Contacts of the helix formed by residues 21 - 33 (chain R) 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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12R VAL 5.7 2.0 - - - +
13R SER* 4.4 7.6 - - - -
14R THR 3.5 18.2 - - - +
15R PHE* 3.6 24.7 - - + -
20R ARG* 1.3 71.7 - - - +
22R PHE* 1.3 68.4 + - - +
23R GLN* 3.2 2.7 - - + +
24R VAL* 2.7 43.5 + - + +
25R GLU* 2.9 15.1 + - - +
81S LEU* 4.4 17.0 - - + +
130S ARG* 3.8 42.8 - - - +
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Residues in contact with PHE 22 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14R THR* 3.5 36.5 + - + +
15R PHE 3.8 14.8 - - - -
16R SER* 3.6 30.5 - - - -
17R PRO* 4.8 5.6 - - + -
20R ARG 3.5 4.2 + - - -
21R LEU* 1.3 70.4 - - - +
23R GLN* 1.3 62.3 + - + +
25R GLU* 3.1 4.8 + - - +
26R TYR* 2.9 68.1 + + + -
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Residues in contact with GLN 23 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14Q ILE* 3.8 21.1 - - - +
15Q PHE* 3.0 67.8 + - - +
12R VAL* 3.6 42.1 + - + +
14R THR 5.2 0.2 + - - -
21R LEU* 3.2 1.7 - - + +
22R PHE* 1.3 83.4 - - + +
24R VAL* 1.3 58.1 + - + +
26R TYR* 3.9 9.7 - - - -
27R SER* 3.0 27.5 + - - -
130R ARG* 4.6 2.0 - - - +
131R PRO* 3.9 20.1 - - + +
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Residues in contact with VAL 24 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21R LEU* 2.7 44.2 + - + +
23R GLN* 1.3 72.4 - - + +
25R GLU* 1.3 74.4 + - - +
27R SER* 3.2 9.0 - - - -
28R LEU* 3.2 29.2 + - + +
131R PRO* 4.4 13.7 - - + -
153R PRO 4.7 3.1 - - - +
154R SER* 3.8 40.4 - - - +
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Residues in contact with GLU 25 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20R ARG* 3.5 51.7 + - + +
21R LEU 2.9 14.7 + - - +
22R PHE* 3.6 9.0 - - - +
24R VAL* 1.3 84.4 - - - +
26R TYR* 1.3 67.5 + - + +
28R LEU* 3.2 33.2 + - - +
29R GLU* 3.3 16.0 + - - +
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Residues in contact with TYR 26 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15Q PHE* 3.6 23.3 - - + -
16Q SER 3.3 24.7 - - - +
17Q PRO* 3.5 42.1 - - + +
19Q GLY* 3.4 8.1 - - - -
22R PHE* 2.9 59.8 + + + +
23R GLN* 3.9 9.9 - - - +
25R GLU* 1.3 78.4 - - + +
27R SER* 1.3 65.7 + - - +
29R GLU* 3.1 19.0 + - + +
30R ALA* 3.1 9.7 + - - +
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Residues in contact with SER 27 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15Q PHE* 3.7 23.5 - - - -
23R GLN 3.0 16.8 + - - -
24R VAL* 3.2 14.4 - - - -
26R TYR* 1.3 77.3 - - - +
28R LEU* 1.3 56.9 + - - +
30R ALA* 3.1 21.7 + - - +
31R ILE* 3.3 11.4 + - - +
131R PRO* 4.3 4.9 - - - -
132R PHE 2.7 25.5 + - - -
133R GLY* 4.6 0.7 - - - -
153R PRO* 3.4 15.3 - - - +
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Residues in contact with LEU 28 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24R VAL* 3.2 22.5 + - + +
25R GLU* 3.3 31.4 - - - +
26R TYR 3.2 0.4 - - - -
27R SER* 1.3 78.6 - - - +
29R GLU* 1.3 63.7 + - - +
31R ILE* 3.4 13.8 + - + +
32R LYS* 3.3 30.1 + - + +
152R GLU* 4.3 30.1 - - + +
153R PRO* 4.0 26.5 - - + -
154R SER 5.4 0.4 - - - +
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Residues in contact with GLU 29 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Q PRO 3.5 25.4 - - - +
18Q ASP* 4.0 6.0 - - - +
19Q GLY* 3.9 8.7 - - - +
25R GLU 3.3 11.4 + - - +
26R TYR* 3.1 12.4 + - + +
28R LEU* 1.3 77.2 - - - +
30R ALA* 1.3 63.0 + - - +
32R LYS* 3.0 51.9 + - - +
33R LEU* 3.5 13.0 + - - +
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Residues in contact with ALA 30 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15Q PHE* 4.0 17.5 - - + -
19Q GLY* 3.2 30.4 - - - +
26R TYR 3.1 5.9 + - - +
27R SER 3.1 13.1 + - - +
29R GLU* 1.3 76.3 - - - +
31R ILE* 1.3 60.4 + - - +
33R LEU* 3.3 19.3 + - - +
34R GLY 3.9 2.8 + - - -
80R GLY* 4.2 9.1 - - - -
81R LEU* 4.7 9.3 + - + +
133R GLY 4.7 8.1 - - - +
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Residues in contact with ILE 31 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27R SER 3.3 12.7 + - - +
28R LEU* 3.6 19.5 - - + +
29R GLU 3.1 0.6 - - - -
30R ALA* 1.3 74.0 - - - +
32R LYS* 1.3 60.3 + - + +
33R LEU 3.1 2.0 - - - -
34R GLY* 3.0 19.8 + - - -
79R SER* 3.7 13.9 + - - +
80R GLY* 4.1 5.8 - - - -
133R GLY 3.9 2.0 - - - +
134R VAL* 3.9 11.7 - - - +
135R ALA* 3.5 39.7 - - + +
150R HIS* 5.9 0.2 - - - +
152R GLU* 6.1 0.2 - - + -
153R PRO* 3.6 31.9 - - + -
165R ILE* 5.1 2.7 - - + -
166R GLY* 3.6 21.4 - - - +
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Residues in contact with LYS 32 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28R LEU* 3.3 14.6 + - - +
29R GLU* 3.0 43.6 + - - +
31R ILE* 1.3 79.8 - - + +
33R LEU* 1.3 59.6 + - + +
34R GLY 3.2 0.7 - - - -
166R GLY* 4.4 7.6 - - - +
167R SER* 3.1 30.1 - - - -
169R SER* 5.3 8.1 - - - +
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Residues in contact with LEU 33 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18Q ASP 4.3 6.3 - - - +
19Q GLY 4.6 5.6 - - - +
20Q HIS* 3.3 37.7 - - + +
29R GLU 3.5 12.1 + - - +
30R ALA* 3.3 10.9 + - - +
31R ILE 3.1 1.2 - - - -
32R LYS* 1.3 80.9 - - + +
34R GLY* 1.3 56.7 + - - +
53R ARG* 3.4 19.7 + - - -
167R SER* 4.7 3.3 - - - -
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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