Contacts of the helix formed by residues 343 - 354 (chain A) in PDB entry 1UD8
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 343 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292A PHE* 4.0 30.3 - + - -
295A ALA* 3.5 29.4 - - + -
296A SER* 4.2 9.4 - - - -
304A MET* 4.0 18.2 - - + -
307A ILE* 4.0 12.6 - - + -
339A VAL* 4.0 19.7 - - + -
340A ALA 3.2 2.2 + - - +
342A TRP* 1.3 108.1 - + + +
344A LYS* 1.3 66.2 + - - +
345A PRO* 3.1 3.8 - - - -
346A LEU* 3.0 43.4 + - + +
347A ALA* 3.0 13.0 + - + -
427A ASN* 4.1 6.5 - - + -
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Residues in contact with LYS 344 (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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324A VAL* 3.9 7.2 - - + -
325A ASP* 3.0 21.5 + - - -
338A TRP* 3.4 13.9 - - + -
339A VAL* 3.3 36.5 + - - +
340A ALA 2.9 15.5 + - - +
341A ASP* 3.9 7.2 - - - +
343A PHE* 1.3 77.0 - - - +
345A PRO* 1.3 66.2 - - + +
347A ALA* 3.9 2.6 - - - +
348A TYR* 3.2 35.8 + - + -
365A ASP* 2.9 46.2 + - + +
377A LYS* 4.9 11.4 - - + +
380A MET* 4.2 7.6 - - + -
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Residues in contact with PRO 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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341A ASP 3.0 20.0 - - - +
342A TRP 3.0 15.7 - - - +
343A PHE 3.2 1.3 - - - -
344A LYS* 1.3 92.5 - - + +
346A LEU* 1.3 62.3 + - + +
348A TYR* 3.5 2.1 + - - +
349A ALA* 3.1 24.1 + - - +
380A MET* 3.4 34.3 - - + -
384A LEU* 4.0 3.9 - - + +
452A ASN* 6.1 1.8 - - - +
474A VAL* 4.0 17.1 - - + +
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Residues in contact with LEU 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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304A MET* 4.8 0.7 - - + -
342A TRP* 4.1 17.9 - - + +
343A PHE* 3.0 40.8 + - + +
345A PRO* 1.3 76.7 - - + +
347A ALA* 1.3 64.9 + - - +
349A ALA* 3.3 4.2 + - - +
350A THR* 3.0 25.9 + - - -
425A MET* 3.8 27.1 - - - +
426A SER 4.0 20.4 - - - +
427A ASN* 4.3 8.7 - - + -
472A GLY 4.6 0.9 - - - -
473A SER* 3.7 33.4 - - - +
474A VAL* 3.7 12.8 - - + -
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Residues in contact with ALA 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A PHE* 3.7 38.4 - - + -
324A VAL* 3.5 31.6 - - + -
339A VAL* 4.8 0.2 - - + -
343A PHE* 3.0 20.0 + - + +
344A LYS* 4.0 2.5 - - - +
345A PRO 3.4 0.2 - - - -
346A LEU* 1.3 76.5 - - - +
348A TYR* 1.3 64.2 + - - +
350A THR* 3.0 13.6 + - - -
351A ILE* 3.2 12.0 + - - +
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Residues in contact with TYR 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A VAL* 3.5 28.4 + - + +
344A LYS* 3.2 39.5 + - + +
345A PRO 3.9 0.7 - - - +
346A LEU 3.4 0.2 - - - -
347A ALA* 1.3 78.1 - - - +
349A ALA* 1.3 57.1 + - - +
351A ILE* 3.4 7.2 + - + +
352A LEU* 2.9 55.3 + - + +
360A ASN 4.2 5.0 + - - -
361A VAL* 4.1 21.3 - - + -
362A PHE* 3.2 22.5 + - - +
365A ASP* 2.8 30.8 + - - +
380A MET* 4.0 9.9 - - + -
381A ILE* 3.9 22.9 - - + -
384A LEU* 3.9 16.4 - - + -
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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 PRO 3.1 14.3 + - - +
346A LEU 3.6 7.9 - - - +
347A ALA 3.2 0.2 - - - -
348A TYR* 1.3 76.0 - - - +
350A THR* 1.3 64.7 + - - +
353A THR* 2.7 37.5 + - - +
384A LEU* 3.7 23.0 - - + +
408A TRP* 4.0 1.1 - - - -
423A THR* 4.6 6.7 - - + -
425A MET* 4.3 4.5 - - + -
474A VAL* 3.9 24.0 - - + -
476A VAL* 4.7 1.3 - - + -
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Residues in contact with THR 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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288A LEU* 5.5 0.4 - - + -
292A PHE* 4.1 19.3 - - + -
304A MET* 5.8 0.9 - - - +
307A ILE* 5.5 7.5 - - + +
308A LEU* 4.0 24.9 - - + -
346A LEU 3.0 15.1 + - - -
347A ALA* 3.0 11.9 + - - -
349A ALA* 1.3 78.3 - - - +
351A ILE* 1.3 59.8 + - + +
354A ARG* 3.1 43.9 - - - +
400A PHE* 5.9 0.4 - - + -
408A TRP* 3.5 21.8 - - + -
425A MET* 3.9 5.7 - - - +
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Residues in contact with ILE 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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288A LEU* 4.0 6.7 - - + -
292A PHE* 3.9 29.6 - - + -
322A THR* 3.4 49.9 + - + +
323A PHE* 3.7 14.8 - - - +
324A VAL* 4.1 12.3 - - + -
347A ALA 3.2 4.0 + - - +
348A TYR* 3.6 16.2 - - + +
350A THR* 1.3 77.2 - - + +
352A LEU* 1.3 68.9 + - + +
354A ARG* 4.7 3.7 - - - +
356A GLY 4.8 3.8 - - - +
359A PRO* 3.0 23.7 - - + +
360A ASN 4.0 16.6 - - - +
388A ARG* 3.6 4.3 + - - -
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Residues in contact with LEU 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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6A THR* 3.8 28.5 - - + -
348A TYR* 2.9 43.5 + - + +
349A ALA* 4.4 0.7 - - - +
351A ILE* 1.3 84.8 - - + +
353A THR* 1.3 60.8 + - + +
359A PRO* 3.9 13.2 - - + -
360A ASN 5.6 0.2 - - - +
361A VAL* 4.6 6.3 - - + -
381A ILE* 4.7 7.0 - - + -
384A LEU* 3.8 32.5 - - + +
385A LEU* 3.9 17.0 - - + -
388A ARG* 2.9 46.6 + - - +
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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* 2.7 22.9 + - - +
352A LEU* 1.3 81.5 - - + +
354A ARG* 1.3 63.6 + - - +
384A LEU* 4.7 8.3 - - + -
387A ALA* 3.9 27.6 - - + -
388A ARG 4.8 0.4 - - - +
392A ALA* 3.6 7.2 - - - +
408A TRP* 3.1 19.8 + - - -
410A ARG* 3.1 28.8 + - - +
421A LEU* 4.0 12.6 - - + -
423A THR* 3.1 16.2 + - - +
476A VAL* 4.3 11.2 - - + -
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Residues in contact with ARG 354 (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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308A LEU* 3.5 26.6 - - - +
350A THR* 3.1 33.1 + - - +
351A ILE* 4.7 1.7 - - - +
352A LEU 3.6 1.0 - - - -
353A THR* 1.3 82.0 - - - +
355A GLU* 1.3 63.2 + - - +
356A GLY* 3.5 10.8 + - - +
388A ARG* 3.7 18.2 + - - -
396A GLN* 3.0 27.4 - - - +
398A ASP* 3.0 32.1 + - - -
400A PHE* 3.8 9.0 - - - -
408A TRP* 3.2 53.6 - - + +
410A ARG* 4.0 3.0 + - - -
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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