Contacts of the helix formed by residues 338 - 349 (chain A) in PDB entry 5UFL
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 LEU 338 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320A MET 6.2 0.4 - - - -
334A HIS* 3.3 49.8 - - + +
335A THR* 3.4 11.8 + - + +
336A LYS 3.2 0.2 - - - -
337A CYS* 1.3 79.5 - - - +
339A GLU* 1.3 61.5 - - - +
340A PRO* 3.5 4.9 - - - -
341A THR* 3.5 13.8 + - - +
342A VAL* 3.2 33.5 + - + +
388A LEU* 4.9 16.2 - - + -
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Residues in contact with GLU 339 (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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286A GLY* 5.5 4.5 - - - -
289A ASN* 3.7 32.8 + - - +
335A THR* 3.3 25.7 + - + +
336A LYS* 3.5 34.4 + - - +
338A LEU* 1.3 75.9 - - - +
340A PRO* 1.4 71.3 - - + +
342A VAL* 3.6 3.2 + - - +
343A ALA* 3.0 26.7 + - - +
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Residues in contact with PRO 340 (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 HIS* 5.4 10.3 - - + -
285A LEU* 4.4 32.1 - - + +
288A LEU* 4.8 2.5 - - + +
289A ASN* 5.6 0.2 - - - +
319A MET 4.6 11.0 - - - +
320A MET* 3.5 33.5 - - + +
336A LYS 4.4 5.8 - - - +
337A CYS 5.1 1.6 - - - +
338A LEU* 3.5 6.7 - - - -
339A GLU* 1.4 95.2 - - + +
341A THR* 1.3 61.9 + - - +
343A ALA* 3.5 6.7 - - + +
344A LEU* 3.4 24.1 + - - +
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Residues in contact with THR 341 (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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320A MET* 3.9 30.2 + - + +
321A PHE* 4.1 7.6 - - + -
338A LEU* 3.5 20.8 + - - +
340A PRO* 1.3 76.8 - - - +
342A VAL* 1.3 63.6 + - - +
344A LEU* 3.2 9.8 + - - +
345A LEU* 2.9 32.1 + - - +
366A PHE* 4.3 3.4 - - + -
385A PHE* 3.4 46.4 - - + -
388A LEU* 5.4 1.6 - - - +
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Residues in contact with VAL 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A LEU* 3.2 37.3 + - + +
339A GLU* 4.2 3.8 - - - +
341A THR* 1.3 77.0 + - - +
343A ALA* 1.3 64.9 + - - +
345A LEU* 3.7 17.6 - - + +
346A ARG* 3.2 22.2 + - - +
388A LEU* 4.7 10.3 - - + -
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Residues in contact with ALA 343 (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 LEU 5.0 0.2 - - - +
288A LEU* 3.6 32.9 - - + +
289A ASN* 3.8 15.5 - - - +
339A GLU 3.0 19.3 + - - +
340A PRO* 3.5 8.3 - - + +
341A THR 3.2 0.2 - - - -
342A VAL* 1.3 79.5 - - - +
344A LEU* 1.3 58.8 - - - +
346A ARG* 3.4 15.4 + - - +
347A TRP* 3.1 23.6 + - - -
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Residues in contact with LEU 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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288A LEU* 3.9 15.7 - - + -
300A LEU* 3.4 33.7 - - + -
320A MET* 4.3 25.1 - - + -
340A PRO 3.4 13.4 + - - +
341A THR* 3.2 5.5 + - - +
343A ALA* 1.3 76.8 - - - +
345A LEU* 1.3 66.6 + - - +
347A TRP* 3.2 17.1 + - + +
348A LEU* 3.6 9.2 + - - +
362A ALA* 3.9 13.6 - - + +
365A LEU* 4.0 19.3 - - + -
366A PHE* 3.5 40.2 - - + -
369A ILE* 5.1 1.3 - - + -
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Residues in contact with LEU 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 THR 2.9 20.1 + - - +
342A VAL* 3.7 16.8 - - + +
343A ALA 3.4 0.2 - - - -
344A LEU* 1.3 74.2 - - - +
346A ARG* 1.3 65.1 + - - +
348A LEU* 3.3 19.2 + - + +
349A SER* 3.4 12.5 + - - -
366A PHE* 4.6 2.9 - - + -
385A PHE* 4.3 9.4 - - + -
388A LEU* 4.3 31.0 - - + +
389A LEU* 3.4 35.0 - - + -
392A THR* 4.0 30.7 - - + +
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Residues in contact with ARG 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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288A LEU 2.7 28.9 + - - -
289A ASN* 3.3 15.9 + - - +
290A GLY 3.1 14.3 + - - -
291A LYS* 4.0 32.5 + - - +
342A VAL 3.2 12.2 + - - +
343A ALA* 3.4 13.0 + - - +
344A LEU 3.2 0.4 - - - -
345A LEU* 1.3 74.9 - - - +
347A TRP* 1.3 88.9 + - - +
349A SER* 2.7 23.9 + - - +
350A GLN* 3.4 23.2 + - - +
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Residues in contact with TRP 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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288A LEU* 3.7 16.7 + - + +
290A GLY 3.7 2.2 - - - -
291A LYS 4.3 3.4 - - - -
292A ASP 3.7 15.0 - - - -
293A PRO* 3.9 14.8 - - + -
296A SER* 3.2 36.1 - - - -
300A LEU* 4.3 12.8 - - + -
343A ALA 3.1 28.6 + - - -
344A LEU* 3.2 13.7 + - + +
346A ARG* 1.3 109.6 - - - +
348A LEU* 1.3 57.5 + - - +
350A GLN* 3.6 31.7 + - + +
358A CYS* 3.5 46.2 - - + +
359A SER* 2.6 32.1 + - - -
362A ALA* 4.2 2.9 - - + -
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Residues in contact with LEU 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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344A LEU 3.9 8.7 - - - +
345A LEU* 3.3 9.6 + - + +
347A TRP* 1.3 78.9 - - - +
349A SER* 1.3 56.4 + - - +
359A SER* 3.5 26.7 - - - +
362A ALA* 3.7 16.8 - - + -
363A LEU* 3.6 31.0 - - + +
366A PHE* 4.2 15.7 - - + -
389A LEU* 4.4 4.3 - - + -
392A THR* 4.0 22.7 - - + +
393A ILE* 4.3 15.0 - - + -
396A GLN* 2.9 24.3 + - + +
415A ARG* 2.8 27.0 + - - -
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Residues in contact with SER 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 LEU 3.4 6.0 + - - -
346A ARG* 2.7 29.6 + - - +
348A LEU* 1.3 75.3 - - - +
350A GLN* 1.3 65.0 + - - +
351A PRO* 3.7 2.4 - - - +
392A THR* 4.9 6.5 - - - +
396A GLN* 4.7 2.2 - - - +
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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