Contacts of the helix formed by residues 289 - 303 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281A GLY* 3.8 13.5 + - - -
282A TYR* 3.3 62.5 + - + +
283A GLY 4.2 0.6 - - - +
286A ASP* 3.9 24.4 + - - +
287A PHE* 3.1 1.4 - - - +
288A GLY* 1.3 83.9 - - - +
290A VAL* 1.3 63.8 + - - +
291A PRO* 3.4 2.9 - - - -
292A GLN* 3.2 38.0 + - + +
293A LEU* 3.1 28.0 + - + +
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Residues in contact with VAL 290 (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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37A LEU* 3.8 27.1 - - + -
82A ALA* 4.1 13.9 - - + +
83A LEU* 3.7 15.7 - - + -
87A TRP* 4.1 17.0 - - + +
287A PHE* 3.5 21.1 - - - +
288A GLY 3.6 1.4 - - - -
289A ARG* 1.3 74.1 - - - +
291A PRO* 1.3 73.4 - - + +
293A LEU* 2.8 21.5 + - - +
294A ILE* 2.9 35.4 + - + +
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Residues in contact with PRO 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 3.9 21.1 - - + -
288A GLY 4.9 2.7 - - - +
289A ARG* 3.4 5.2 - - - -
290A VAL* 1.3 94.0 - - + +
292A GLN* 1.3 65.3 + - - +
294A ILE* 3.5 6.4 + - + +
295A ASP* 2.9 28.5 + - - +
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Residues in contact with GLN 292 (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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282A TYR* 3.3 31.2 + - + +
289A ARG* 3.2 37.7 - - - +
290A VAL 3.1 0.2 - - - -
291A PRO* 1.3 91.9 - - - +
293A LEU* 1.3 59.5 + - - +
295A ASP* 3.3 6.5 + - - +
296A ALA* 2.8 30.8 + - - +
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Residues in contact with LEU 293 (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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34A ALA* 3.4 23.1 - - + +
35A ARG* 4.0 22.2 - - + +
37A LEU* 4.2 15.9 - - + -
38A ALA* 3.2 26.9 - - - +
279A LEU* 3.9 16.8 - - + -
282A TYR* 3.7 29.8 - - + -
283A GLY 5.9 0.4 - - - +
286A ASP 4.1 17.0 - - - +
287A PHE* 5.2 0.7 - - - -
289A ARG* 3.1 22.9 + - + +
290A VAL* 2.8 12.9 + - + +
292A GLN* 1.3 71.6 - - - +
294A ILE* 1.3 61.9 + - - +
296A ALA* 3.2 18.6 + - - +
297A GLY 3.3 0.5 + - - -
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Residues in contact with ILE 294 (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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37A LEU* 3.7 20.2 - - + +
38A ALA* 4.3 0.9 - - - +
40A ILE* 3.8 17.0 - - + -
41A GLY* 3.3 26.5 - - - +
44A LYS* 4.3 16.8 - - - +
79A GLU* 3.8 35.4 - - + +
82A ALA* 4.7 1.1 - - + -
83A LEU* 4.6 4.7 - - + -
290A VAL* 2.9 40.8 + - + +
291A PRO* 3.9 6.1 - - + +
293A LEU* 1.3 74.7 - - - +
295A ASP* 1.3 59.0 + - - +
297A GLY 3.3 1.9 + - - -
298A TYR* 2.9 25.2 + - - +
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Residues in contact with ASP 295 (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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44A LYS* 6.5 0.2 - - - +
291A PRO 2.9 19.3 + - - +
292A GLN* 3.3 8.0 + - - +
294A ILE* 1.3 77.7 - - - +
296A ALA* 1.3 52.2 + - - +
298A TYR* 3.2 12.6 + - - +
299A ARG* 2.6 82.3 + - - +
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Residues in contact with ALA 296 (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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277A PRO* 4.1 4.3 - - + -
278A PRO* 3.7 21.1 - - + +
279A LEU* 3.4 28.7 - - + -
282A TYR* 5.1 3.1 - - - +
292A GLN 2.8 16.8 + - - +
293A LEU 3.2 11.2 - - - +
295A ASP* 1.3 72.8 + - - +
297A GLY* 1.3 57.7 + - - +
299A ARG* 4.1 3.3 - - - +
300A ALA* 3.0 31.5 + - - +
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Residues in contact with GLY 297 (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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38A ALA* 3.5 22.2 - - - +
41A GLY 3.7 7.0 - - - -
42A VAL* 3.6 7.5 + - - +
277A PRO* 4.0 13.0 - - - -
293A LEU 3.3 8.3 + - - -
294A ILE 3.3 0.4 + - - -
296A ALA* 1.3 76.1 - - - +
298A TYR* 1.3 61.0 + - - +
300A ALA* 3.9 0.7 - - - +
301A THR* 2.6 33.4 + - - -
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Residues in contact with TYR 298 (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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41A GLY* 3.2 23.5 - - - +
44A LYS* 4.3 22.0 - - + -
45A ALA* 3.7 22.4 - - + -
48A GLU* 2.7 33.5 + - - -
294A ILE 2.9 14.7 + - - +
295A ASP* 3.3 18.8 - - - +
297A GLY* 1.3 77.4 - - - +
299A ARG* 1.3 69.8 + - + +
301A THR* 3.7 1.7 - - - -
302A THR* 2.8 55.5 + - + +
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Residues in contact with ARG 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A PRO* 5.8 4.3 - - + -
295A ASP* 2.6 53.8 + - - +
296A ALA* 4.1 3.8 - - - +
298A TYR* 1.3 79.0 - - + +
300A ALA* 1.3 65.1 + - - +
302A THR* 3.3 8.1 + - - -
303A VAL* 3.0 33.5 + - + +
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Residues in contact with ALA 300 (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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275A ILE* 4.2 13.4 - - + +
276A GLN 4.6 3.1 - - - +
277A PRO* 3.7 26.0 - - + -
278A PRO* 3.8 8.2 - - + +
296A ALA 3.0 18.8 + - - +
297A GLY 3.9 4.0 - - - +
299A ARG* 1.3 77.7 - - - +
301A THR* 1.3 59.6 + - - +
303A VAL* 3.6 11.0 - - - +
304A LEU* 3.5 22.3 - - - +
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Residues in contact with THR 301 (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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42A VAL* 3.4 21.0 - - + +
45A ALA* 3.6 23.8 - - + -
46A LEU* 3.9 15.5 - - + -
49A GLN* 3.4 5.8 + - - +
275A ILE* 3.9 16.8 - - + +
297A GLY 2.6 22.7 + - - -
299A ARG 3.2 0.2 - - - -
300A ALA* 1.3 73.2 - - - +
302A THR* 1.3 65.8 + - - +
303A VAL 3.1 2.2 - - - -
304A LEU* 3.0 15.2 + - - +
305A ALA 3.4 6.9 + - - -
308A LEU* 3.8 21.6 - - + +
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Residues in contact with THR 302 (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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45A ALA* 4.2 2.8 - - - +
48A GLU* 4.9 2.2 + - - +
49A GLN* 3.6 11.5 + - - +
298A TYR* 2.8 52.8 + - + +
299A ARG* 3.5 9.0 - - - -
301A THR* 1.3 75.8 - - - +
303A VAL* 1.3 63.8 + - + +
305A ALA* 3.3 18.4 + - + +
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Residues in contact with VAL 303 (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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299A ARG* 3.0 24.4 + - + +
300A ALA* 3.6 9.9 - - - +
301A THR 3.1 0.2 - - - -
302A THR* 1.3 79.0 - - + +
304A LEU* 1.3 72.6 + - + +
305A ALA* 3.2 2.8 + - - +
306A ALA* 4.7 4.2 + - - +
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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