Contacts of the helix formed by residues 15 - 28 (chain A) in PDB entry 1OFD
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 HIS 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ASP* 1.3 74.7 - - - +
16A THR* 1.3 66.7 + - - +
17A LEU 3.3 0.7 - - - -
18A VAL* 2.9 19.6 + - + +
19A GLU* 3.1 46.5 + - + +
191A LEU 3.2 22.5 + - - -
192A LYS* 4.1 11.4 - - - -
193A ASN 3.2 20.5 + - - -
194A PRO* 3.5 28.8 - - + +
196A TYR* 2.7 30.1 - - + +
197A THR* 3.8 3.4 - - - +
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Residues in contact with THR 16 (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 ASP* 3.4 16.6 + - - +
15A HIS* 1.3 77.7 - - - +
17A LEU* 1.3 56.7 + - - +
19A GLU* 3.3 20.7 + - + +
20A GLN* 2.9 49.9 + - + +
361A TYR* 5.3 1.3 - - - +
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Residues in contact with LEU 17 (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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6A ILE* 3.4 33.5 - - + +
8A ASN* 3.7 26.0 - - + +
14A ASP* 3.2 15.5 + - - +
15A HIS 3.3 0.2 - - - -
16A THR* 1.3 77.9 - - - +
18A VAL* 1.3 62.4 + - + +
20A GLN* 3.4 6.6 + - - +
21A ALA* 2.9 23.7 + - - +
198A SER 3.3 18.8 - - - +
199A ASN 3.8 7.6 - - - +
200A PHE 3.5 26.7 - - - +
201A ALA* 3.7 14.1 - - + +
361A TYR* 3.4 20.8 + - + +
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Residues in contact with VAL 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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14A ASP 4.1 8.5 - - - +
15A HIS* 2.9 15.3 + - + +
17A LEU* 1.3 78.8 - - + +
19A GLU* 1.3 64.8 + - - +
21A ALA* 3.2 8.1 + - + +
22A LEU* 3.0 27.0 + - + +
46A VAL* 5.9 3.1 - - + -
48A THR* 5.1 7.6 - - + -
191A LEU* 4.0 33.9 - - + +
196A TYR* 3.9 39.7 - - + +
198A SER* 4.3 17.3 - - - +
201A ALA* 5.6 0.7 - - - -
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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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15A HIS* 3.1 38.9 + - + +
16A THR* 3.4 25.1 + - + +
18A VAL* 1.3 75.0 - - - +
20A GLN* 1.3 59.1 + - + +
22A LEU* 3.2 12.4 + - + +
23A LYS* 2.9 30.4 + - - +
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Residues in contact with GLN 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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6A ILE* 3.8 14.8 - - + +
16A THR* 2.9 34.5 + - + +
17A LEU* 3.5 8.6 - - - +
19A GLU* 1.3 76.0 - - + +
21A ALA* 1.3 57.0 + - - +
23A LYS* 3.3 8.4 + - - +
24A ALA* 2.8 29.8 + - - +
361A TYR* 2.6 40.9 + - - -
371A VAL* 3.7 30.2 - - + +
372A ASP 4.8 5.9 + - - -
373A LEU* 4.5 6.5 - - - +
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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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6A ILE* 3.6 12.5 - - + +
17A LEU 2.9 14.6 + - - +
18A VAL* 3.2 10.1 + - - +
20A GLN* 1.3 75.4 - - - +
22A LEU* 1.3 59.5 + - + +
24A ALA* 3.3 4.8 + - - +
25A LEU* 2.9 31.5 + - - +
46A VAL* 4.3 12.8 - - + -
201A ALA* 3.7 27.4 - - + -
203A TYR* 4.2 10.8 - - + -
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Residues in contact with LEU 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 VAL* 3.0 21.7 + - + +
19A GLU* 3.2 10.9 + - + +
21A ALA* 1.3 75.5 - - + +
23A LYS* 1.3 65.1 + - - +
25A LEU* 3.4 12.5 - - + +
26A GLY* 3.1 17.8 + - - -
46A VAL* 5.2 7.2 - - + -
181A SER 4.8 7.0 - - - +
182A ILE* 5.7 1.2 - - - +
184A LEU* 4.0 28.0 - - + -
185A GLY* 4.2 18.6 - - - +
191A LEU* 4.0 40.6 - - + +
192A LYS* 4.4 14.6 - - - +
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Residues in contact with LYS 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 16.4 + - - +
20A GLN* 3.3 9.2 + - - +
22A LEU* 1.3 74.5 - - - +
24A ALA* 1.3 64.5 + - - +
26A GLY* 3.0 12.5 + - - +
27A CYS* 3.0 23.7 + - - -
370A VAL 4.5 7.4 - - - +
371A VAL* 6.2 1.3 - - + -
372A ASP* 5.3 10.5 - - - +
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Residues in contact with ALA 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 GLN 2.8 21.0 + - - +
21A ALA* 3.6 6.1 - - - +
23A LYS* 1.3 71.1 - - - +
25A LEU* 1.3 63.5 + - - +
27A CYS 3.0 10.9 + - - -
28A MET* 3.3 12.6 + - - +
203A TYR* 3.6 31.6 - - + +
370A VAL* 3.3 35.5 + - + +
371A VAL* 4.2 6.3 - - + -
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Residues in contact with LEU 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 2.9 9.7 + - - +
22A LEU* 3.4 17.5 - - + +
24A ALA* 1.3 74.6 - - - +
26A GLY* 1.3 55.5 + - - +
28A MET* 3.0 23.1 + - + +
29A GLU 3.6 0.3 + - - -
44A ALA* 4.2 11.9 - - + -
45A GLY 4.1 7.0 - - - +
46A VAL* 5.5 1.1 - - + -
181A SER* 2.7 31.6 + - - +
184A LEU* 3.7 30.7 - - + -
203A TYR* 3.9 22.8 - - + -
204A HIS 3.4 38.8 - - - +
205A ARG* 3.8 14.1 - - + +
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Residues in contact with GLY 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 LEU 3.1 10.7 + - - -
23A LYS* 3.0 9.3 + - - -
25A LEU* 1.3 77.7 - - - +
27A CYS* 1.3 60.6 + - - +
28A MET 3.1 0.9 + - - -
29A GLU* 3.4 17.3 + - - +
181A SER* 3.6 12.7 - - - -
182A ILE* 4.4 17.0 - - - +
1276A THR* 4.6 4.7 - - - +
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Residues in contact with CYS 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 LYS* 3.0 22.7 + - - -
24A ALA 3.0 0.4 + - - -
26A GLY* 1.3 75.6 - - - +
28A MET* 1.3 60.0 + - - +
29A GLU 3.5 0.7 - - - -
30A HIS* 3.2 14.7 + - - -
369A GLY 5.2 1.1 - - - -
370A VAL* 3.0 39.0 - - + -
1274A VAL* 6.2 1.1 - - - -
1275A ASN* 2.9 45.5 - - - +
1276A THR* 3.7 10.1 - - - +
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Residues in contact with MET 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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2A GLY* 3.1 41.7 - - - +
3A VAL 3.8 5.8 - - - +
24A ALA 3.3 6.5 + - - +
25A LEU* 3.0 16.4 + - + +
27A CYS* 1.3 82.9 - - - +
29A GLU* 1.3 63.2 + - - +
30A HIS* 3.3 6.5 - - - -
31A ARG* 2.9 26.0 + - + +
32A GLY 3.7 2.3 + - - -
203A TYR* 3.0 43.3 - - + -
205A ARG* 3.9 8.4 - - + +
366A SER* 4.0 18.4 - - - -
367A GLU* 4.8 11.9 - - + -
370A VAL* 4.8 7.2 - - + -
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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