - +
133O GLY* 4.4 1.5 - - - -
153O PRO* 3.7 20.9 - - + -
15U PHE* 3.8 27.7 - - + -
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Residues in contact with LEU 28 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24O ILE* 2.9 30.6 + - + +
25O ASP* 3.0 19.9 + - - +
27O ALA* 1.3 72.2 - - - +
29O THR* 1.3 56.4 + - - +
31O VAL* 3.0 10.6 + - + +
32O LYS* 2.8 32.9 + - + +
135O SER* 4.8 4.0 - - - +
152O ASP* 4.2 22.2 - - + +
153O PRO* 4.2 19.3 - - + -
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Residues in contact with THR 29 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25O ASP* 2.9 17.0 + - - +
26O TYR* 3.2 10.6 + - - -
28O LEU* 1.3 76.3 - - - +
30O ALA* 1.3 62.0 + - - +
32O LYS* 3.1 22.8 + - + +
33O GLN* 3.2 24.2 - - - +
17U PRO 3.9 15.3 + - - +
18U GLU* 3.8 24.0 - - - +
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Residues in contact with ALA 30 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26O TYR 2.9 12.3 + - - +
27O ALA 3.1 9.2 + - - +
29O THR* 1.3 74.8 - - - +
31O VAL* 1.3 63.4 + - - +
33O GLN* 3.2 21.8 + - - +
34O GLY 3.5 6.2 + - - -
80O GLY* 4.0 8.8 - - - -
81O MET* 4.6 13.2 - - + -
133O GLY 4.7 3.6 - - - +
15U PHE* 4.2 15.0 - - + -
19U GLY* 3.7 23.7 - - - +
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Residues in contact with VAL 31 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27O ALA 2.9 19.8 + - - +
28O LEU* 3.3 11.9 - - + +
30O ALA* 1.3 74.6 - - - +
32O LYS* 1.3 58.4 + - - +
34O GLY* 2.9 19.8 + - - -
79O SER* 3.4 20.0 - - - +
80O GLY* 3.9 8.7 + - - -
133O GLY 3.9 0.9 - - - +
134O VAL* 3.5 38.4 - - - +
135O SER* 3.5 24.0 - - - +
153O PRO* 4.2 7.0 - - + -
165O ILE* 5.0 2.2 - - + -
166O GLY* 3.5 16.8 - - - +
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Residues in contact with LYS 32 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28O LEU* 2.8 15.0 + - + +
29O THR* 3.2 19.3 - - + +
31O VAL* 1.3 76.9 - - - +
33O GLN* 1.3 60.7 + - - +
34O GLY 3.2 0.2 - - - -
166O GLY* 3.3 19.8 - - - +
167O LYS* 2.9 51.5 + - - +
169O SER* 3.4 16.8 + - - -
170O VAL* 4.0 15.4 - - - +
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Residues in contact with GLN 33 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29O THR* 3.2 26.9 + - - +
30O ALA* 3.2 13.6 + - - +
32O LYS* 1.3 77.9 - - - +
34O GLY* 1.3 64.1 + - - +
35O VAL* 3.8 0.5 + - - +
167O LYS* 4.2 17.1 + - - +
18U GLU* 3.2 23.1 - - - +
19U GLY 5.6 1.1 - - - +
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Residues in contact with GLY 34 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30O ALA 3.5 3.4 + - - -
31O VAL 2.9 15.8 + - - -
33O GLN* 1.3 80.2 - - - +
35O VAL* 1.3 63.3 + - - +
79O SER* 4.7 0.2 - - - -
80O GLY* 3.9 23.3 - - - -
166O GLY* 4.4 0.2 - - - -
167O LYS* 2.7 34.3 + - - +
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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