Contacts of the helix formed by residues 350 - 368 (chain E) 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 GLY 350 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345E SER 3.8 1.0 + - - -
346E ARG* 3.1 40.7 + - - +
347E LEU 4.6 0.2 - - - +
349E THR* 1.3 82.4 + - - +
351E GLU* 1.3 60.2 + - - -
352E ASP 3.2 3.1 - - - -
353E GLY* 3.0 18.7 + - - -
354E TYR* 3.1 11.6 - - - -
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Residues in contact with GLU 351 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292E THR* 4.8 0.2 - - + -
296E LYS* 3.1 34.9 + - - +
346E ARG* 5.0 0.9 - - - +
349E THR 3.6 1.8 + - - -
350E GLY* 1.3 66.7 - - - -
352E ASP* 1.3 68.2 + - - +
353E GLY 3.0 2.5 - - - -
354E TYR* 2.8 34.1 + - - +
355E TYR* 3.0 38.2 + - + +
57F PHE* 3.9 16.5 - - + -
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Residues in contact with ASP 352 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288E LEU* 3.8 35.8 - - + +
291E ILE* 3.4 5.2 - - + +
292E THR* 2.7 29.7 + - - +
346E ARG* 2.3 44.7 + - + +
351E GLU* 1.3 79.9 - - - +
353E GLY* 1.3 56.1 + - - +
355E TYR* 3.6 4.0 - - - -
356E PHE* 2.9 32.0 + - - +
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Residues in contact with GLY 353 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346E ARG 3.2 17.8 + - - -
347E LEU* 3.4 32.0 - - - +
350E GLY 3.0 6.7 + - - -
351E GLU 3.0 1.4 - - - -
352E ASP* 1.3 76.2 - - - +
354E TYR* 1.3 58.3 + - - +
356E PHE* 3.4 1.7 + - - +
357E THR* 2.8 34.5 + - - -
22F LYS* 5.2 0.2 - - - -
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Residues in contact with TYR 354 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347E LEU 5.0 0.4 - - - -
348E MET 2.7 13.7 + - - -
349E THR 3.2 12.0 + - - -
350E GLY 3.1 22.4 - - - -
351E GLU* 2.8 17.3 + - - +
353E GLY* 1.3 68.8 - - - -
355E TYR* 1.3 64.5 - - + +
357E THR* 3.8 5.5 - - - -
358E ASN* 2.6 36.2 + - - +
22F LYS* 3.8 29.2 - - + +
57F PHE* 3.2 45.3 - + + -
70F LYS* 3.5 0.3 + - - -
72F GLU* 2.7 46.0 + - + +
73F ILE 5.6 0.2 - - - -
74F TRP* 4.9 26.6 + + + -
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Residues in contact with TYR 355 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291E ILE* 3.5 15.9 - - + -
292E THR* 3.1 24.9 - - + -
295E SER* 3.1 35.7 - - - +
296E LYS* 3.4 29.3 - - + +
299E PHE* 5.0 13.3 - + - -
351E GLU* 3.0 43.9 + - + +
352E ASP 3.6 0.7 - - - +
354E TYR* 1.3 80.7 - - + +
356E PHE* 1.3 62.7 + - - +
358E ASN* 2.9 31.2 - - - +
359E LEU* 2.9 12.3 + - + +
57F PHE* 4.9 17.3 - + + +
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Residues in contact with PHE 356 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288E LEU* 4.6 3.6 - - + -
291E ILE* 3.2 9.1 - - + +
335E ILE* 3.9 17.5 - - + -
338E ILE* 3.6 46.2 - - + -
339E THR* 4.3 16.4 - - + -
347E LEU* 3.9 24.7 - - + -
352E ASP 2.9 21.2 + - - +
353E GLY* 3.8 4.5 - - - +
355E TYR* 1.3 75.1 - - - +
357E THR* 1.3 69.4 + - - +
359E LEU* 3.0 31.8 + - + +
360E CYS* 3.1 39.6 + - - -
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Residues in contact with THR 357 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347E LEU* 4.9 4.5 + - - +
353E GLY 2.8 24.1 + - - -
354E TYR* 3.8 6.5 - - - -
356E PHE* 1.3 85.1 - - - +
358E ASN* 1.3 64.6 + - - +
359E LEU 3.1 0.5 + - - -
360E CYS* 3.2 5.1 + - - +
361E CYS* 3.1 19.1 + - + +
22F LYS* 4.6 11.5 + - - +
88F MET* 5.0 25.5 - - + +
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Residues in contact with ASN 358 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295E SER* 6.0 0.7 - - - -
319E LEU* 3.9 25.0 - - + +
354E TYR* 2.6 30.1 + - - +
355E TYR* 2.9 28.7 + - - +
357E THR* 1.3 78.2 - - - +
359E LEU* 1.3 72.2 + - - +
361E CYS* 3.1 16.7 - - - -
362E ALA* 3.0 19.9 + - - +
74F TRP* 4.4 24.8 - - + +
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Residues in contact with LEU 359 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275E ILE* 5.5 9.4 - - + -
291E ILE* 3.5 32.8 - - + -
295E SER* 5.4 7.2 - - - -
319E LEU* 5.6 3.8 - - + -
355E TYR* 2.9 36.4 + - + +
356E PHE* 3.0 19.9 + - + +
358E ASN* 1.3 83.8 + - - +
360E CYS* 1.3 58.5 + - - +
362E ALA* 2.6 30.1 + - - +
363E VAL* 2.9 17.7 + - + +
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Residues in contact with CYS 360 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335E ILE* 4.2 15.3 - - + -
339E THR* 6.0 0.4 - - - -
356E PHE* 3.1 50.7 + - - -
357E THR* 4.0 5.8 - - - +
359E LEU* 1.3 82.0 - - - +
361E CYS* 1.3 63.1 + - - +
363E VAL* 3.6 13.4 - - + +
364E ALA* 3.0 27.5 + - - +
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Residues in contact with CYS 361 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319E LEU* 4.1 13.0 - - - -
357E THR* 3.1 12.2 + - + +
358E ASN* 3.1 20.0 - - - +
359E LEU 3.0 0.2 - - - -
360E CYS* 1.3 77.3 - - - +
362E ALA* 1.3 80.7 + - - +
365E PHE* 3.0 31.9 + - - +
85F LEU* 3.7 31.6 - - + +
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Residues in contact with ALA 362 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319E LEU* 3.9 30.7 - - + +
320E ILE* 4.2 13.2 - - + +
323E VAL* 5.6 5.8 - - + -
358E ASN 3.8 6.3 - - - +
359E LEU* 2.6 18.4 + - - +
361E CYS* 1.3 82.4 - - - +
363E VAL* 1.3 54.8 + - + +
365E PHE* 3.1 9.6 - - - -
366E ILE* 3.0 38.1 + - + +
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Residues in contact with VAL 363 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238E ILE* 5.3 11.7 - - + -
323E VAL* 6.1 8.1 - - + -
331E LEU* 5.9 7.0 - - + -
335E ILE* 4.7 23.3 - - + -
359E LEU* 2.9 19.2 + - + +
360E CYS* 3.6 16.2 - - + +
362E ALA* 1.3 73.6 - - + +
364E ALA* 1.3 64.6 + - - +
365E PHE 3.0 1.1 - - - -
366E ILE* 2.8 25.0 + - - +
367E GLU* 2.9 17.1 + - + +
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Residues in contact with ALA 364 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360E CYS 3.0 13.3 + - - +
361E CYS 4.3 0.9 - - - +
363E VAL* 1.3 81.0 - - - +
365E PHE* 1.3 61.8 + - - +
367E GLU* 3.8 20.9 + - - +
368E LYS* 4.0 9.4 + - - +
85F LEU* 4.6 16.4 - - + -
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Residues in contact with PHE 365 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320E ILE* 3.4 33.0 - - + -
361E CYS* 3.0 18.1 + - - +
362E ALA* 3.1 22.4 - - - +
364E ALA* 1.3 79.7 - - - +
366E ILE* 1.3 81.0 + - + +
368E LYS* 3.8 2.4 + - - +
369E LEU* 3.4 45.3 + - + -
370E ASP* 5.3 1.6 - - - +
373E SER* 3.8 26.2 - - - -
374E LEU* 5.8 1.3 - - + -
82F TYR* 4.0 31.0 - + + -
85F LEU* 4.9 4.8 - - + +
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Residues in contact with ILE 366 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241E ARG* 3.4 11.5 + - + -
242E ILE* 5.7 3.6 - - + -
245E LEU* 4.6 10.9 - - + +
320E ILE* 4.3 20.4 - - + +
323E VAL* 5.1 10.5 - - + -
324E LEU* 3.7 34.1 - - + -
362E ALA* 3.0 18.4 + - + +
363E VAL* 2.8 15.2 + - - +
365E PHE* 1.3 92.1 - - + +
367E GLU* 1.3 59.9 + - - +
369E LEU* 2.8 39.1 + - + +
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Residues in contact with GLU 367 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237E ALA* 6.3 2.9 - - + -
241E ARG* 2.5 35.7 + - - +
363E VAL* 2.9 17.6 + - + +
364E ALA* 4.0 15.4 - - - +
365E PHE 3.4 0.4 - - - -
366E ILE* 1.3 76.4 - - - +
368E LYS* 1.3 87.9 + - - +
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Residues in contact with LYS 368 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241E ARG* 4.0 7.9 - - - +
364E ALA 4.0 6.5 + - - +
365E PHE 3.8 5.9 + - - +
366E ILE 3.2 0.6 - - - -
367E GLU* 1.3 110.8 + - + +
369E LEU* 1.3 64.5 + - - +
370E ASP* 3.2 15.5 - - - +
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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