Contacts of the helix formed by residues 21 - 33 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A THR* 3.7 14.6 - - + -
14A THR 3.5 26.0 - - - +
15A PHE* 3.9 24.2 - - + -
19A GLY 3.9 1.7 + - - +
20A LYS* 1.3 71.3 - - - +
22A GLY* 1.3 64.8 + - - +
23A GLN 3.4 2.2 - - - -
24A ILE* 3.0 43.1 + - + +
25A ASP* 3.2 15.1 + - - +
30B SER* 5.9 0.2 - - - +
81B LEU* 4.0 34.1 - - + -
130B ARG* 3.8 24.0 - - - +
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Residues in contact with GLY 22 (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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14A THR 4.0 7.1 + - - +
16A SER* 5.4 2.7 + - - -
20A LYS* 3.6 8.2 + - - -
21A LEU* 1.3 70.1 - - - +
23A GLN* 1.3 58.8 + - - +
25A ASP* 3.1 8.8 + - - +
26A TYR* 2.8 53.3 + - - -
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Residues in contact with GLN 23 (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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12A LEU* 3.7 22.4 - - + +
13A THR* 3.6 22.6 - - + +
21A LEU 3.2 1.0 + - - -
22A GLY* 1.3 74.9 - - - +
24A ILE* 1.3 57.2 + - - +
26A TYR* 3.9 13.2 - - - -
27A ALA* 2.9 30.5 + - - +
130A ARG* 4.4 1.1 - - - +
131A PRO* 3.8 13.4 - - + +
14G ILE* 3.6 27.9 - - + +
15G PHE* 2.7 64.8 + - - +
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Residues in contact with ILE 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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13A THR* 4.0 8.9 - - + +
21A LEU* 3.0 37.6 + - + +
23A GLN* 1.3 73.8 - - - +
25A ASP* 1.3 62.2 + - - +
27A ALA* 3.4 6.9 + - - +
28A LEU* 2.9 42.9 + - + +
124A THR* 3.7 40.6 - - + +
131A PRO* 4.3 6.1 - - + -
153A PRO* 4.7 3.5 - - + +
154A SER* 3.7 36.8 - - - +
81B LEU* 5.7 1.6 - - + -
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Residues in contact with ASP 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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20A LYS* 3.5 46.6 + - - +
21A LEU* 3.2 12.2 + - - +
22A GLY* 3.1 10.2 + - - +
24A ILE* 1.3 77.9 - - - +
26A TYR* 1.3 71.7 + - + +
28A LEU* 3.0 18.8 + - - +
29A THR* 3.0 23.5 + - - -
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Residues in contact with TYR 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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22A GLY* 2.8 36.3 + - - +
23A GLN* 3.9 13.5 - - - +
24A ILE 3.3 0.2 - - - -
25A ASP* 1.3 80.0 - - + +
27A ALA* 1.3 62.7 + - - +
29A THR* 3.1 19.1 + - - -
30A ALA 3.1 9.4 + - - -
15G PHE* 3.5 31.2 - - + -
16G SER 3.3 19.5 - - - +
17G PRO* 3.6 40.7 - - + +
19G GLY* 3.5 9.0 - - - -
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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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23A GLN 2.9 18.1 + - - +
24A ILE* 3.6 5.6 - - - +
26A TYR* 1.3 77.3 - - - +
28A LEU* 1.3 63.1 + - - +
30A ALA* 3.0 14.6 + - - +
31A VAL* 3.1 16.6 + - - +
131A PRO* 4.4 2.7 - - + -
132A PHE 3.8 17.7 - - - +
133A GLY* 4.4 0.9 - - - -
153A PRO* 3.9 10.3 - - + -
15G PHE* 3.4 31.2 - - + -
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Residues in contact with LEU 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 ILE* 2.9 34.8 + - + +
25A ASP* 3.0 17.2 + - - +
27A ALA* 1.3 75.9 - - - +
29A THR* 1.3 61.0 + - - +
31A VAL* 3.2 12.1 + - + +
32A LYS* 3.1 24.6 + - - +
135A SER* 4.8 3.1 - - - +
152A ASP* 4.2 18.6 - - + +
153A PRO* 4.0 24.4 - - + +
154A SER* 6.2 0.4 - - - -
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Residues in contact with THR 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 ASP 3.0 12.6 + - - -
26A TYR* 3.1 12.6 + - - -
28A LEU* 1.3 73.4 - - - +
30A ALA* 1.3 64.0 + - - +
32A LYS* 3.1 19.2 + - + +
33A GLN* 3.2 23.0 + - + +
17G PRO 3.9 13.4 + - - +
18G GLU* 3.5 28.3 - - - +
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Residues in contact with ALA 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 TYR 3.1 8.3 + - - +
27A ALA* 3.0 17.4 + - - +
29A THR* 1.3 77.1 - - - +
31A VAL* 1.3 58.7 + - - +
33A GLN* 3.4 18.3 + - - +
34A GLY* 3.5 6.8 + - - -
80A GLY* 4.0 9.6 - - - -
81A MET* 4.6 9.0 - - + -
133A GLY 4.5 9.4 - - - +
15G PHE* 4.4 9.9 - - + -
19G GLY* 3.6 24.8 - - - +
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Residues in contact with VAL 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 3.1 14.2 + - - +
28A LEU* 3.5 11.9 - - + +
29A THR 3.2 0.4 - - - -
30A ALA* 1.3 72.8 - - - +
32A LYS* 1.3 65.9 + - - +
34A GLY* 3.0 13.7 + - - -
79A SER* 3.4 21.5 - - - +
80A GLY* 4.2 5.8 - - - -
133A GLY 3.8 3.6 - - - +
134A VAL* 3.6 32.5 - - - +
135A SER* 3.7 21.5 - - - +
153A PRO* 4.2 9.9 - - + -
165A ILE* 5.0 2.5 - - + -
166A GLY* 3.4 18.4 - - - +
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Residues in contact with LYS 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 LEU 3.1 14.6 + - - +
29A THR* 3.1 15.3 + - + +
31A VAL* 1.3 74.9 - - - +
33A GLN* 1.3 69.4 + - - +
34A GLY 3.1 0.2 - - - -
166A GLY* 3.4 12.1 - - - +
167A LYS* 3.1 50.9 + - - +
169A SER* 3.2 22.4 + - - -
170A VAL* 4.1 17.8 - - - +
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Residues in contact with GLN 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 THR* 3.2 27.1 + - - +
30A ALA* 3.7 10.8 - - - +
31A VAL 3.2 0.8 - - - -
32A LYS* 1.3 82.9 - - - +
34A GLY* 1.3 61.8 + - - +
35A VAL 4.0 0.2 + - - -
167A LYS* 3.3 26.3 + - - +
18G GLU 4.6 10.7 - - - +
19G GLY 6.4 0.2 - - - -
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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