Contacts of the helix formed by residues 344 - 353 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A ASP* 3.7 16.8 - - + -
247A MET* 3.8 10.8 - - + -
248A LEU* 3.6 44.6 - - + -
251A GLN* 2.8 28.3 + - - +
303A LEU* 3.7 27.6 - - + -
323A THR* 5.3 1.1 - - + -
334A ILE* 3.4 37.2 - - + -
342A LYS* 3.9 24.7 - - + -
343A ASP* 1.3 70.1 - - - +
345A SER* 1.3 65.0 + - - +
346A ALA 3.2 2.9 - - - -
347A ILE* 3.0 31.6 - - + +
348A ILE* 3.0 14.4 + - + +
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Residues in contact with SER 345 (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 GLN* 4.0 2.2 + - - -
343A ASP* 2.9 29.5 + - - -
344A PHE* 1.3 78.0 - - - +
346A ALA* 1.3 59.9 + - - +
348A ILE* 3.4 10.3 + - - +
349A ALA* 3.0 28.8 + - - +
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Residues in contact with ALA 346 (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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321A TYR* 4.0 14.5 + - + +
332A LYS* 6.4 0.2 - - + -
343A ASP 4.9 3.0 + - - +
344A PHE 3.2 0.6 - - - -
345A SER* 1.3 79.8 + - - +
347A ILE* 1.3 61.6 + - - +
349A ALA* 3.4 6.3 + - - +
350A HIS* 2.9 28.9 + - - +
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Residues in contact with ILE 347 (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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235A ILE* 3.9 30.7 - - + -
248A LEU* 4.5 1.8 - - + -
301A PRO* 3.5 24.0 - - + +
302A VAL 4.4 1.6 - - - +
303A LEU* 4.0 16.8 - - + -
321A TYR* 3.5 48.5 + - + -
334A ILE* 4.6 2.8 - - + +
344A PHE* 3.0 46.4 - - + +
346A ALA* 1.3 78.1 - - - +
348A ILE* 1.3 58.1 + - - +
350A HIS* 3.3 2.0 + - - +
351A ALA* 2.9 27.9 + - - +
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Residues in contact with ILE 348 (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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235A ILE* 4.0 11.7 - - + -
248A LEU* 4.7 0.2 - - + -
251A GLN* 3.5 42.2 - - + +
252A THR* 3.8 19.5 - - + -
255A THR* 4.2 20.0 - - + +
257A VAL* 4.0 16.1 - - + +
344A PHE* 3.0 23.8 + - + +
345A SER* 3.7 8.3 - - - +
346A ALA 3.3 0.2 - - - -
347A ILE* 1.3 74.8 - - + +
349A ALA* 1.3 66.6 + - - +
351A ALA* 3.2 12.4 + - - +
352A LYS* 3.2 22.4 + - - +
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Residues in contact with ALA 349 (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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345A SER 3.0 17.6 + - - +
346A ALA* 3.8 6.5 - - - +
348A ILE* 1.3 76.7 - - - +
350A HIS* 1.3 63.6 + - - +
352A LYS* 3.2 25.5 + - - +
353A THR* 3.6 12.2 - - - +
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Residues in contact with HIS 350 (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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301A PRO* 4.0 6.5 - - + -
318A ASP* 3.2 39.0 + - - -
319A ARG* 3.6 19.1 - - + +
321A TYR* 2.7 26.2 + - - +
332A LYS* 4.7 1.8 - - - -
346A ALA 2.9 17.9 + - - +
347A ILE 3.4 5.4 - - - +
349A ALA* 1.3 78.0 - - - +
351A ALA* 1.3 61.3 + - - +
353A THR* 2.7 36.3 + - - -
354A CYS* 3.5 16.0 - - - -
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Residues in contact with ALA 351 (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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233A PRO* 3.2 17.7 - - + +
234A GLY 3.8 6.9 + - - +
235A ILE* 3.7 17.3 - - + -
257A VAL* 3.8 13.9 - - + -
301A PRO* 3.5 24.6 - - + +
347A ILE 2.9 14.6 + - - +
348A ILE 3.2 9.4 + - - +
350A HIS* 1.3 76.9 - - - +
352A LYS* 1.3 62.0 + - - +
354A CYS* 3.0 15.8 + - - +
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Residues in contact with LYS 352 (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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233A PRO* 4.3 12.2 - - + +
255A THR* 3.5 30.4 + - - +
257A VAL* 3.7 11.4 - - + -
348A ILE* 3.6 29.0 - - - +
349A ALA* 3.2 14.6 + - - +
350A HIS 3.2 1.0 - - - -
351A ALA* 1.3 76.3 - - - +
353A THR* 1.3 61.2 + - + +
354A CYS 3.3 4.2 + - - +
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Residues in contact with THR 353 (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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349A ALA 3.6 14.6 - - - +
350A HIS* 2.7 31.1 + - - -
352A LYS* 1.3 77.8 - - + +
354A CYS* 1.3 60.4 + - - +
355A PRO* 4.5 2.3 - - - +
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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