Contacts of the helix formed by residues 297 - 314 (chain O) in PDB entry 5A31
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 297 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C SER* 4.0 11.2 - - - -
294O GLU* 3.6 10.5 - - - +
296O TYR* 1.3 82.1 + - - +
298O ARG* 1.3 67.1 + - - +
299O SER* 3.1 10.9 + - - -
300O LEU* 3.3 21.8 + - - +
301O ARG* 4.2 6.1 + - - -
330O ILE* 5.6 0.9 - - - +
334O SER* 5.3 0.3 + - - -
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Residues in contact with ARG 298 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283O LEU* 4.2 19.0 - - + +
284O THR 3.1 34.8 + - - +
285O GLY 4.7 0.8 + - - -
286O ALA* 3.5 20.4 - - - +
291O ASN* 3.2 32.5 + - - +
292O GLY 3.0 21.0 + - - -
294O GLU* 3.8 33.9 - - + +
297O GLY* 1.3 72.9 - - - -
299O SER* 1.3 66.7 + - - +
300O LEU 3.1 0.9 + - - -
301O ARG* 2.9 48.9 + - - +
302O TYR* 3.3 35.2 + - + -
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Residues in contact with SER 299 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C SER* 5.2 5.2 + - - -
278O PHE* 4.0 26.8 - - - -
281O LEU* 4.0 21.5 + - - -
282O ILE* 5.6 0.2 - - - -
283O LEU* 4.4 17.6 + - - +
297O GLY* 3.9 6.6 - - - -
298O ARG* 1.3 78.8 + - - +
300O LEU* 1.3 65.7 + - - +
302O TYR* 3.0 6.6 + - - +
303O ALA* 2.9 28.6 + - - +
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Residues in contact with LEU 300 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C THR* 4.5 4.0 - - + -
382C SER* 6.5 0.2 - - - -
385C ILE* 4.4 11.9 - - + -
409C TYR* 4.0 19.5 - - + +
412C LEU* 3.7 21.3 - - + -
414C MET* 3.2 33.3 - - + +
278O PHE 6.1 0.7 - - - +
296O TYR* 4.0 23.3 - - + -
297O GLY* 3.6 16.6 - - - +
298O ARG 3.1 1.0 - - - -
299O SER* 1.3 83.5 - - - +
301O ARG* 1.3 68.4 + - - +
303O ALA* 3.4 8.1 + - + +
304O ALA* 3.3 21.0 + - - +
330O ILE* 4.0 16.7 - - + +
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Residues in contact with ARG 301 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293O GLU 2.7 24.7 + - - -
294O GLU* 3.0 23.4 + - - +
297O GLY 4.2 2.6 + - - -
298O ARG* 2.9 54.8 + - - +
299O SER 3.2 0.4 - - - -
300O LEU* 1.3 78.3 - - - +
302O TYR* 1.3 69.4 + - + +
304O ALA* 3.4 2.6 + - - +
305O LEU* 3.1 22.7 + - - +
327O ALA* 4.1 5.5 - - - +
330O ILE* 3.6 26.7 - - + -
331O ALA* 3.9 9.9 - - + +
334O SER* 3.0 22.2 + - - -
336O ASP* 3.3 35.8 + - - +
339O CYS* 3.9 16.6 - - - -
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Residues in contact with TYR 302 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D LEU* 3.2 36.9 - - + +
17D TRP* 3.9 30.3 - + + -
278O PHE* 4.1 11.4 - - + -
283O LEU* 3.3 37.4 - - + +
291O ASN* 4.1 4.2 + - - -
298O ARG* 3.3 46.4 + - + -
299O SER 3.0 4.1 + - - +
301O ARG* 1.3 75.7 - - + +
303O ALA* 1.3 57.0 + - - +
305O LEU* 3.4 6.2 - - + +
306O ASN* 2.7 40.1 + - - +
336O ASP* 4.0 7.6 + - - -
339O CYS* 3.8 27.8 - - + -
342O HIS* 5.8 0.9 - + - -
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Residues in contact with ALA 303 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C TYR* 5.9 0.7 - - + +
414C MET* 6.3 0.4 - - - -
417C TYR* 3.9 21.5 - - + +
274O LEU* 4.5 2.3 - - - +
278O PHE* 3.6 39.9 - - + -
299O SER 2.9 13.4 + - - +
300O LEU* 3.8 11.2 - - + +
301O ARG 3.2 0.4 - - - -
302O TYR* 1.3 77.4 - - - +
304O ALA* 1.3 52.6 + - - +
306O ASN* 3.3 1.9 + - - +
307O LEU* 2.7 35.5 + - - +
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Residues in contact with ALA 304 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C MET* 4.7 2.2 - - - -
417C TYR* 4.4 17.0 - - + -
300O LEU 3.3 12.0 + - - +
302O TYR 3.3 0.4 - - - -
303O ALA* 1.3 80.1 - - - +
305O LEU* 1.3 58.6 + - - +
307O LEU* 3.2 4.3 + - + +
308O ALA* 2.8 29.8 + - - +
323O ALA* 4.0 5.7 - - + +
326O GLU* 4.2 12.1 - - + -
327O ALA* 3.6 29.8 - - + +
330O ILE* 4.3 6.7 - - + -
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Residues in contact with LEU 305 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D TRP* 4.2 25.8 - - + -
301O ARG 3.1 17.1 + - - +
302O TYR* 3.4 13.9 - - + +
304O ALA* 1.3 78.3 - - - +
306O ASN* 1.3 59.4 + - - +
308O ALA* 3.4 5.0 + - - +
309O ALA* 3.0 25.0 + - + +
324O LEU* 4.0 5.8 - - + -
327O ALA* 3.4 10.6 - - + +
339O CYS* 4.5 5.8 - - - -
342O HIS* 3.9 20.6 - - + -
343O CYS* 3.8 31.0 - - - +
346O TRP* 3.9 26.2 - - + +
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Residues in contact with ASN 306 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D VAL* 6.0 1.2 - - - +
13D THR 5.4 0.2 + - - -
17D TRP* 3.3 52.2 + - - -
255O TYR* 4.0 5.2 + - - -
258O TYR* 4.6 7.5 + - - +
274O LEU* 4.0 19.6 - - + +
278O PHE* 3.7 20.0 - - + -
302O TYR 2.7 31.4 + - - +
303O ALA 3.6 3.6 - - - +
305O LEU* 1.3 72.4 - - - +
307O LEU* 1.3 62.0 + - - +
309O ALA* 3.2 8.5 + - - +
310O LEU* 2.8 29.1 + - - +
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Residues in contact with LEU 307 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C PHE* 3.5 31.9 - - + +
417C TYR* 3.5 36.8 - - + +
420C TYR* 6.5 0.4 - - + -
271O THR* 4.6 10.8 - - - +
274O LEU* 4.0 11.4 - - + +
275O LEU* 4.3 17.5 - - + -
303O ALA 2.7 22.0 + - - +
304O ALA* 3.7 4.3 - - - +
306O ASN* 1.3 71.0 - - - +
308O ALA* 1.3 63.4 + - - +
310O LEU* 3.4 10.6 + - + +
311O HIS* 3.2 49.1 + - + +
323O ALA* 4.4 1.6 - - + -
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Residues in contact with ALA 308 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304O ALA 2.8 13.5 + - - +
305O LEU 3.5 8.5 - - - +
307O LEU* 1.3 76.7 - - - +
309O ALA* 1.3 62.4 + - - +
311O HIS 3.1 3.6 + - - -
312O CYS* 3.1 19.8 + - - -
320O ALA* 3.4 20.0 - - + +
323O ALA* 3.8 8.7 - - - +
324O LEU* 3.6 44.2 - - + +
346O TRP* 5.9 0.9 - - + -
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Residues in contact with ALA 309 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258O TYR* 5.7 1.8 - - - +
305O LEU* 3.0 16.5 + - + +
306O ASN* 3.2 10.1 + - - +
308O ALA* 1.3 73.1 - - - +
310O LEU* 1.3 66.6 + - - +
312O CYS* 3.1 8.3 + - - +
313O ARG* 3.0 37.2 + - - +
346O TRP* 3.5 36.0 - - + +
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Residues in contact with LEU 310 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258O TYR* 3.7 21.0 + - + +
262O LEU* 3.6 29.8 - - + -
267O VAL 5.2 0.7 - - - +
270O SER* 4.2 4.3 - - - +
271O THR* 3.8 38.4 - - - +
274O LEU* 4.8 9.0 - - + -
306O ASN 2.8 13.8 + - - +
307O LEU* 3.5 20.6 - - + +
309O ALA* 1.3 77.5 - - - +
311O HIS* 1.3 70.3 + - + +
313O ARG* 3.3 6.3 + - - +
314O PHE* 3.2 34.8 + - + -
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Residues in contact with HIS 311 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A HIS* 6.4 0.2 - - - -
166A GLY 4.8 4.9 - - - -
168A ASP* 5.4 6.3 - - - -
416C PHE* 3.7 27.3 - + - -
267O VAL* 6.6 0.4 - - + -
271O THR* 6.1 2.7 - - - -
307O LEU* 3.2 38.3 + - + +
308O ALA* 3.1 7.2 + - - +
310O LEU* 1.3 86.8 - - + +
312O CYS* 1.3 61.7 + - - +
314O PHE* 3.3 3.2 + - - -
315O GLY 3.1 4.7 + - - -
316O HIS* 2.8 64.8 + + + +
319O GLN* 4.0 21.8 - - + -
320O ALA* 3.8 6.5 - - + +
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Residues in contact with CYS 312 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D PHE* 4.2 6.2 - - + -
308O ALA* 3.1 21.1 + - - -
309O ALA* 3.1 5.6 + - - +
311O HIS* 1.3 74.5 - - - +
313O ARG* 1.3 65.1 + - - +
315O GLY* 3.0 14.7 + - - -
317O TYR* 3.7 27.1 + - + -
320O ALA* 3.9 2.9 - - - +
346O TRP* 3.1 47.8 - - + -
349O VAL* 5.0 0.7 - - - -
350O LEU* 3.4 29.8 - - - -
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Residues in contact with ARG 313 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D PHE* 3.8 41.1 + - + +
10D PRO 3.1 23.8 + - - -
11D ARG* 3.9 1.0 + - - +
12D VAL* 3.2 39.5 - - - +
258O TYR* 4.4 5.7 + - - -
262O LEU* 4.3 25.6 - - + -
309O ALA* 3.0 21.8 + - - +
310O LEU* 3.8 6.7 - - - +
311O HIS 3.3 0.2 - - - -
312O CYS* 1.3 76.0 - - + +
314O PHE* 1.3 61.8 + - + +
315O GLY* 3.2 4.2 + - - -
346O TRP* 3.8 15.1 - - - -
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Residues in contact with PHE 314 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A TYR* 5.5 4.0 + - - -
115A LYS* 4.5 15.6 - - + -
262O LEU* 3.8 16.8 - - + -
265O GLN* 3.9 33.9 - - + -
266O ASP 3.3 24.0 - - - -
267O VAL* 4.0 26.7 - - + -
270O SER* 3.6 16.8 - - - -
310O LEU* 3.2 38.0 + - + +
311O HIS* 3.3 1.7 + - - +
313O ARG* 1.3 77.8 - - + +
315O GLY* 1.3 60.0 + - - +
316O HIS* 3.4 33.5 + + + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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