Contacts of the helix formed by residues 17 - 30 (chain A) 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 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ASP* 1.3 73.1 + - - +
19A GLU* 3.2 7.5 - - - +
20A GLU* 2.9 32.3 + - - +
21A ALA* 3.1 20.8 + - - +
98D ARG* 3.7 23.3 + - - -
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Residues in contact with ASP 18 (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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17A SER* 1.3 83.6 + - - +
19A GLU* 1.3 62.2 + - - +
21A ALA* 3.4 3.0 + - - +
22A ASN* 3.0 19.9 + - - +
116C LYS* 3.4 43.3 + - - +
117C PHE* 3.3 17.1 - - + -
357C PHE* 4.1 9.5 - - + -
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Residues in contact with GLU 19 (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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17A SER 3.2 4.1 - - - +
18A ASP* 1.3 78.7 - - - +
20A GLU* 1.3 60.4 + - + +
22A ASN* 3.2 3.1 + - - +
23A LEU* 2.9 49.0 + - + +
193C LYS* 2.5 32.9 + - - +
355C CYS* 4.9 5.0 - - - -
356C ALA* 4.0 0.5 - - - -
357C PHE* 3.0 27.5 + - - -
358C ASN* 2.9 26.3 + - - +
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Residues in contact with GLU 20 (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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17A SER* 2.9 35.7 + - - +
18A ASP 3.4 0.2 - - - -
19A GLU* 1.3 77.5 - - + +
21A ALA* 1.3 57.1 + - - +
23A LEU* 3.4 7.7 + - - +
24A PHE* 2.9 31.1 + - - +
311C ILE* 5.3 1.4 - - - +
98D ARG* 3.4 32.7 + - - +
99D GLU 4.5 3.1 - - - +
100D LEU* 5.5 2.8 - - - +
101D PRO* 4.4 29.2 - - + +
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Residues in contact with ALA 21 (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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17A SER 3.1 14.3 + - - +
18A ASP* 3.6 9.2 - - - +
20A GLU* 1.3 73.3 - - - +
22A ASN* 1.3 65.2 + - - +
24A PHE* 3.4 4.8 + - - -
25A ALA* 3.0 19.9 + - - +
113C PRO* 4.0 17.5 - - + +
114C VAL* 3.5 16.5 - - - +
116C LYS* 5.3 1.3 - - + -
117C PHE* 3.7 17.3 - - + -
98D ARG* 3.9 15.0 - - - +
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Residues in contact with ASN 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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18A ASP 3.0 12.0 + - - +
19A GLU 3.6 0.4 - - - +
21A ALA* 1.3 74.8 - - - +
23A LEU* 1.3 68.6 + - - +
25A ALA* 3.2 4.5 + - - +
26A MET* 3.1 32.4 + - - +
117C PHE* 3.5 18.5 - - + -
127C LEU* 3.6 17.4 - - - +
186C ASN* 5.5 1.9 + - - +
189C ILE* 3.6 29.9 - - - +
190C THR* 5.2 1.8 + - - -
357C PHE* 3.5 45.4 - - + +
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Residues in contact with LEU 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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19A GLU* 2.9 44.0 + - + +
20A GLU* 4.0 7.0 - - - +
22A ASN* 1.3 82.7 - - - +
24A PHE* 1.3 57.7 + - - +
26A MET* 3.3 5.2 + - + -
27A GLN* 2.9 24.8 + - - +
301C TYR* 6.1 0.2 - - - +
311C ILE* 3.8 14.8 - - + -
312C ALA* 4.0 26.7 - - + +
315C VAL* 3.3 19.7 - - + +
357C PHE* 3.9 11.7 - - - +
358C ASN* 3.7 32.3 - - + +
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Residues in contact with PHE 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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20A GLU 2.9 18.7 + - - +
21A ALA* 3.8 4.5 - - - +
22A ASN 3.3 0.2 - - - -
23A LEU* 1.3 78.0 - - - +
25A ALA* 1.3 56.7 + - - +
27A GLN* 3.2 21.4 + - - +
28A LEU* 2.9 61.9 + - + +
90C TYR* 3.3 24.2 - + + -
91C SER* 3.8 24.5 - - - -
92C VAL* 4.1 0.7 - - + -
114C VAL* 3.6 29.2 - - + -
311C ILE* 4.0 13.8 - - + +
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Residues in contact with ALA 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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21A ALA 3.0 14.1 + - - +
22A ASN 3.2 8.5 + - - +
24A PHE* 1.3 77.3 - - - +
26A MET* 1.3 57.0 + - - +
28A LEU* 3.4 8.3 + - - +
29A ALA* 3.0 27.7 + - - +
114C VAL* 3.5 17.3 - - + +
117C PHE* 4.2 6.3 - - + -
118C LEU* 4.1 21.1 - - + +
127C LEU* 3.9 18.6 - - + +
131C LEU* 5.2 0.9 - - - +
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Residues in contact with MET 26 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ASN* 3.1 29.6 + - - +
23A LEU* 3.6 11.4 - - + +
24A PHE 3.3 0.2 - - - -
25A ALA* 1.3 74.0 - - - +
27A GLN* 1.3 63.0 + - - +
29A ALA* 3.4 11.2 + - - +
30A SER* 3.2 17.7 + - - -
127C LEU* 3.9 15.9 - - + -
130C PHE* 3.5 43.3 - - + -
186C ASN* 3.7 24.9 - - - +
269C TRP* 3.9 6.5 - - + -
301C TYR* 3.7 23.1 - - - +
315C VAL* 4.0 20.1 - - + +
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Residues in contact with GLN 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 LEU 2.9 13.8 + - - +
24A PHE* 3.2 25.7 + - - +
26A MET* 1.3 73.8 - - - +
28A LEU* 1.3 64.8 + - - +
30A SER 3.5 0.9 + - - -
31A ALA* 3.0 20.2 + - + +
90A TYR* 2.9 25.4 + - - +
311C ILE* 2.9 38.5 - - + +
314C LYS* 3.6 18.3 - - + +
315C VAL* 3.7 10.9 - - + +
318C HIS* 3.4 28.8 - - + +
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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 PHE* 2.9 48.6 + - + +
25A ALA* 3.6 13.0 - - - +
26A MET 3.4 0.2 - - - -
27A GLN* 1.3 73.2 - - - +
29A ALA* 1.3 67.2 + - - +
31A ALA* 3.1 19.5 + - - +
34C LEU* 3.5 33.9 - - + -
35C PRO* 3.7 13.6 - - + +
38C LEU* 3.9 22.0 - - + -
90C TYR* 5.4 0.2 - - + -
92C VAL* 3.7 28.7 - - + -
114C VAL* 4.2 7.9 - - + -
118C LEU* 4.6 4.7 - - + -
131C LEU* 4.7 2.4 - - + +
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Residues in contact with ALA 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 ALA 3.0 17.4 + - - +
26A MET* 3.6 7.6 - - - +
27A GLN 3.3 0.4 - - - -
28A LEU* 1.3 77.6 - - - +
30A SER* 1.3 58.8 + - - +
31A ALA 3.7 0.5 + - - -
32A ALA* 5.1 0.3 + - - +
35C PRO* 4.6 1.0 - - - +
127C LEU 5.8 0.4 - - - +
130C PHE* 4.0 23.1 - - + -
131C LEU* 3.9 36.3 - - + -
134C ALA* 3.3 18.9 - - + +
135C THR* 3.8 14.6 - - - +
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Residues in contact with SER 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 MET 3.2 12.5 + - - -
27A GLN 3.7 0.4 - - - -
28A LEU 3.2 0.4 - - - -
29A ALA* 1.3 76.5 - - - +
31A ALA* 1.3 64.7 + - - +
32A ALA* 3.2 4.5 - - - -
33A VAL* 3.1 27.3 + - - +
130C PHE* 5.8 3.4 - - - -
134C ALA* 4.6 7.4 - - - -
315C VAL* 5.9 0.3 - - - +
318C HIS* 2.8 33.6 + - - +
319C THR* 5.6 2.2 - - - +
322C LEU* 4.1 28.7 - - - -
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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