Contacts of the helix formed by residues 351 - 368 (chain A) in PDB entry 4Q9U
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 GLU 351 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A THR* 4.5 5.5 + - - +
296A LYS* 2.7 34.2 + - - -
350A GLY* 1.3 70.3 - - - -
352A ASP* 1.3 77.5 + - - +
354A TYR* 3.0 16.8 + - - -
355A TYR* 2.9 25.7 + - + +
57B PHE* 3.2 24.4 - - + -
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Residues in contact with ASP 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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288A LEU* 3.3 39.0 - - + +
289A ALA* 5.2 0.2 - - - -
291A ILE* 4.8 1.8 - - + +
292A THR* 3.3 29.6 - - + +
346A ARG* 2.9 40.9 + - - +
347A LEU* 5.3 5.4 - - + -
350A GLY* 3.9 4.5 - - - -
351A GLU* 1.3 85.5 + - - +
353A GLY* 1.3 61.4 + - - +
354A TYR 3.3 0.3 + - - -
355A TYR* 3.4 3.3 + - - +
356A PHE* 3.0 27.0 + - + +
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Residues in contact with GLY 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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346A ARG 4.4 1.2 + - - -
347A LEU* 3.0 30.7 + - - -
348A MET 5.0 0.2 - - - -
350A GLY 3.2 9.6 + - - -
351A GLU 3.0 2.6 + - - -
352A ASP* 1.3 77.3 - - - +
354A TYR* 1.3 55.6 + - - +
356A PHE* 4.0 5.3 - - - +
357A THR* 2.6 38.2 + - - -
74B TRP* 3.9 4.9 - - - -
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Residues in contact with TYR 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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348A MET 3.8 7.2 - - - -
349A THR 3.2 7.0 + - - -
350A GLY 2.8 22.2 - - - -
351A GLU 3.0 13.9 - - - -
353A GLY* 1.3 70.8 - - - +
355A TYR* 1.3 58.0 + - + +
357A THR* 3.5 1.4 - - - -
358A ASN* 2.3 46.2 + - - +
57B PHE* 3.3 57.2 - + + -
59B THR* 4.1 1.9 - - - +
72B GLU* 2.7 43.3 + - + +
73B ILE 4.5 1.8 - - - -
74B TRP* 3.3 56.4 - + + -
89B TYR* 6.0 0.2 - - + -
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Residues in contact with TYR 355 (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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291A ILE* 3.6 15.9 - - + -
292A THR* 3.3 33.7 - - + -
295A SER* 3.3 32.3 - - - +
296A LYS* 4.2 17.5 - - + +
299A PHE* 4.5 19.7 - + - -
315A PHE* 5.7 1.1 - + - -
351A GLU* 2.9 36.6 + - + +
352A ASP* 3.6 1.3 - - - +
353A GLY 3.4 0.2 - - - -
354A TYR* 1.3 73.4 - - + +
356A PHE* 1.3 68.5 + - - +
357A THR 3.0 0.9 - - - -
358A ASN* 3.2 13.2 - - - +
359A LEU* 2.8 24.3 + - - +
56B ALA* 4.6 6.1 - - + +
57B PHE* 3.0 32.4 - + - -
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Residues in contact with PHE 356 (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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291A ILE* 3.6 32.1 - - + +
335A ILE* 3.6 27.8 - - + -
338A ILE* 3.4 28.9 - - + -
339A THR* 3.6 34.3 - - + -
347A LEU* 5.7 12.1 - - + -
352A ASP* 3.0 16.2 + - + +
353A GLY* 4.1 4.9 - - - +
355A TYR* 1.3 77.9 - - - +
357A THR* 1.3 63.0 + - - +
359A LEU* 3.0 14.1 - - + +
360A CYS* 2.9 44.9 + - - -
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Residues in contact with THR 357 (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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353A GLY 2.6 23.2 + - - -
354A TYR 3.5 0.4 - - - -
355A TYR 3.0 0.2 - - - -
356A PHE* 1.3 78.3 - - - +
358A ASN* 1.3 68.1 + - - +
359A LEU 2.8 5.4 + - - -
360A CYS* 2.9 15.7 + - - +
361A CYS* 3.0 16.0 + - - +
74B TRP* 3.1 29.3 - - + -
88B MET* 4.1 20.9 - - + +
89B TYR* 4.0 19.3 - - + +
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Residues in contact with ASN 358 (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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295A SER* 5.6 0.7 - - - -
315A PHE* 3.5 29.3 - - - -
316A LEU* 4.1 10.4 - - + +
319A LEU* 3.6 10.1 - - + +
354A TYR* 2.3 41.8 + - - +
355A TYR* 3.2 17.9 - - - +
357A THR* 1.3 79.6 - - - +
359A LEU* 1.3 55.9 + - - +
361A CYS* 3.4 9.0 - - - +
362A ALA* 2.9 29.1 + - - +
75B ASP 5.6 0.4 + - - -
89B TYR* 2.9 34.9 + - + +
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Residues in contact with LEU 359 (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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275A ILE* 5.6 11.0 - - + -
291A ILE* 3.9 33.9 - - + -
319A LEU* 4.2 17.3 - - + -
323A VAL* 6.1 1.8 - - + -
331A LEU* 5.8 2.0 - - + -
335A ILE* 3.9 21.5 - - + -
355A TYR 2.8 12.4 + - - +
356A PHE* 3.0 16.4 - - + +
357A THR 2.8 0.4 + - - -
358A ASN* 1.3 74.5 + - - +
360A CYS* 1.3 99.4 + - - +
362A ALA* 2.8 14.9 + - - +
363A VAL* 2.9 21.2 + - + +
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Residues in contact with CYS 360 (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 ILE* 3.7 26.9 - - + -
356A PHE* 2.9 35.5 + - - -
357A THR* 2.9 10.1 + - - +
359A LEU* 1.3 88.8 - - - +
361A CYS* 1.3 63.2 + - - +
363A VAL* 3.1 7.3 + - - +
364A ALA* 2.9 27.8 + - + +
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Residues in contact with CYS 361 (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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316A LEU* 6.5 0.7 - - + -
357A THR* 3.0 16.7 + - - +
358A ASN* 3.4 13.2 - - - +
360A CYS* 1.3 77.4 - - - +
362A ALA* 1.3 64.9 + - - +
363A VAL 2.9 0.2 + - - -
364A ALA* 4.5 1.9 - - - +
365A PHE 2.9 20.8 + - - -
85B LEU* 3.1 47.7 - - + +
88B MET* 4.5 18.6 - - - -
89B TYR* 4.7 16.8 - - + -
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Residues in contact with ALA 362 (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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316A LEU* 5.9 2.5 - - + -
319A LEU* 3.6 22.7 - - + -
320A ILE* 3.3 33.2 - - + +
323A VAL* 5.4 0.7 - - + -
358A ASN 2.9 13.0 + - - +
359A LEU 2.8 13.6 + - - +
361A CYS* 1.3 72.2 - - - +
363A VAL* 1.3 57.9 + - + +
365A PHE* 3.4 5.7 - - - +
366A ILE* 2.9 33.3 + - + +
85B LEU* 4.7 2.2 - - - -
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Residues in contact with VAL 363 (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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238A ILE* 5.6 9.2 - - + -
323A VAL* 4.9 18.8 - - + -
331A LEU* 4.8 20.6 - - + -
335A ILE* 4.8 12.8 - - + -
359A LEU* 2.9 32.1 + - + +
360A CYS* 3.2 10.1 - - - +
361A CYS 2.9 0.8 + - - -
362A ALA* 1.3 77.0 - - + +
364A ALA* 1.3 57.6 + - + +
365A PHE 2.9 3.4 - - - -
366A ILE* 2.3 41.5 + - + +
367A GLU* 3.1 8.5 + - + +
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Residues in contact with ALA 364 (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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360A CYS* 2.9 13.5 + - + +
361A CYS* 4.5 1.6 - - - +
363A VAL* 1.3 79.2 - - + +
365A PHE* 1.3 60.7 + - - +
367A GLU* 3.7 12.9 + - - +
368A LYS* 3.5 42.4 + - - +
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Residues in contact with PHE 365 (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 ILE* 4.1 17.7 - - + -
361A CYS 2.9 18.3 + - - +
362A ALA 3.4 7.2 - - - +
363A VAL 2.8 0.8 + - - -
364A ALA* 1.3 75.5 - - - +
366A ILE* 1.3 71.1 + - + +
368A LYS* 2.7 36.1 + - - +
369A LEU* 3.0 29.6 - - + +
370A ASP* 5.0 0.4 - - + -
373A SER* 3.8 26.2 - - - -
81B ARG 4.7 7.4 - - - -
82B TYR* 4.3 27.4 - + + -
84B SER* 4.8 1.8 - - - -
85B LEU* 3.4 35.8 - - + +
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Residues in contact with ILE 366 (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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241A ARG* 3.0 19.7 + - + -
242A ILE* 5.5 4.5 - - + -
245A LEU* 3.7 29.6 - - + -
320A ILE* 3.5 38.6 - - + +
323A VAL* 4.8 15.5 - - + -
324A LEU* 5.1 10.1 - - + +
362A ALA* 2.9 20.7 + - + +
363A VAL* 2.3 28.1 + - + +
365A PHE* 1.3 74.5 - - + +
367A GLU* 1.3 63.2 + - + +
369A LEU* 3.0 28.3 - - + +
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Residues in contact with GLU 367 (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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234A LYS* 5.4 2.4 - - - +
237A ALA* 4.5 8.5 - - - +
238A ILE* 3.1 35.0 + - + +
241A ARG* 2.3 59.0 + - + +
363A VAL* 3.1 10.8 + - + +
364A ALA* 4.0 13.1 - - - +
365A PHE 3.2 0.4 - - - -
366A ILE* 1.3 77.2 - - - +
368A LYS* 1.3 66.3 + - + +
369A LEU 3.5 2.8 + - - -
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Residues in contact with LYS 368 (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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364A ALA* 3.5 29.2 + - - +
365A PHE* 2.7 30.2 + - - +
367A GLU* 1.3 82.2 - - + +
369A LEU* 1.3 57.5 + - - +
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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