Contacts of the helix formed by residues 323 - 339 (chain F) in PDB entry 4U0Z
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 HIS 323 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313F GLN* 3.8 25.6 + - + +
321F PRO 3.6 0.8 + - - -
322F PRO* 1.3 73.7 - - - +
324F PRO* 1.4 76.6 - - + +
325F GLN* 3.0 56.2 + - + +
326F ASP* 2.7 43.9 + - - +
327F VAL* 3.3 5.8 + - - -
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Residues in contact with PRO 324 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309F PHE* 6.0 0.7 - - - +
310F ARG* 3.3 33.0 - - - +
311F THR* 3.3 21.3 - - - +
312F THR* 3.2 28.7 - - - +
313F GLN* 4.2 2.5 - - - -
322F PRO 3.6 0.2 - - - -
323F HIS* 1.4 105.4 - - + +
325F GLN* 1.3 58.6 + - + +
326F ASP 3.3 0.6 + - - -
327F VAL* 3.6 23.8 + - + +
328F GLU* 4.7 2.4 + - - +
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Residues in contact with GLN 325 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323F HIS* 2.8 32.0 + - + +
324F PRO* 1.3 75.1 - - + +
326F ASP* 1.3 67.1 + - - +
328F GLU* 4.9 5.3 + - - +
329F LYS* 5.3 2.1 + - - +
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Residues in contact with ASP 326 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322F PRO* 4.6 2.9 - - + -
323F HIS* 2.7 39.5 + - - +
325F GLN* 1.3 79.1 - - - +
327F VAL* 1.4 61.7 + - - -
328F GLU 3.3 3.1 - - - -
329F LYS* 3.1 13.5 + - + +
330F GLN* 3.0 37.0 + - - +
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Residues in contact with VAL 327 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309F PHE* 3.9 25.4 - - + -
310F ARG* 3.6 32.5 - - + +
322F PRO* 4.0 5.1 - - + +
323F HIS 3.3 11.3 + - - +
324F PRO* 3.6 16.6 + - + +
325F GLN 3.6 0.8 - - - -
326F ASP* 1.4 74.1 - - - +
328F GLU* 1.3 53.5 + - - +
330F GLN* 3.2 7.0 + - - +
331F MET* 2.8 37.5 + - + +
362F ILE* 4.5 8.7 - - + +
364F PRO* 3.7 31.9 - - + +
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Residues in contact with GLU 328 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287F ILE* 4.4 3.5 - - + +
309F PHE* 4.4 28.1 - - + -
324F PRO 4.7 1.8 + - - -
325F GLN 4.9 4.9 + - - +
326F ASP 3.3 0.6 - - - -
327F VAL* 1.3 77.6 - - - +
329F LYS* 1.3 56.9 + - - +
331F MET* 3.4 2.8 + - - +
332F GLN* 3.1 54.4 + - + +
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Residues in contact with LYS 329 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325F GLN 5.3 1.5 + - - +
326F ASP* 3.1 15.0 + - + +
328F GLU* 1.3 80.0 - - - +
330F GLN* 1.4 60.7 + - - +
332F GLN* 3.2 19.6 + - + +
333F GLU* 3.1 49.7 + - + +
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Residues in contact with GLN 330 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322F PRO* 3.3 28.1 - - + +
326F ASP* 3.0 21.9 + - - +
327F VAL* 3.7 4.7 - - - +
329F LYS* 1.4 77.7 - - - +
331F MET* 1.4 59.7 + - - +
333F GLU* 3.6 26.5 + - - +
334F PHE* 3.1 26.7 + - - +
361F TYR* 5.9 2.9 - - + -
362F ILE* 3.8 30.8 - - + +
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Residues in contact with MET 331 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287F ILE* 3.7 24.7 - - + -
290F VAL* 4.2 28.9 - - + -
309F PHE* 3.9 31.2 - - + -
327F VAL* 2.8 19.5 + - + +
328F GLU 3.8 2.2 - - - +
330F GLN* 1.4 73.9 - - - +
332F GLN* 1.4 59.2 + - - +
334F PHE* 3.5 22.7 + - + +
335F VAL* 3.0 36.3 + - + +
359F LEU* 4.0 20.9 - - + -
362F ILE* 4.2 13.5 - - + -
364F PRO* 4.0 15.9 - - + -
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Residues in contact with GLN 332 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287F ILE* 4.2 11.8 - - + +
328F GLU* 3.1 42.7 + - - +
329F LYS* 3.2 21.2 + - + +
331F MET* 1.4 76.6 - - - +
333F GLU* 1.4 56.1 + - + +
335F VAL* 3.2 12.3 - - + +
336F GLN* 3.2 28.4 + - - +
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Residues in contact with GLU 333 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329F LYS* 3.1 47.5 + - + +
330F GLN* 3.8 26.5 + - + +
332F GLN* 1.4 73.8 - - + +
334F PHE* 1.4 54.3 + - - +
336F GLN* 3.4 13.9 + - - +
337F TRP* 2.9 33.1 + - - +
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Residues in contact with PHE 334 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290F VAL* 5.1 3.4 - - + -
330F GLN 3.1 18.0 + - - +
331F MET* 3.6 25.8 - - + +
333F GLU* 1.4 72.7 - - - +
335F VAL* 1.4 70.3 + - + +
337F TRP* 3.0 21.1 + + - +
338F LEU* 2.9 40.7 + - + +
355F ALA* 3.4 34.1 - - - -
358F LYS* 3.7 25.6 - - + -
359F LEU* 3.8 23.1 - - + -
362F ILE* 3.9 11.4 - - + -
376F LEU* 3.6 21.3 - - + -
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Residues in contact with VAL 335 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285F VAL 4.2 11.7 - - - +
286F THR* 4.0 5.8 - - - +
287F ILE* 3.8 40.2 - - + +
290F VAL* 4.9 3.6 - - + -
331F MET* 3.0 24.2 + - + +
332F GLN* 3.2 22.7 - - + +
334F PHE* 1.4 83.6 - - + +
336F GLN* 1.4 61.7 + - + +
338F LEU* 3.1 23.9 + - + +
339F ASN* 3.0 23.9 + - - +
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Residues in contact with GLN 336 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332F GLN 3.2 19.5 + - - +
333F GLU* 3.4 13.2 + - - +
335F VAL* 1.4 76.4 - - - +
337F TRP* 1.3 58.7 + - - +
339F ASN* 3.4 8.1 + - - +
340F SER* 3.1 30.4 + - - -
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Residues in contact with TRP 337 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333F GLU 2.9 14.5 + - - +
334F PHE* 3.0 16.4 + + - +
336F GLN* 1.3 76.1 - - - +
338F LEU* 1.4 74.3 + - + +
340F SER* 2.7 30.1 + - - -
342F GLU* 4.4 11.6 - - + +
343F ALA* 3.2 31.1 - - + +
346F LEU* 4.2 8.9 - - + +
351F PHE* 3.5 29.2 - + - -
354F LEU* 3.7 15.9 - - + -
355F ALA* 3.6 33.7 - - - -
358F LYS* 3.7 33.7 - - + +
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Residues in contact with LEU 338 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285F VAL* 4.4 24.0 - - + -
290F VAL* 5.6 1.3 - - + -
334F PHE* 2.9 44.3 + - + +
335F VAL* 3.1 17.9 + - + +
337F TRP* 1.4 89.0 - - + +
339F ASN* 1.4 65.3 + - - +
340F SER 3.3 6.5 + - - +
343F ALA* 4.8 0.2 - - - +
344F MET* 5.5 1.6 + - - +
351F PHE* 3.6 42.2 - - + -
355F ALA* 4.0 9.9 - - + -
376F LEU* 4.8 6.3 - - + -
380F ILE* 3.9 17.5 - - + -
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Residues in contact with ASN 339 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284F SER* 3.4 25.5 - - - -
285F VAL* 2.7 49.7 + - - +
286F THR* 5.5 1.0 - - - +
335F VAL* 3.0 21.6 + - - +
336F GLN* 3.4 9.4 + - - +
337F TRP 3.3 0.2 - - - -
338F LEU* 1.4 76.8 - - - +
340F SER* 1.3 59.2 + - - +
341F GLU* 5.7 0.3 - - - +
344F MET* 5.2 5.4 - - - +
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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