Contacts of the helix formed by residues 278 - 291 (chain B) in PDB entry 1FLO
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 ASN 278 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B ARG* 5.4 2.8 + - - -
276B LYS* 3.0 6.0 + - + +
277B ASP* 1.3 79.2 - - - +
279B LEU* 1.3 64.1 + - - +
280B VAL* 3.2 3.4 - - - -
281B ARG* 3.3 18.1 + - - +
282B SER* 3.8 5.2 + - - -
-13G T 4.7 6.4 + - + +
-12G T 2.8 74.7 + - + +
-11G C 4.6 8.7 - - - -
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Residues in contact with LEU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B THR* 6.3 1.1 - - + -
177B LEU* 4.1 33.9 - - + -
178B TYR* 4.2 17.9 - - + -
181B LEU* 3.7 28.3 - - + -
192B PHE* 4.3 2.7 - - + -
275B LEU* 4.1 32.5 - - + -
276B LYS* 2.9 23.6 + - + +
278B ASN* 1.3 77.2 - - - +
280B VAL* 1.3 63.4 + - - +
282B SER* 3.0 17.9 + - - +
283B TYR* 2.9 20.6 + - - +
-13G T 5.3 4.3 - - - +
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Residues in contact with VAL 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B PHE* 3.7 39.2 - - + -
277B ASP 4.0 10.8 - - - +
278B ASN* 3.2 1.1 - - - +
279B LEU* 1.3 78.1 - - - +
281B ARG* 1.3 65.1 + - + +
283B TYR* 4.3 5.8 - - + -
284B ASN* 2.9 41.8 + - - +
304B SER* 3.7 26.5 - - - +
8H T 5.0 7.0 - - + -
9H A 4.1 14.4 - - + +
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Residues in contact with ARG 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ASN* 3.3 4.9 + - - +
279B LEU 3.2 1.2 - - - -
280B VAL* 1.3 86.9 - - + +
282B SER* 1.3 63.1 + - - +
284B ASN* 4.4 11.9 - - - +
285B LYS* 3.3 45.8 + - - +
-13G T 4.4 6.3 - - + -
-12G T 3.6 37.0 + - + +
-11G C 4.1 2.7 - - - +
10H G 3.2 46.8 + - - +
11H G 2.8 47.5 + - - -
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Residues in contact with SER 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B THR* 5.7 0.3 - - - +
178B TYR* 3.4 28.4 + - - -
278B ASN 3.8 3.6 + - - -
279B LEU* 3.0 16.0 + - - +
281B ARG* 1.3 76.2 - - - +
283B TYR* 1.3 68.0 + - - +
285B LYS* 3.5 4.6 + - - +
286B ALA* 3.1 18.4 + - - +
-14G G 3.7 17.4 + - - -
-13G T 3.3 36.1 + - - +
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Residues in contact with TYR 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B PHE* 3.6 17.6 - + - -
178B TYR* 3.3 52.9 - + + -
181B LEU* 3.9 25.6 - - + -
182B PHE* 3.3 33.6 - - + +
185B THR* 5.4 0.4 + - + -
279B LEU* 2.9 18.3 + - + +
280B VAL* 3.8 5.6 - - - +
282B SER* 1.3 75.8 + - - +
284B ASN* 1.3 68.5 + - - +
286B ALA* 3.1 3.5 + - - +
287B LEU* 2.9 49.2 + - + +
303B LYS 5.1 0.2 + - - -
304B SER* 3.7 34.0 + - - -
306B ILE* 5.1 0.5 - - - +
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Residues in contact with ASN 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B VAL* 2.9 28.3 + - - +
281B ARG* 3.9 14.2 - - - +
283B TYR* 1.3 76.4 - - - +
285B LYS* 1.3 57.6 + - - +
287B LEU* 3.3 6.5 + - - +
288B LYS* 2.9 30.4 + - - +
303B LYS* 3.3 16.3 - - + +
304B SER* 3.3 32.2 + - - -
9H A 3.2 44.6 + - - +
10H G 5.0 6.2 + - - +
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Residues in contact with LYS 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ARG* 3.3 43.1 + - - +
282B SER 3.7 8.1 - - - +
283B TYR 3.2 0.4 - - - -
284B ASN* 1.3 74.4 - - - +
286B ALA* 1.3 66.9 + - - +
288B LYS* 3.0 10.1 + - + +
289B LYS* 3.0 31.5 + - + +
-14G G 4.3 14.4 + - + +
-13G T 3.0 37.4 + - + -
12H A 4.4 4.9 + - - +
13H A 4.0 10.5 - - - +
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Residues in contact with ALA 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B PHE* 3.8 22.2 - - + -
178B TYR* 3.9 19.7 - - + +
282B SER 3.1 12.1 + - - +
283B TYR 3.1 7.6 + - - +
285B LYS* 1.3 77.5 - - - +
287B LEU* 1.3 63.2 + - - +
289B LYS* 5.1 1.3 - - - -
290B ASN* 2.8 39.2 + - - +
-14G G 4.7 5.8 - - - +
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ILE* 4.5 11.9 - - + -
164B SER* 5.1 0.4 - - - +
165B PHE* 4.2 15.7 - - + -
283B TYR* 2.9 52.2 + - + +
284B ASN* 3.4 9.9 - - - +
286B ALA* 1.3 77.7 - - - +
288B LYS* 1.3 62.9 + - - +
291B ALA* 3.0 60.1 + - + +
296B PHE* 4.1 24.9 - - + +
303B LYS* 3.8 23.1 - - + +
306B ILE* 5.1 3.1 - - + -
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Residues in contact with LYS 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B ASN 2.9 17.4 + - - +
285B LYS* 3.0 9.2 + - + +
287B LEU* 1.3 77.3 - - - +
289B LYS* 1.3 60.3 - - + +
290B ASN 3.7 0.2 + - - -
291B ALA 5.1 1.2 + - - +
296B PHE* 3.7 28.5 - - - +
297B ALA* 5.2 14.5 - - - +
298B ILE 6.1 0.2 - - - -
299B LYS* 5.6 6.2 - - - +
303B LYS* 4.2 16.9 - - - +
10H G 4.2 26.4 + - - +
11H G 4.4 14.5 + - - -
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Residues in contact with LYS 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B LYS* 3.0 19.0 + - + +
286B ALA* 6.0 0.4 - - - -
288B LYS* 1.3 79.7 - - + +
290B ASN* 1.3 78.1 + - - +
-15G A 3.7 34.2 + - - +
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Residues in contact with ASN 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B SER* 3.6 29.5 - - - +
165B PHE* 5.7 1.7 - - + -
168B THR* 3.4 36.3 + - + +
286B ALA* 2.8 33.1 + - - +
287B LEU 3.2 0.4 + - - -
288B LYS 3.5 0.4 + - - -
289B LYS* 1.3 95.2 - - - +
291B ALA* 1.3 71.5 + - - +
292B PRO* 3.3 4.5 - - - +
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Residues in contact with ALA 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ILE* 5.0 2.7 - - + -
164B SER* 3.9 6.8 + - - +
287B LEU* 3.0 34.9 + - + +
288B LYS 5.0 1.4 - - - +
289B LYS 5.5 0.2 - - - -
290B ASN* 1.3 77.6 + - - +
292B PRO* 1.3 65.8 - - + +
293B TYR 2.9 14.7 + - - +
296B PHE* 3.0 36.0 - - + +
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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
------------------------------------------------------------
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