Contacts of the helix formed by residues 15 - 27 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ASP* 1.3 74.0 - - - +
16B THR* 1.3 65.5 + - - +
17B LEU 3.3 0.9 - - - -
18B VAL* 3.1 19.6 + - + +
19B GLU* 3.1 43.3 + - + +
191B LEU 3.3 21.3 + - - -
192B LYS* 4.1 11.2 - - - -
193B ASN 3.2 21.3 + - - -
194B PRO* 3.5 30.5 - - + +
196B TYR* 2.8 28.7 - - + +
197B THR* 3.8 3.2 - - - +
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Residues in contact with THR 16 (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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14B ASP* 3.4 18.3 + - - +
15B HIS* 1.3 77.9 - - - +
17B LEU* 1.3 56.2 + - - +
19B GLU* 3.0 21.2 + - + +
20B GLN* 2.8 50.2 + - + +
361B TYR* 5.3 1.1 - - - +
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Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 3.5 30.2 - - + +
8B ASN* 3.7 14.8 - - + +
14B ASP* 3.1 16.2 + - - +
15B HIS 3.3 0.2 - - - -
16B THR* 1.3 75.5 - - - +
18B VAL* 1.3 59.2 + - - +
20B GLN* 3.3 15.5 + - - +
21B ALA* 2.9 24.6 + - - +
198B SER* 3.2 21.3 - - - +
199B ASN 3.6 23.1 - - - +
200B PHE 3.6 26.2 - - - +
201B ALA* 3.6 14.6 - - + +
361B TYR* 3.6 12.0 + - - +
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Residues in contact with VAL 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ASP 4.4 4.7 - - - +
15B HIS* 3.1 15.5 + - + +
17B LEU* 1.3 77.6 - - + +
19B GLU* 1.3 66.3 + - - +
21B ALA* 3.2 7.2 + - + +
22B LEU* 3.1 30.4 + - + +
46B VAL* 6.1 2.9 - - + -
48B THR* 4.9 7.9 - - + -
191B LEU* 3.8 37.5 - - + +
196B TYR* 4.0 33.4 - - + +
198B SER* 4.3 19.7 - - - -
201B ALA* 5.6 0.4 - - - -
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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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15B HIS* 3.1 41.4 + - + +
16B THR* 3.0 25.8 + - + +
18B VAL* 1.3 75.8 - - - +
20B GLN* 1.3 58.2 + - + +
22B LEU* 3.3 10.7 + - + +
23B LYS* 3.0 29.9 + - - +
191B LEU 5.8 0.4 - - - +
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Residues in contact with GLN 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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6B ILE* 3.7 14.6 - - + +
16B THR* 2.8 33.0 + - + +
17B LEU* 3.5 8.1 - - - +
19B GLU* 1.3 77.6 - - + +
21B ALA* 1.3 56.5 + - - +
23B LYS* 3.3 6.1 + - - +
24B ALA* 2.9 30.7 + - - +
361B TYR* 2.6 40.3 + - - -
370B VAL 4.9 0.2 - - - +
371B VAL* 3.8 30.3 - - + +
372B ASP 4.8 4.2 + - - -
373B LEU* 4.7 6.3 - - - +
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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
----------------------------------------------------------
6B ILE* 3.5 12.3 - - + +
17B LEU 2.9 16.5 + - - +
18B VAL* 3.2 7.6 + - + +
20B GLN* 1.3 76.5 - - - +
22B LEU* 1.3 60.5 + - + +
24B ALA* 3.5 3.6 + - - +
25B LEU* 3.0 32.1 + - - +
46B VAL* 4.4 12.3 - - + -
201B ALA* 3.7 27.1 - - + -
203B TYR* 4.2 10.3 - - + -
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Residues in contact with LEU 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 VAL* 3.1 19.2 + - + +
19B GLU* 3.7 10.5 - - + +
21B ALA* 1.3 77.0 - - + +
23B LYS* 1.3 56.8 + - - +
25B LEU* 3.4 12.3 - - + +
26B GLY* 3.0 22.7 + - - -
46B VAL* 5.0 6.5 - - + -
181B SER 4.9 7.0 - - - +
182B ILE* 5.7 1.6 - - - +
184B LEU* 4.1 27.6 - - + -
185B GLY* 4.2 10.3 - - - +
191B LEU* 4.0 37.5 - - + +
192B LYS* 3.7 27.1 - - - +
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Residues in contact with LYS 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 3.0 17.8 + - - +
20B GLN* 3.7 6.5 - - - +
22B LEU* 1.3 74.9 - - - +
24B ALA* 1.3 65.3 + - - +
26B GLY* 3.1 5.4 + - - +
27B CYS* 3.0 27.8 + - - -
370B VAL 4.6 8.5 - - - +
371B VAL* 6.2 0.7 - - - -
372B ASP* 6.2 0.2 - - - +
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Residues in contact with ALA 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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6B ILE* 4.8 0.2 - - + -
20B GLN 2.9 18.0 + - - +
21B ALA* 3.7 4.3 - - - +
23B LYS* 1.3 74.9 - - - +
25B LEU* 1.3 63.1 + - - +
27B CYS* 3.0 13.7 + - - +
28B MET* 3.0 18.8 - - - +
203B TYR* 3.6 31.6 - - + +
370B VAL* 3.7 29.0 + - + +
371B VAL* 4.3 6.3 - - + -
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Residues in contact with LEU 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 3.0 17.8 + - - +
22B LEU* 3.4 19.1 - - + +
24B ALA* 1.3 76.7 - - - +
26B GLY* 1.3 58.8 + - - +
28B MET* 3.0 19.8 + - + +
44B ALA* 4.6 6.1 - - + -
45B GLY 3.7 18.2 - - - +
46B VAL* 5.0 1.8 - - + -
181B SER* 2.6 28.8 + - - +
184B LEU* 3.9 25.4 - - + -
203B TYR* 3.8 15.8 - - + -
204B HIS 3.4 38.6 - - - +
205B ARG* 3.7 13.9 - - + +
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Residues in contact with GLY 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU 3.0 14.3 + - - -
23B LYS* 3.1 6.2 + - - -
25B LEU* 1.3 75.7 - - - +
27B CYS* 1.3 59.1 + - - +
28B MET 3.1 1.3 + - - -
29B GLU* 3.4 18.4 + - - +
181B SER* 3.5 13.9 - - - -
182B ILE* 4.3 17.6 - - - +
1276B THR* 5.6 1.6 + - - +
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Residues in contact with CYS 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 LYS* 3.0 21.5 + - - -
24B ALA 3.0 11.3 + - - +
26B GLY* 1.3 74.5 - - - +
28B MET* 1.3 59.3 + - - +
29B GLU 3.5 0.9 - - - -
30B HIS* 3.2 14.6 - - - -
369B GLY 5.2 0.7 - - - -
370B VAL* 3.5 30.5 - - + -
1274B VAL* 6.4 0.4 - - - -
1275B ASN* 2.9 47.7 - - - +
1276B THR* 5.1 8.1 + - - -
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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