Contacts of the helix formed by residues 16 - 30 (chain B) in PDB entry 3REO
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 SER 16 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B SER* 1.3 63.8 + - - +
18B ASP* 3.4 5.4 + - - +
19B GLU* 3.6 31.2 + - - +
20B GLU* 2.7 40.1 + - - +
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Residues in contact with SER 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B SER* 1.3 77.1 - - - +
18B ASP* 1.3 68.1 + - - +
20B GLU* 3.5 12.6 + - - +
21B ALA* 3.1 26.9 + - - +
98C ARG* 3.7 28.1 + - - +
113D PRO* 6.0 0.7 - - - +
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Residues in contact with ASP 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B SER 4.1 4.3 + - - +
17B SER* 1.3 81.2 + - - +
19B GLU* 1.3 61.8 + - - +
21B ALA* 4.6 1.3 - - - -
22B ASN* 2.9 27.4 + - - +
116D LYS* 2.8 39.6 + - - +
117D PHE* 3.2 17.2 - - + -
357D PHE* 4.0 9.0 - - + -
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Residues in contact with GLU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B SER* 3.5 27.2 + - - +
17B SER 3.3 0.2 - - - -
18B ASP* 1.3 77.6 - - - +
20B GLU* 1.3 65.0 + - - +
22B ASN* 3.2 2.6 + - - +
23B LEU* 2.9 38.7 + - + +
193D LYS* 2.8 32.5 + - - -
355D CYS* 4.7 4.0 - - - +
356D ALA* 3.7 1.6 + - - -
357D PHE* 2.7 48.7 + - - -
358D ASN 4.0 3.1 + - - +
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Residues in contact with GLU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B SER* 2.7 31.5 + - - +
17B SER* 3.6 10.4 - - - +
19B GLU* 1.3 74.7 - - - +
21B ALA* 1.3 58.1 + - - +
23B LEU* 3.4 9.6 + - - +
24B PHE* 3.0 28.9 + - - +
98C ARG* 3.2 40.9 + - - +
99C GLU 3.1 25.2 + - - +
100C LEU* 4.8 2.2 - - - +
101C PRO* 3.7 20.6 - - + +
311D ILE* 5.2 1.4 - - - +
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B SER 3.1 15.3 + - - +
18B ASP* 4.6 0.9 - - - -
19B GLU 3.3 0.2 - - - -
20B GLU* 1.3 76.7 - - - +
22B ASN* 1.3 65.8 + - - +
24B PHE* 3.4 5.1 + - - -
25B ALA* 3.1 19.6 + - - +
113D PRO* 3.8 27.8 - - + +
114D VAL* 3.5 17.0 - - - +
116D LYS* 5.4 1.8 - - + -
117D PHE* 3.8 19.6 - - + -
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Residues in contact with ASN 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ASP 2.9 18.5 + - - +
19B GLU 3.6 0.2 - - - +
21B ALA* 1.3 77.9 - - - +
23B LEU* 1.3 67.9 + - - +
25B ALA* 3.1 5.5 + - - +
26B MET* 3.0 31.7 + - - +
117D PHE* 3.5 21.9 - - + -
127D LEU* 3.8 14.5 - - - +
186D ASN* 5.3 1.9 + - - +
189D ILE* 3.7 27.5 - - - +
190D THR* 5.2 1.4 + - - -
357D PHE* 3.5 39.5 - - + +
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLU* 2.9 35.3 + - + +
20B GLU* 3.9 6.5 - - - +
21B ALA 3.3 0.2 - - - -
22B ASN* 1.3 83.6 - - - +
24B PHE* 1.3 58.9 + - - +
26B MET* 3.3 4.1 + - + +
27B GLN* 3.0 24.1 + - - +
301D TYR* 5.6 0.7 - - + +
311D ILE* 3.9 14.6 - - + -
312D ALA* 3.9 25.8 - - + +
315D VAL* 3.2 22.1 - - + +
357D PHE 3.9 9.6 - - - +
358D ASN* 3.5 39.7 - - + +
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Residues in contact with PHE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLU 3.0 18.3 + - - +
21B ALA* 3.8 5.2 - - - +
23B LEU* 1.3 75.8 - - - +
25B ALA* 1.3 57.1 + - - +
27B GLN* 3.1 22.3 + - - -
28B LEU* 2.9 61.6 + - + +
90D TYR* 3.3 29.6 - + + -
91D SER* 3.8 20.4 - - - -
92D VAL* 4.3 0.9 - - + -
114D VAL* 3.3 24.9 - - + -
311D ILE* 3.9 15.3 - - + +
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Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ALA 3.1 13.5 + - - +
22B ASN 3.1 9.2 + - - +
24B PHE* 1.3 75.8 - - - +
26B MET* 1.3 57.8 + - - +
28B LEU* 3.3 8.1 + - - +
29B ALA* 3.0 27.9 + - - +
114D VAL* 3.5 15.2 - - + +
117D PHE* 4.0 11.0 - - + -
118D LEU* 4.3 16.8 - - + +
127D LEU* 3.6 21.5 - - + +
131D LEU* 5.1 2.3 - - - +
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Residues in contact with MET 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ASN* 3.0 30.4 + - - +
23B LEU* 3.6 9.4 - - + +
25B ALA* 1.3 75.9 - - - +
27B GLN* 1.3 65.3 + - - +
29B ALA* 3.3 5.2 + - - +
30B SER* 3.0 24.9 + - - -
127D LEU* 3.9 19.5 - - + -
130D PHE* 3.4 44.1 - - + -
186D ASN* 4.0 15.0 - - - +
269D TRP* 4.1 9.9 - - + -
301D TYR* 3.7 22.4 - - + +
315D VAL* 4.1 17.9 - - + -
319D THR* 5.7 3.8 - - + -
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Residues in contact with GLN 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU 3.0 13.8 + - - +
24B PHE* 3.5 28.7 - - + +
26B MET* 1.3 76.8 - - - +
28B LEU* 1.3 63.6 + - + +
30B SER 3.4 1.4 + - - -
31B ALA* 3.0 23.0 + - + +
90B TYR* 2.9 26.2 + - - +
311D ILE* 3.4 28.7 - - + +
314D LYS* 3.5 22.8 - - + +
315D VAL* 3.9 12.5 - - + +
318D HIS* 3.5 22.9 - - + -
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B PHE* 2.9 60.1 + - + +
25B ALA* 3.7 7.0 - - - +
27B GLN* 1.3 78.2 - - + +
29B ALA* 1.3 64.7 + - - +
31B ALA* 3.2 19.4 + - + +
34D LEU* 3.6 32.1 - - + -
35D PRO* 3.6 14.1 - - + +
38D LEU* 3.9 20.9 - - + -
90D TYR* 5.2 0.9 - - + -
92D VAL* 3.8 22.9 - - + -
114D VAL* 4.0 13.2 - - + -
118D LEU* 4.5 5.8 - - + -
131D LEU* 4.5 2.8 - - + +
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Residues in contact with ALA 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ALA 3.0 16.2 + - - +
26B MET* 3.6 8.1 - - - +
27B GLN 3.3 0.2 - - - -
28B LEU* 1.3 78.0 - - - +
30B SER* 1.4 58.0 + - - +
31B ALA 3.8 0.2 + - - -
32B ALA* 5.2 1.0 + - - +
35D PRO* 4.7 1.2 - - - +
127D LEU* 5.5 1.6 - - + +
130D PHE* 3.8 22.9 - - + -
131D LEU* 3.7 36.8 - - + +
134D ALA* 3.2 20.1 - - + +
135D THR* 4.0 13.7 - - - +
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Residues in contact with SER 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B MET 3.0 13.7 + - - -
27B GLN 3.6 1.1 - - - -
28B LEU 3.2 0.4 - - - -
29B ALA* 1.4 79.1 - - - +
31B ALA* 1.3 61.9 + - - +
32B ALA* 3.2 3.6 - - - -
33B VAL* 3.0 25.5 + - - +
130D PHE* 5.6 3.1 - - - -
134D ALA* 4.7 5.2 - - - -
315D VAL* 5.8 0.2 - - - -
318D HIS* 2.9 31.9 + - - +
319D THR* 5.7 1.4 - - - +
322D LEU* 4.0 31.5 - - - +
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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