Contacts of the helix formed by residues 318 - 331 (chain f) in PDB entry 5T0J
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 MET 318 (chain f).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282f LYS* 3.6 29.4 - - + -
286f LEU* 4.0 29.3 + - + +
287f LEU 4.6 0.4 - - - -
289f CYS* 3.7 7.9 - - + +
290f GLY* 3.4 35.2 - - - +
307f LEU* 5.6 3.8 - - + -
310f TYR* 3.6 39.0 - - + +
311f VAL* 5.0 1.8 - - + -
315f SER* 3.6 12.5 + - - +
316f ASN* 3.4 2.8 - - - +
317f THR* 1.3 78.7 - - - +
319f ARG* 1.3 61.8 + - + +
320f LEU 3.0 2.5 + - - -
321f GLY 3.9 5.0 + - - -
322f SER* 4.2 8.9 + - - -
689f GLN* 3.4 11.9 + - - +
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Residues in contact with ARG 319 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311f VAL* 3.3 44.9 + - + +
312f LEU* 5.2 11.2 - - - +
314f ASN* 3.2 34.7 + - - +
315f SER 4.9 3.4 - - - +
317f THR 2.9 1.2 + - - -
318f MET* 1.3 75.9 - - + +
320f LEU* 1.3 63.6 + - - +
321f GLY 3.6 0.2 - - - -
322f SER 4.0 1.1 - - - -
323f ILE* 3.0 48.5 + - + +
344f PRO* 4.9 11.7 - - - +
348f ASP* 2.5 33.3 + - - +
354f GLU 4.2 10.3 - - - +
355f VAL 2.9 16.3 + - - -
358f VAL* 3.2 15.6 - - + +
359f THR* 5.0 2.2 - - - +
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Residues in contact with LEU 320 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317f THR* 2.9 23.4 + - - +
318f MET 3.0 2.2 + - - -
319f ARG* 1.3 80.7 - - - +
321f GLY* 1.3 62.4 + - - +
324f PHE* 3.2 20.6 + - + +
353f MET* 4.0 21.1 - - + -
358f VAL* 3.5 28.4 - - + +
361f LEU* 4.0 16.8 - - + -
398f TRP* 5.0 2.9 - - + +
689f GLN* 3.3 45.1 - - + +
690f ALA* 4.1 6.5 - - + -
693f VAL* 3.8 16.4 - - + -
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Residues in contact with GLY 321 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290f GLY* 3.2 7.5 - - - -
291f ILE* 3.6 29.2 - - - -
294f SER* 2.6 26.9 + - - -
318f MET 3.9 4.0 + - - -
320f LEU* 1.3 80.7 - - - +
322f SER* 1.3 60.2 + - - +
324f PHE* 3.6 4.3 + - - +
325f GLY 3.2 5.5 + - - -
689f GLN* 4.6 2.8 - - - +
692f ASP* 5.3 3.9 + - - -
693f VAL* 5.6 3.4 - - - -
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Residues in contact with SER 322 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290f GLY* 3.4 16.9 + - - -
307f LEU* 3.2 44.4 - - - +
308f SER* 4.9 0.3 - - - -
311f VAL* 3.3 32.1 - - - +
318f MET* 4.3 4.3 - - - -
319f ARG 3.5 3.2 + - - -
320f LEU 3.2 0.6 - - - -
321f GLY* 1.3 75.8 - - - +
323f ILE* 1.3 62.8 + - - +
325f GLY* 2.9 17.3 + - - -
326f LEU* 3.2 9.5 + - - +
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Residues in contact with ILE 323 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308f SER* 6.2 0.7 - - - -
311f VAL* 4.3 13.9 - - + -
319f ARG* 3.0 55.3 + - + +
322f SER* 1.3 76.0 - - - +
324f PHE* 1.3 61.0 + - - +
326f LEU* 3.0 35.4 + - + +
327f GLY 3.7 3.6 + - - -
341f LEU* 5.1 0.7 - - + -
344f PRO* 5.8 3.1 - - + -
358f VAL* 3.6 22.0 - - + -
359f THR* 3.9 31.9 - - - +
362f ALA* 4.3 9.8 - - + +
366f ILE* 4.2 3.6 - - - +
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Residues in contact with PHE 324 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291f ILE* 3.5 26.0 - - + -
294f SER* 4.3 0.2 - - - -
320f LEU* 3.2 19.3 + - + +
321f GLY* 3.7 7.2 - - - +
322f SER 3.2 0.4 - - - -
323f ILE* 1.3 76.0 - - - +
325f GLY* 1.3 59.0 + - - +
328f LEU* 3.3 41.3 - - + +
358f VAL* 5.0 0.8 - - - +
361f LEU* 5.5 6.1 - - + -
362f ALA* 5.1 4.9 - - - -
365f MET* 3.5 44.2 - - + -
366f ILE* 3.2 46.6 - - + +
693f VAL* 4.1 17.5 - - + -
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Residues in contact with GLY 325 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293f ASN 5.3 0.4 - - - +
294f SER* 3.4 31.2 + - - +
297f ARG 5.1 1.7 - - - +
304f LEU* 3.9 4.0 - - - +
307f LEU* 4.9 7.3 - - - +
321f GLY 3.2 6.1 + - - -
322f SER 2.9 11.6 + - - -
324f PHE* 1.3 76.8 - - - +
326f LEU* 1.3 62.8 + - - +
327f GLY 3.4 0.2 - - - -
328f LEU* 4.0 3.1 - - - -
329f ALA* 3.4 22.7 + - - +
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Residues in contact with LEU 326 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304f LEU* 3.3 49.0 - - + +
308f SER* 5.2 14.4 - - - -
322f SER 3.2 5.0 + - - +
323f ILE* 3.0 29.2 + - + +
325f GLY* 1.3 77.1 - - - +
327f GLY* 1.3 60.3 + - - +
329f ALA* 4.0 3.1 + - - +
330f TYR* 4.1 7.6 - - + -
337f ASP* 3.4 24.0 - - - +
340f THR* 4.9 9.9 - - - +
341f LEU* 4.0 15.9 - - + -
344f PRO* 5.2 9.6 - - + -
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Residues in contact with GLY 327 (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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323f ILE 3.7 5.7 + - - -
324f PHE 3.9 0.6 + - - -
326f LEU* 1.3 76.5 - - - +
328f LEU* 1.3 61.2 + - - +
329f ALA 3.2 2.8 + - - -
330f TYR* 3.4 3.6 + - - +
331f ALA* 2.9 30.5 + - - +
336f GLU 4.7 1.5 - - - +
337f ASP* 3.7 13.9 - - - -
341f LEU* 3.9 12.8 - - - +
366f ILE* 3.6 19.3 - - - -
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Residues in contact with LEU 328 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291f ILE* 5.8 0.2 - - + -
294f SER* 3.9 24.5 - - - +
295f GLY* 4.0 9.2 - - - +
298f ASN* 3.3 14.6 - - - +
324f PHE* 3.3 45.4 + - + +
325f GLY* 4.3 3.6 - - - -
326f LEU 3.5 0.4 - - - -
327f GLY* 1.3 75.6 - - - +
329f ALA* 1.3 64.2 + - - +
331f ALA* 3.8 3.4 - - + +
332f GLY* 3.2 19.8 + - - +
366f ILE* 3.4 17.4 - - + +
368f VAL* 6.4 1.6 - - + -
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Residues in contact with ALA 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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297f ARG 4.1 3.1 - - - +
298f ASN* 3.4 35.4 - - - +
299f GLU* 3.7 28.7 - - - +
304f LEU* 3.7 21.8 - - + -
325f GLY 3.4 18.2 + - - +
326f LEU 4.0 0.2 - - - +
327f GLY 3.2 0.4 - - - -
328f LEU* 1.3 81.2 - - - +
330f TYR* 1.3 63.3 + - + +
332f GLY 3.4 5.7 + - - -
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Residues in contact with TYR 330 (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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299f GLU* 3.8 26.6 - - + +
301f ASP* 3.6 25.3 - - + +
304f LEU* 3.8 28.1 - - + +
326f LEU* 4.1 7.0 - - + -
327f GLY 3.4 2.6 + - - +
329f ALA* 1.3 82.6 - - - +
331f ALA* 1.3 59.4 + - - +
332f GLY 3.2 1.7 + - - -
333f SER* 4.0 4.5 + - - -
334f ASN 3.9 10.7 + - - +
336f GLU* 3.3 34.7 - - + +
337f ASP* 3.8 34.3 - - + -
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Residues in contact with ALA 331 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255f LEU* 4.9 4.7 - - - +
327f GLY 2.9 22.7 + - - +
328f LEU* 3.8 5.8 - - + +
330f TYR* 1.3 73.8 - - - +
332f GLY* 1.3 64.2 + - - +
333f SER 3.1 10.1 + - - +
335f ARG 4.1 7.1 - - - +
336f GLU 3.8 24.7 - - - +
366f ILE* 4.2 21.5 - - + +
367f ALA 5.8 0.7 - - - +
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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