Contacts of the helix formed by residues 341 - 347 (chain B) in PDB entry 1FUU
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 GLU 341 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339B ASN* 2.9 18.3 + - - +
340B LYS* 1.3 78.9 - - - +
342B ASN* 1.3 88.8 + - - +
343B TYR 3.2 0.6 + - - -
344B ILE* 3.0 32.1 - - + +
345B HIS* 2.7 25.9 + - - -
377B PHE* 4.3 21.3 - - + -
378B TYR* 4.1 4.0 - - - -
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Residues in contact with ASN 342 (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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317B ASP* 3.7 37.8 + - - +
318B LEU* 5.9 0.6 - - - +
320B ALA* 5.5 0.4 - - - +
337B PRO* 4.7 1.6 - - + -
339B ASN* 2.8 36.2 + - + +
341B GLU* 1.3 93.0 + - - +
343B TYR* 1.3 64.1 + - - +
344B ILE 3.4 0.7 - - - -
345B HIS* 3.5 16.2 + - + +
346B ARG* 3.2 27.3 + - - +
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Residues in contact with TYR 343 (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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230B LEU* 4.4 15.7 - - + -
235B GLN* 3.2 28.2 - - + +
333B ASN* 4.1 5.6 - - - -
337B PRO* 4.1 18.6 - - + +
339B ASN 4.0 1.2 + - - -
340B LYS 3.0 17.8 + - - +
341B GLU 3.2 0.2 - - - -
342B ASN* 1.3 77.9 - - - +
344B ILE* 1.3 63.7 + - - +
346B ARG* 3.1 8.2 + - - +
347B ILE* 3.1 48.7 + - + +
359B ALA* 5.1 0.2 - - - +
361B ASN* 3.3 34.5 + - - -
374B LEU* 3.6 38.8 - - + -
378B TYR* 3.6 18.2 - + - +
380B THR* 5.1 1.1 - - + -
382B ILE* 3.9 10.3 - - + +
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Residues in contact with ILE 344 (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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228B LEU* 3.3 39.9 - - + -
229B THR 4.8 0.9 - - - +
230B LEU* 3.4 16.8 - - + -
341B GLU* 3.0 20.0 - - + +
343B TYR* 1.3 70.9 - - + +
345B HIS* 1.3 96.2 + - + +
346B ARG 2.9 5.8 - - - -
347B ILE* 4.1 5.6 - - - +
348B GLY* 2.7 34.5 + - - -
378B TYR* 3.1 41.3 - - + +
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Residues in contact with HIS 345 (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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265B PHE* 5.4 0.2 - - - -
320B ALA* 3.2 34.4 - - + +
321B ARG* 4.3 21.9 - - + +
325B VAL* 5.6 3.5 - - - +
341B GLU* 2.7 42.6 + - - -
342B ASN* 3.7 17.5 - - + +
343B TYR 3.3 0.8 - - - -
344B ILE* 1.3 101.9 - - + +
346B ARG* 1.3 60.1 + - - +
348B GLY 4.9 0.7 + - - -
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Residues in contact with ARG 346 (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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265B PHE* 3.0 51.3 + - + +
267B ASN* 3.6 9.1 - - - +
317B ASP* 3.5 24.2 + - - +
320B ALA* 3.7 19.7 - - + -
325B VAL* 4.2 17.3 - - - +
331B VAL* 3.9 10.7 - - - +
333B ASN* 2.8 35.6 + - - +
335B ASP 2.9 20.0 + - - -
337B PRO* 2.9 40.1 - - - +
342B ASN 3.2 17.3 - - - +
343B TYR* 3.1 7.1 + - + +
344B ILE 2.9 0.2 - - - -
345B HIS* 1.3 81.4 - - - +
347B ILE* 1.3 66.9 - - + +
348B GLY 3.8 0.8 + - - -
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Residues in contact with ILE 347 (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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230B LEU* 3.1 22.0 - - + +
233B ILE* 3.5 22.0 - - + +
235B GLN* 3.6 21.5 - - - +
331B VAL* 3.7 21.8 - - + -
333B ASN* 4.4 10.1 - - - +
343B TYR* 3.1 53.8 + - + +
344B ILE 3.1 3.1 + - - -
346B ARG* 1.3 84.7 - - + +
348B GLY* 1.3 59.6 + - - +
359B ALA* 3.7 24.9 - - + -
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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