Contacts of the helix formed by residues 329 - 350 (chain A) in PDB entry 5U2H
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 ASN 329 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A TYR* 3.1 11.7 + - - +
53A LYS* 4.4 11.4 - - + -
327A LYS 3.3 6.5 + - - +
328A PHE* 1.3 75.2 - - - +
330A VAL* 1.3 65.4 + - - +
331A ILE* 4.4 4.7 - - + +
332A GLN* 3.4 17.2 + - + +
333A LEU* 3.3 19.2 + - - +
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Residues in contact with VAL 330 (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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329A ASN* 1.3 70.2 - - - +
331A ILE* 1.3 66.5 + - - +
333A LEU* 3.3 6.7 + - - +
334A ALA* 2.9 25.7 + - - +
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Residues in contact with ILE 331 (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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329A ASN* 3.3 5.0 - - + +
330A VAL* 1.3 78.5 - - - +
332A GLN* 1.3 56.7 + - - +
334A ALA* 3.3 6.9 + - - +
335A VAL* 2.9 29.9 + - - +
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Residues in contact with GLN 332 (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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50A ARG 3.7 23.6 - - - +
51A TYR* 3.7 7.4 - - - +
52A GLN 5.4 2.2 - - - +
53A LYS* 5.6 2.2 - - - +
329A ASN* 3.4 18.3 + - + +
330A VAL 3.2 0.6 - - - -
331A ILE* 1.3 78.0 - - - +
333A LEU* 1.3 62.7 + - - +
335A VAL* 3.1 8.1 + - - +
336A TYR* 2.9 23.8 + - - +
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Residues in contact with LEU 333 (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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51A TYR* 4.4 20.7 - - + +
329A ASN 3.3 9.1 + - - +
330A VAL* 3.3 9.7 + - - +
332A GLN* 1.3 78.8 - - - +
334A ALA* 1.3 57.6 + - - +
336A TYR* 3.3 6.6 + - - +
337A ILE* 2.9 30.8 + - - +
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Residues in contact with ALA 334 (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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330A VAL 2.9 16.8 + - - +
331A ILE* 3.7 7.0 - - - +
333A LEU* 1.3 77.5 - - - +
335A VAL* 1.3 57.0 + - - +
337A ILE* 3.9 5.3 - - - +
338A GLY* 2.9 26.3 + - - -
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Residues in contact with VAL 335 (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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331A ILE 2.9 17.6 + - - +
332A GLN* 3.5 7.0 - - - +
334A ALA* 1.3 74.8 - - - +
336A TYR* 1.3 66.2 + - - +
338A GLY* 3.2 2.6 + - - -
339A SER* 2.9 23.4 + - - -
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Residues in contact with TYR 336 (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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45A LEU* 5.6 8.1 - - + -
50A ARG* 4.8 18.6 - - + -
51A TYR 5.9 0.4 - - - +
332A GLN 2.9 16.2 + - - +
333A LEU* 3.8 7.0 - - - +
335A VAL* 1.3 76.4 - - - +
337A ILE* 1.3 61.6 + - - +
339A SER* 3.1 8.2 + - - -
340A VAL* 2.9 24.2 + - - +
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Residues in contact with ILE 337 (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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333A LEU 2.9 17.0 + - - +
334A ALA* 3.9 6.3 - - - +
336A TYR* 1.3 75.5 - - - +
338A GLY* 1.3 58.7 + - - +
340A VAL* 3.2 5.8 + - - +
341A ILE* 2.9 31.6 + - - +
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Residues in contact with GLY 338 (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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334A ALA 2.9 15.8 + - - -
335A VAL* 3.2 4.0 + - - -
337A ILE* 1.3 77.8 - - - +
339A SER* 1.3 59.6 + - - +
341A ILE* 3.7 15.1 + - - +
342A SER* 4.1 6.9 + - - -
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Residues in contact with SER 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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335A VAL 2.9 16.1 + - - -
336A TYR* 3.6 7.4 - - - -
338A GLY* 1.3 77.4 - - - +
340A VAL* 1.3 63.5 + - - +
341A ILE 3.6 0.2 + - - -
342A SER* 3.9 9.5 + - - -
343A TYR* 3.9 9.4 + - - +
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Residues in contact with VAL 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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41A ILE* 4.3 23.8 - - + -
336A TYR 2.9 15.9 + - - +
337A ILE* 3.9 5.6 - - - +
339A SER* 1.3 76.1 - - - +
341A ILE* 1.3 66.7 + - - +
343A TYR* 3.1 9.7 + - + +
344A PHE* 2.9 24.0 + - - +
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Residues in contact with ILE 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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337A ILE 2.9 16.1 + - - +
338A GLY* 3.9 9.6 - - - +
339A SER 3.3 0.4 - - - -
340A VAL* 1.3 76.9 - - - +
342A SER* 1.3 64.3 + - - +
344A PHE* 3.2 8.0 + - - +
345A GLY* 2.9 20.4 + - - -
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Residues in contact with SER 342 (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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338A GLY 4.1 6.4 + - - -
339A SER* 3.9 8.4 + - - -
340A VAL 3.3 0.6 - - - -
341A ILE* 1.3 76.9 - - - +
343A TYR* 1.3 57.8 + - - +
345A GLY* 3.3 1.4 + - - +
346A LEU* 2.9 31.2 + - - +
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Residues in contact with TYR 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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37A VAL* 5.5 2.5 - - + -
339A SER 3.9 7.2 + - - +
340A VAL* 3.1 15.2 + - - +
342A SER* 1.3 78.7 - - - +
344A PHE* 1.3 56.5 + - - +
346A LEU* 3.4 5.5 + - - +
347A ALA* 2.9 28.8 + - - +
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Residues in contact with PHE 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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34A HIS* 5.2 9.3 - - - +
37A VAL* 4.7 12.6 - - + -
38A PHE* 5.5 7.9 - - + +
340A VAL 2.9 13.3 + - - +
341A ILE* 3.6 9.9 - - - +
343A TYR* 1.3 76.2 - - - +
345A GLY* 1.3 63.0 + - - +
347A ALA* 3.1 9.5 + - - +
348A THR* 2.9 22.8 + - - -
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Residues in contact with GLY 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 ILE 2.9 14.4 + - - -
342A SER* 3.7 2.9 - - - -
344A PHE* 1.3 77.4 - - - +
346A LEU* 1.3 55.7 + - - +
348A THR* 3.1 9.7 + - - -
349A VAL* 2.9 27.4 + - - +
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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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342A SER 2.9 17.4 + - - +
343A TYR* 3.8 6.7 - - - +
345A GLY* 1.3 74.8 - - - +
347A ALA* 1.3 61.8 + - - +
349A VAL* 3.1 8.0 + - - +
350A PHE* 3.0 23.0 + - - +
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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
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34A HIS* 4.8 13.4 + - - +
37A VAL* 4.1 24.0 - - + -
343A TYR 2.9 14.3 + - - +
344A PHE 3.1 8.5 + - - +
346A LEU* 1.3 77.1 - - - +
348A THR* 1.3 60.6 + - - +
349A VAL 3.6 0.2 + - - -
350A PHE* 3.7 12.9 + - - +
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Residues in contact with THR 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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34A HIS* 4.6 18.6 - - - +
344A PHE 2.9 13.3 + - - -
345A GLY* 3.5 10.3 - - - -
347A ALA* 1.3 75.4 - - - +
349A VAL* 1.3 65.3 + - - +
350A PHE* 4.4 2.6 - - - +
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Residues in contact with VAL 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 GLY 2.9 13.0 + - - +
346A LEU* 3.6 11.2 - - - +
348A THR* 1.3 76.9 - - - +
350A PHE* 1.3 75.5 + - - +
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Residues in contact with PHE 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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346A LEU 3.0 14.7 + - - +
347A ALA* 3.7 11.2 + - - +
348A THR 3.5 2.9 - - - +
349A VAL* 1.3 86.6 - - - +
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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