Contacts of the helix formed by residues 280 - 289 (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 PRO 280 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A GLN 3.0 11.2 - - - +
279A ALA* 1.3 89.4 - - + +
281A LEU* 1.3 70.1 + - - +
282A ALA* 3.0 12.8 + - + +
283A GLN* 3.2 7.4 + - + +
284A CYS* 3.0 14.4 + - - +
318A LYS* 5.2 4.3 - - + -
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Residues in contact with LEU 281 (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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280A PRO* 1.3 71.6 - - + +
282A ALA* 1.3 56.0 + - - +
284A CYS* 2.9 9.4 + - - -
285A VAL* 2.2 48.9 + - + +
318A LYS* 5.3 10.0 - - + +
321A ALA* 4.9 17.3 - - + -
322A VAL* 5.0 5.6 - - + +
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Residues in contact with ALA 282 (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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280A PRO* 3.0 12.9 + - + +
281A LEU* 1.3 74.7 - - - +
283A GLN* 1.3 58.3 + - - +
285A VAL* 3.1 9.9 - - - +
286A ALA* 2.8 31.5 + - - +
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Residues in contact with GLN 283 (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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279A ALA* 3.7 23.1 - - + -
280A PRO* 3.2 5.9 + - + +
282A ALA* 1.3 74.6 - - - +
284A CYS* 1.3 56.2 + - - +
286A ALA* 3.4 5.6 - - - +
287A LEU* 2.5 43.5 + - + +
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Residues in contact with CYS 284 (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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274A ILE* 3.4 36.7 - - + +
276A SER* 5.0 2.9 - - - -
279A ALA* 3.9 14.1 - - + +
280A PRO 3.0 13.7 + - - +
281A LEU* 2.9 12.3 + - - +
283A GLN* 1.3 77.2 - - - +
285A VAL* 1.3 50.8 + - - +
287A LEU* 3.1 8.0 + - - +
288A ALA* 2.5 35.9 + - - +
318A LYS* 4.6 18.2 - - + -
319A LEU* 6.1 0.2 - - - -
322A VAL* 3.8 17.5 - - - -
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Residues in contact with VAL 285 (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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281A LEU* 2.2 47.0 + - + +
282A ALA* 3.1 11.7 - - - +
284A CYS* 1.3 69.0 - - - +
286A ALA* 1.3 59.0 + - + +
288A ALA* 3.1 7.4 + - - +
289A GLN* 2.8 48.3 + - + +
322A VAL* 4.0 14.1 - - + +
325A ALA* 3.5 33.0 - - + -
326A VAL* 4.4 8.1 - - + +
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Residues in contact with ALA 286 (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 ALA 2.8 20.7 + - - +
283A GLN* 3.6 5.8 - - - +
285A VAL* 1.3 78.9 - - + +
287A LEU* 1.3 58.0 + - - +
289A GLN* 2.9 30.2 + - - +
290A ARG* 3.9 2.4 + - - +
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Residues in contact with LEU 287 (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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273A GLY 3.0 30.1 - - - +
274A ILE* 4.6 16.8 - - + -
275A GLY 5.7 0.4 - - - +
283A GLN* 2.5 25.2 + - + +
284A CYS* 3.4 6.1 - - - +
286A ALA* 1.3 72.2 - - - +
288A ALA* 1.3 59.7 + - - +
289A GLN 3.4 0.5 + - - -
290A ARG* 4.1 7.3 + - - +
293A VAL* 3.9 10.6 - - - +
534A THR* 4.3 8.3 - - - +
535A GLY* 3.3 26.9 - - - +
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Residues in contact with ALA 288 (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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272A ALA 4.7 0.2 - - - +
274A ILE* 4.1 8.9 - - + +
284A CYS 2.5 18.1 + - - +
285A VAL* 3.1 13.0 + - - +
287A LEU* 1.3 71.9 - - - +
289A GLN* 1.3 57.0 + - - +
290A ARG 3.5 0.9 - - - -
293A VAL* 3.1 27.2 - - + +
294A ARG* 3.3 14.7 + - - +
297A TRP* 5.1 1.9 - - + +
322A VAL* 3.5 30.5 - - + -
326A VAL* 4.1 10.8 - - + +
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Residues in contact with GLN 289 (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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285A VAL* 2.8 29.1 + - + +
286A ALA* 2.9 17.7 + - - +
288A ALA* 1.3 77.8 - - - +
290A ARG* 1.3 53.3 + - - +
294A ARG* 2.8 74.7 + - - +
325A ALA 4.6 4.9 + - - -
326A VAL* 3.4 39.3 + - + +
525B HIS* 5.1 1.2 - - - -
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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