Contacts of the helix formed by residues 289 - 303 (chain B) in PDB entry 5FQU
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 ARG 289 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B GLY* 3.8 13.5 + - - -
282B TYR* 3.3 62.0 + - + +
283B GLY 4.2 0.6 - - - +
286B ASP* 3.9 24.6 + - - +
287B PHE* 3.2 1.6 - - - +
288B GLY* 1.3 82.1 - - - +
290B VAL* 1.3 65.7 + - - +
291B PRO* 3.4 3.1 - - - -
292B GLN* 3.2 38.9 + - + +
293B LEU* 3.1 28.4 + - + +
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Residues in contact with VAL 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 3.8 27.6 - - + -
82B ALA* 4.1 14.4 - - + +
83B LEU* 3.7 15.9 - - + -
87B TRP* 4.1 16.4 - - + +
287B PHE* 3.5 20.9 - - - +
288B GLY 3.6 1.2 - - - -
289B ARG* 1.3 74.9 - - - +
291B PRO* 1.4 65.5 - - + +
293B LEU* 2.8 26.7 + - - +
294B ILE* 2.9 35.7 + - + +
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Residues in contact with PRO 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LEU* 3.9 21.5 - - + -
288B GLY 4.9 2.5 - - - +
289B ARG* 3.4 5.4 - - - -
290B VAL* 1.4 93.6 - - + +
292B GLN* 1.3 67.0 + - - +
294B ILE* 3.5 7.0 + - + +
295B ASP* 3.0 28.8 + - - +
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Residues in contact with GLN 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B TYR* 3.4 31.0 + - + +
289B ARG* 3.2 39.1 - - - +
291B PRO* 1.3 91.3 - - - +
293B LEU* 1.3 61.0 + - - +
295B ASP* 3.3 7.1 + - - +
296B ALA* 2.8 30.1 + - - +
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Residues in contact with LEU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ALA* 3.4 23.1 - - + +
35B ARG* 4.0 22.4 - - + +
37B LEU* 4.2 14.8 - - + -
38B ALA* 3.2 20.8 - - - +
279B LEU* 3.9 16.8 - - + -
282B TYR* 3.7 29.4 - - + -
283B GLY 5.8 0.4 - - - +
286B ASP 4.1 17.9 - - - +
287B PHE* 5.2 0.4 - - - -
289B ARG* 3.1 22.5 + - + +
290B VAL* 2.8 11.9 + - + +
292B GLN* 1.3 71.9 - - - +
294B ILE* 1.3 62.8 + - - +
296B ALA* 3.2 18.9 + - - +
297B GLY 3.2 6.1 + - - -
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Residues in contact with ILE 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 3.7 21.1 - - + +
38B ALA* 4.3 0.9 - - - +
40B ILE* 3.8 16.8 - - + -
41B GLY* 3.3 27.3 - - - +
44B LYS* 4.3 16.6 - - - +
79B GLU* 3.8 35.9 - - + +
82B ALA* 4.7 1.1 - - + -
83B LEU* 4.6 4.3 - - + -
290B VAL* 2.9 39.3 + - + +
291B PRO* 3.9 5.8 - - + +
293B LEU* 1.3 72.8 - - - +
295B ASP* 1.3 67.0 + - - +
297B GLY 3.3 1.9 + - - -
298B TYR* 2.9 19.3 + - - +
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Residues in contact with ASP 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B PRO 3.0 19.0 + - - +
292B GLN* 3.6 7.9 - - - +
293B LEU 3.3 0.2 - - - -
294B ILE* 1.3 77.6 - - - +
296B ALA* 1.3 52.8 + - - +
298B TYR* 3.2 13.4 + - - +
299B ARG* 2.6 81.3 + - - +
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Residues in contact with ALA 296 (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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277B PRO* 4.1 4.9 - - + -
278B PRO* 3.7 22.7 - - + +
279B LEU* 3.4 27.8 - - + -
282B TYR* 5.1 3.4 - - - +
292B GLN 2.8 17.1 + - - +
293B LEU 3.2 11.9 + - - +
295B ASP* 1.3 73.0 - - - +
297B GLY* 1.3 57.4 + - - +
299B ARG* 4.0 3.4 - - - +
300B ALA* 3.0 31.2 + - - +
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Residues in contact with GLY 297 (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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38B ALA* 3.5 22.5 - - - +
41B GLY 3.7 7.4 - - - -
42B VAL* 3.6 8.0 + - - +
277B PRO* 4.0 12.6 - - - -
293B LEU 3.2 8.3 + - - -
294B ILE 3.3 0.6 + - - -
296B ALA* 1.3 75.4 - - - +
298B TYR* 1.3 60.9 + - - +
300B ALA* 3.6 0.9 + - - +
301B THR* 2.6 33.3 + - - -
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Residues in contact with TYR 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLY* 3.2 22.2 - - - +
44B LYS* 4.3 23.1 - - + -
45B ALA* 3.7 21.9 - - + +
48B GLU* 2.7 37.1 + - - -
294B ILE 2.9 14.7 + - - +
295B ASP* 3.3 18.8 - - - +
297B GLY* 1.3 77.7 - - - +
299B ARG* 1.3 70.2 + - + +
301B THR* 3.7 1.9 - - - -
302B THR* 2.8 56.3 + - + +
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Residues in contact with ARG 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B PRO* 5.8 3.8 - - + -
295B ASP* 2.6 53.7 + - - +
296B ALA* 4.0 4.5 - - - +
298B TYR* 1.3 78.3 - - + +
300B ALA* 1.3 65.7 + - - +
302B THR* 3.3 7.9 + - - -
303B VAL* 3.0 33.0 + - + +
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Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ILE* 4.2 13.8 - - + +
276B GLN 4.7 2.9 - - - +
277B PRO* 3.7 26.7 - - + -
278B PRO* 3.9 7.5 - - + +
296B ALA 3.0 18.9 + - - +
297B GLY 3.9 4.3 - - - +
299B ARG* 1.3 77.2 - - - +
301B THR* 1.3 59.4 + - - +
303B VAL* 3.6 11.3 - - - +
304B LEU* 3.5 22.2 - - - +
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Residues in contact with THR 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 3.4 22.4 - - + +
45B ALA* 3.6 24.2 - - + -
46B LEU* 3.9 15.0 - - + -
49B GLN* 3.4 6.1 + - - +
275B ILE* 3.9 16.1 - - + +
297B GLY 2.6 22.6 + - - -
299B ARG 3.2 0.2 - - - -
300B ALA* 1.3 74.7 - - - +
302B THR* 1.3 65.8 + - - +
303B VAL 3.1 1.6 - - - -
304B LEU* 3.0 16.5 + - - +
305B ALA 3.4 7.4 + - - -
308B LEU* 3.8 21.6 - - + +
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Residues in contact with THR 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ALA* 4.2 2.1 - - - +
48B GLU* 4.8 2.1 + - - +
49B GLN* 3.6 11.5 + - - +
298B TYR* 2.8 53.9 + - + +
299B ARG* 3.6 9.2 - - - +
301B THR* 1.3 76.0 - - - +
303B VAL* 1.3 63.8 + - + +
305B ALA* 3.3 18.3 + - + +
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Residues in contact with VAL 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ARG* 3.0 24.1 + - + +
300B ALA* 3.6 8.7 - - - +
301B THR 3.1 0.2 - - - -
302B THR* 1.3 79.4 - - + +
304B LEU* 1.3 72.1 + - + +
305B ALA* 3.2 3.0 + - - +
306B ALA* 4.7 4.3 + - - +
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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