Contacts of the helix formed by residues 290 - 300 (chain A) in PDB entry 5FHH
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 290 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286A ALA 3.9 2.7 + - - +
287A LEU* 4.5 9.0 - - - +
288A ALA 3.5 2.2 - - - -
289A GLN* 1.3 77.6 - - - +
291A PRO* 1.3 92.2 - - + +
292A GLY 4.0 0.4 - - - -
293A VAL* 4.4 1.8 - - + +
294A ARG* 3.0 26.2 + - - +
534A THR 5.1 0.4 + - - -
535A GLY* 2.9 46.6 + - - -
536A GLY 4.6 1.6 - - - +
526B ALA* 5.0 1.3 - - - -
542B GLN* 3.6 11.7 + - - +
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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
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290A ARG* 1.3 98.5 - - + +
292A GLY* 1.3 64.2 + - - +
293A VAL 3.2 0.3 + - - -
294A ARG* 4.6 0.9 - - + -
295A GLN* 2.7 39.3 + - - +
536A GLY* 5.1 0.4 - - - -
526B ALA* 3.2 47.0 - - + +
527B ASP* 3.7 11.7 - - - +
528B ARG* 4.4 0.4 - - + +
542B GLN* 3.4 37.7 - - + +
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Residues in contact with GLY 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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291A PRO* 1.3 83.7 - - - +
293A VAL* 1.3 63.4 + - - +
295A GLN* 4.7 3.6 - - - -
296A GLY* 3.3 16.5 + - - -
532A GLN* 6.3 2.7 - - - -
536A GLY* 4.4 8.0 - - - -
528B ARG* 3.2 40.4 + - - +
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Residues in contact with VAL 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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271A PHE 4.7 7.2 - - - +
272A ALA 3.0 28.9 - - - +
273A GLY* 3.8 19.7 - - - +
287A LEU 3.9 11.0 - - - +
288A ALA* 3.1 29.6 - - + +
290A ARG* 3.9 5.3 + - + +
291A PRO 3.1 0.6 - - - -
292A GLY* 1.3 78.1 - - - +
294A ARG* 1.3 51.0 + - - +
296A GLY 3.6 0.5 - - - -
297A TRP* 2.7 39.4 + - + +
532A GLN* 6.5 1.1 - - + -
533A ALA 4.8 2.0 - - - +
535A GLY 4.2 0.9 - - - +
536A GLY* 3.2 29.3 - - - +
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Residues in contact with ARG 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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288A ALA 3.3 4.4 + - - +
289A GLN* 2.8 76.3 + - - +
290A ARG 3.0 23.3 + - - +
291A PRO* 3.6 2.2 - - + +
293A VAL* 1.3 75.7 - - - +
295A GLN* 1.3 58.5 + - - +
297A TRP* 2.5 26.6 + - - +
298A LEU* 2.6 21.5 + - + +
326A VAL* 4.6 5.8 - - + -
525B HIS* 2.9 60.8 + - - -
526B ALA 5.6 2.2 - - - +
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Residues in contact with GLN 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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291A PRO* 2.7 18.4 + - + +
292A GLY* 4.6 2.7 - - - +
294A ARG* 1.3 77.9 - - - +
296A GLY* 1.3 58.6 + - - +
298A LEU* 4.2 4.7 - - - +
299A ASN* 2.6 36.2 + - - +
526B ALA 5.1 0.9 - - - +
527B ASP* 3.0 29.4 - - - +
528B ARG* 5.6 2.0 - - + +
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Residues in contact with GLY 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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251A VAL* 5.1 0.9 - - - +
271A PHE* 4.1 19.4 - - - -
292A GLY 3.3 16.1 + - - -
293A VAL 3.8 0.4 - - - -
294A ARG 3.0 1.0 - - - -
295A GLN* 1.3 78.2 - - - +
297A TRP* 1.3 63.9 + - - +
298A LEU 3.4 0.3 + - - -
299A ASN* 3.6 9.8 + - - +
300A CYS* 3.8 7.8 + - - +
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Residues in contact with TRP 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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271A PHE* 3.4 40.3 + + - +
272A ALA* 5.0 8.1 - - - -
288A ALA* 5.1 2.5 - - + +
293A VAL* 2.7 21.9 + - + +
294A ARG* 2.5 14.6 + - - +
296A GLY* 1.3 73.3 - - - +
298A LEU* 1.3 59.1 + - - +
300A CYS* 3.6 9.5 - - - -
303A LEU* 4.5 8.5 - - + -
319A LEU* 4.2 23.1 - - + -
322A VAL* 3.2 10.4 + - + -
323A ALA* 2.2 69.5 + - + +
326A VAL* 2.9 35.9 - - + -
327A ARG* 3.5 21.3 + - + +
333A PHE* 4.7 5.6 - + - -
336A ILE* 4.5 11.2 - - + -
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Residues in contact with LEU 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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294A ARG* 2.6 19.0 + - + +
295A GLN* 4.2 5.6 - - - +
297A TRP* 1.3 73.2 - - - +
299A ASN* 1.3 68.2 + - - +
300A CYS 3.3 0.7 + - - -
326A VAL* 4.9 8.7 - - + +
327A ARG* 3.6 30.8 + - + +
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Residues in contact with ASN 299 (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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248A THR 3.9 18.0 - - - +
295A GLN* 2.6 26.5 + - - +
296A GLY* 3.6 3.7 + - - +
297A TRP 3.5 0.6 - - - -
298A LEU* 1.3 80.6 - - - +
300A CYS* 1.3 63.2 + - - +
301A GLN* 3.5 12.5 + - - +
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Residues in contact with CYS 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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249A GLY 3.3 9.6 - - - +
251A VAL* 3.6 29.8 - - + -
271A PHE* 4.4 12.6 - - - -
296A GLY 3.8 7.1 + - - +
297A TRP* 3.6 10.8 - - - -
298A LEU 3.3 2.0 - - - -
299A ASN* 1.3 77.8 - - - +
301A GLN* 1.3 53.0 + - - +
302A ARG 4.8 1.1 - - - +
303A LEU* 4.5 7.0 - - - -
327A ARG* 2.3 57.1 + - - -
336A ILE* 3.9 23.8 - - - -
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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