Contacts of the helix formed by residues 344 - 353 (chain B) in PDB entry 1UPX
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 PHE 344 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244B ASP* 3.6 28.7 - - + -
247B MET* 3.8 11.7 - - + -
248B LEU* 3.7 36.1 - - + -
251B GLN* 2.9 28.5 + - - +
303B LEU* 3.6 29.6 - - + -
323B THR* 5.3 1.1 - - - -
334B ILE* 3.6 35.0 - - + -
342B LYS* 4.0 23.6 - - + -
343B ASP* 1.3 70.1 - - - +
345B SER* 1.3 64.4 + - - +
346B ALA 3.3 2.2 - - - -
347B ILE* 3.1 17.3 - - + +
348B ILE* 3.1 27.0 + - + +
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Residues in contact with SER 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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251B GLN* 4.0 2.3 + - - -
343B ASP* 3.0 26.8 + - - -
344B PHE* 1.3 77.5 - - - +
346B ALA* 1.3 61.8 + - - +
348B ILE* 3.4 9.2 + - - +
349B ALA* 3.0 29.2 + - - +
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Residues in contact with ALA 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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321B TYR* 4.1 13.2 + - + +
343B ASP 4.8 2.6 + - - +
344B PHE 3.3 0.8 - - - -
345B SER* 1.3 83.7 + - - +
347B ILE* 1.3 63.5 + - - +
349B ALA* 3.4 6.4 + - - +
350B HIS* 3.0 23.2 + - - +
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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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235B ILE* 4.0 28.7 - - + -
248B LEU* 4.6 1.3 - - + -
301B PRO* 3.6 23.6 - - + +
302B VAL 4.5 1.1 - - - +
303B LEU* 4.1 16.8 - - + -
321B TYR* 3.5 50.5 - - + -
334B ILE* 4.3 4.4 - - + +
344B PHE* 3.1 43.0 - - + +
346B ALA* 1.3 78.9 - - - +
348B ILE* 1.3 57.0 + - - +
350B HIS* 3.4 2.3 + - - +
351B ALA* 2.9 27.4 + - - +
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Residues in contact with ILE 348 (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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235B ILE* 4.0 12.6 - - + -
248B LEU* 4.6 0.9 - - + -
251B GLN* 3.5 38.4 - - + +
252B THR* 3.7 22.0 - - + -
255B THR* 4.1 28.5 - - + +
257B VAL* 4.2 8.1 - - + -
344B PHE* 3.1 24.9 + - + +
345B SER* 3.7 6.7 - - - +
347B ILE* 1.3 75.1 - - + +
349B ALA* 1.3 65.4 + - - +
351B ALA* 3.1 11.9 + - - +
352B LYS* 3.1 22.5 + - - +
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Residues in contact with ALA 349 (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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345B SER 3.0 17.6 + - - +
346B ALA* 3.7 7.0 - - - +
348B ILE* 1.3 76.8 - - - +
350B HIS* 1.3 63.3 + - - +
352B LYS* 3.3 24.2 + - - +
353B THR* 3.6 12.6 - - - +
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Residues in contact with HIS 350 (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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301B PRO* 4.1 5.6 - - + -
318B ASP* 3.3 37.4 + - - -
319B ARG* 3.6 20.4 - - + +
321B TYR* 2.7 26.1 + - - +
332B LYS* 4.6 1.5 - - - -
346B ALA 3.0 13.9 + - - +
347B ILE 3.5 9.4 - - - +
349B ALA* 1.3 76.8 - - - +
351B ALA* 1.3 63.8 + - - +
353B THR* 2.7 34.8 + - - -
354B CYS* 3.5 16.8 - - - -
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Residues in contact with ALA 351 (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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233B PRO* 3.1 18.4 - - - +
234B GLY 3.9 4.5 - - - +
235B ILE* 3.7 7.2 - - + -
257B VAL* 3.7 27.1 - - + -
301B PRO* 3.6 25.0 - - + +
347B ILE 2.9 14.7 + - - +
348B ILE 3.1 8.9 + - - +
350B HIS* 1.3 74.5 - - - +
352B LYS* 1.3 64.3 + - - +
354B CYS* 3.0 13.9 + - - +
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Residues in contact with LYS 352 (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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233B PRO* 4.3 10.1 - - - +
255B THR* 3.5 39.8 + - - +
256B GLY 5.9 0.2 - - - -
257B VAL* 3.7 13.2 - - + -
348B ILE* 3.1 22.1 + - - +
349B ALA* 3.6 14.4 - - - +
350B HIS 3.2 0.6 - - - -
351B ALA* 1.3 75.8 - - - +
353B THR* 1.3 60.2 + - + +
354B CYS 3.3 3.9 + - - +
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Residues in contact with THR 353 (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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349B ALA 3.6 15.9 - - - +
350B HIS* 2.7 27.9 + - - -
352B LYS* 1.3 78.0 - - + +
354B CYS* 1.3 60.8 + - - +
355B PRO* 4.5 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