Contacts of the helix formed by residues 355 - 368 (chain E) in PDB entry 5U07
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 SER 355 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338E ALA* 4.2 2.9 - - - -
353E TYR* 3.3 2.0 - - - +
354E ASP* 1.3 88.1 + - - +
356E TYR* 1.3 64.4 + - - +
357E PRO* 4.0 2.2 - - - +
358E ALA* 3.4 21.7 + - - +
359E LEU* 3.0 27.4 + - - +
327I GLU 3.6 11.7 - - - -
328I VAL* 3.2 17.7 - - - +
330I PRO* 4.0 15.8 - - - +
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Residues in contact with TYR 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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264E LEU* 3.7 24.9 - - + -
280E LEU* 4.8 8.7 - - + -
281E PRO* 2.4 43.8 + - + -
282E ASP 4.0 8.8 + - - -
284E VAL* 3.6 26.9 - - + +
338E ALA* 3.5 34.0 + - + -
340E VAL* 4.8 2.4 - - - +
355E SER* 1.3 71.0 - - - +
357E PRO* 1.3 64.0 - - + +
359E LEU* 3.2 6.0 + - + +
360E ILE* 2.9 34.6 + - + +
325I LEU* 6.3 0.2 - - + -
328I VAL* 3.1 34.4 + - + +
329I TRP* 4.2 20.6 - + + -
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Residues in contact with PRO 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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261E ARG* 5.2 13.5 - - + +
355E SER* 3.8 2.5 - - - -
356E TYR* 1.3 94.7 - - + +
358E ALA* 1.3 57.3 + - - +
360E ILE* 4.1 7.5 - - + +
361E ASP* 2.9 34.1 + - - +
328I VAL 3.8 8.7 - - - +
329I TRP* 4.6 17.7 - - + -
330I PRO* 4.0 20.2 - - + +
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Residues in contact with ALA 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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353E TYR* 4.4 11.4 - - + -
354E ASP* 4.1 11.2 - - - +
355E SER* 3.4 22.8 + - - +
356E TYR 3.3 0.4 - - - -
357E PRO* 1.3 79.2 - - - +
359E LEU* 1.3 60.8 + - - +
361E ASP* 2.4 24.4 - - - +
362E ALA* 2.9 14.6 + - - +
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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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284E VAL* 4.0 14.4 - - + -
286E ILE* 3.9 26.2 - - + -
336E GLY 3.9 8.3 - - - +
337E TYR* 3.9 24.2 - - - +
338E ALA* 3.9 9.0 - - + +
353E TYR* 3.5 34.0 - - + +
355E SER 3.0 14.5 + - - +
356E TYR* 3.2 10.1 + - + +
358E ALA* 1.3 77.1 - - - +
360E ILE* 1.3 65.8 + - + +
363E MET* 2.9 47.1 + - - +
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Residues in contact with ILE 360 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E ILE* 5.5 1.1 - - + -
257E ALA* 4.0 22.7 - - + +
260E LEU* 3.7 35.0 - - + -
261E ARG* 3.7 29.8 - - + +
264E LEU* 3.7 29.8 - - + -
286E ILE* 5.1 8.1 - - + -
356E TYR* 2.9 21.0 + - + +
357E PRO* 4.1 5.4 - - + +
359E LEU* 1.3 81.8 - - + +
361E ASP* 1.3 65.4 + - - +
363E MET* 5.3 0.9 - - - -
364E VAL* 2.9 31.0 + - + +
329I TRP* 6.4 0.4 - - + -
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Residues in contact with ASP 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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257E ALA* 5.7 5.2 - - + -
357E PRO 2.9 18.0 + - - +
358E ALA* 2.4 23.2 - - - +
360E ILE* 1.3 79.0 - - - +
362E ALA* 1.3 79.6 + - - +
364E VAL* 4.2 3.2 - - - +
365E ALA* 2.9 32.3 + - - +
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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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353E TYR* 3.6 31.4 - - + +
358E ALA 2.9 18.0 + - - +
359E LEU 3.8 0.7 - - - +
361E ASP* 1.3 90.0 + - - +
363E MET* 1.3 59.4 + - - +
365E ALA* 3.4 5.8 + - - +
366E ALA* 2.9 25.2 + - - +
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Residues in contact with MET 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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286E ILE* 3.2 43.7 - - + -
288E VAL* 4.2 8.3 - - + +
334E ILE* 4.3 12.8 - - + +
335E ARG 2.9 31.9 - - - +
336E GLY* 3.4 9.2 - - - -
351E GLU* 3.1 25.6 - - - +
353E TYR* 3.3 15.7 - - + +
359E LEU* 2.9 22.0 + - + +
360E ILE 4.5 0.4 - - - +
362E ALA* 1.3 73.5 - - - +
364E VAL* 1.3 64.8 + - - +
366E ALA* 2.9 24.9 + - + +
367E ALA* 3.0 13.9 + - - +
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Residues in contact with VAL 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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4E VAL* 5.4 8.3 - - + -
253E ARG* 3.9 32.2 + - + +
256E VAL* 3.7 29.4 - - + -
257E ALA* 4.6 9.2 - - + +
260E LEU* 4.1 17.5 - - + -
360E ILE* 2.9 26.2 + - + +
361E ASP* 4.2 2.9 - - - +
363E MET* 1.3 77.6 - - + +
365E ALA* 1.3 61.7 + - - +
367E ALA* 3.1 16.8 + - + +
368E PHE* 3.1 20.0 + - + -
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Residues in contact with ALA 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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361E ASP 2.9 19.9 + - - +
362E ALA* 3.6 7.0 - - - +
364E VAL* 1.3 77.5 - - - +
366E ALA* 1.3 59.0 + - - +
367E ALA 3.2 0.7 + - - -
368E PHE* 3.4 36.3 + - + +
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Residues in contact with ALA 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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288E VAL* 5.6 1.8 - - + -
290E PHE* 5.7 1.4 - - - -
334E ILE* 4.7 30.9 - - + +
362E ALA 2.9 14.6 + - - +
363E MET* 2.9 19.7 + - + +
365E ALA* 1.3 77.3 - - - +
367E ALA* 1.3 56.7 + - - +
368E PHE 4.7 2.6 - - - +
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Residues in contact with ALA 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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2E THR 6.1 0.2 - - - +
4E VAL* 4.6 2.0 - - + -
239E LEU* 3.7 29.3 - - + +
253E ARG* 4.0 7.0 + - - +
288E VAL* 4.2 21.1 - - + -
290E PHE* 5.8 5.2 - - - -
363E MET 3.0 8.9 + - - +
364E VAL* 3.1 11.8 + - + +
366E ALA* 1.3 79.2 - - - +
368E PHE* 1.3 63.2 + - - +
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Residues in contact with PHE 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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249E ALA* 5.9 4.5 - - + -
253E ARG* 3.0 59.9 - - + +
364E VAL* 3.1 17.5 - - + -
365E ALA* 3.4 38.4 + - + +
366E ALA 4.7 2.8 - - - +
367E ALA* 1.3 82.6 - - - +
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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