Contacts of the helix formed by residues 316 - 334 (chain O) in PDB entry 5G04
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 HIS 316 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A TYR* 6.0 0.2 - - - -
115A LYS* 2.9 28.8 + - - -
162A HIS* 3.6 21.2 - + - -
164A ILE 3.6 22.2 - - - -
165A GLU* 3.0 18.8 - - - +
166A GLY* 3.5 9.4 - - - -
267O VAL* 3.9 5.6 - - + -
311O HIS* 2.8 34.7 + + + +
314O PHE* 3.2 30.5 + + + +
315O GLY* 1.3 69.8 - - - +
317O TYR* 1.3 66.2 + - - +
318O GLN 3.3 2.2 - - - -
319O GLN* 3.2 11.8 + - + -
320O ALA* 2.8 21.3 + - - +
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Residues in contact with TYR 317 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D PHE* 3.9 25.1 - + - -
312O CYS* 4.4 19.2 + - + -
315O GLY* 2.9 40.8 + - - -
316O HIS* 1.3 71.8 - - - +
318O GLN* 1.3 52.8 + - - +
320O ALA* 2.7 24.8 + - - +
321O GLU* 2.7 28.8 + - - +
349O VAL* 4.4 15.9 - - + -
350O LEU* 3.4 20.4 - - + +
353O LYS* 3.6 42.2 - - + +
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Residues in contact with GLN 318 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLU* 3.2 25.3 + - + +
316O HIS 3.3 0.6 - - - -
317O TYR* 1.3 76.0 - - - +
319O GLN* 1.3 62.2 + - - +
321O GLU* 3.5 26.2 + - - +
322O LEU* 3.3 24.7 + - - +
353O LYS* 3.4 24.3 + - - +
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Residues in contact with GLN 319 (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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165A GLU* 2.7 45.5 + - - +
166A GLY 3.9 14.8 - - - +
167A LYS* 3.2 37.7 + - - +
416C PHE* 3.3 28.6 - - + -
448C GLN* 4.0 7.7 - - - +
311O HIS* 4.0 11.9 - - + +
316O HIS* 3.4 20.2 - - + +
318O GLN* 1.3 76.7 - - - +
320O ALA* 1.3 58.4 + - - +
322O LEU* 3.1 26.1 - - - +
323O ALA* 3.1 12.3 + - - +
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Residues in contact with ALA 320 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308O ALA* 3.6 15.6 - - - +
311O HIS* 3.5 18.8 - - + -
312O CYS* 3.7 23.3 - - - +
316O HIS 2.8 15.1 + - - +
317O TYR* 2.7 15.5 + - - +
319O GLN* 1.3 71.0 - - - +
321O GLU* 1.3 54.5 + - - +
322O LEU 3.2 0.2 - - - -
323O ALA* 4.3 1.8 - - - +
324O LEU* 2.8 35.3 + - - +
350O LEU* 3.5 5.1 - - + +
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Residues in contact with GLU 321 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317O TYR* 2.7 32.9 + - - +
318O GLN* 3.5 32.2 + - - +
320O ALA* 1.3 71.0 - - - +
322O LEU* 1.3 62.9 + - - +
324O LEU* 3.4 2.8 + - - +
325O GLN* 3.3 25.5 + - - +
350O LEU* 3.5 40.3 - - + +
353O LYS* 4.4 5.9 - - - +
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Residues in contact with LEU 322 (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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416C PHE* 3.6 27.6 - - + -
446C LEU* 3.6 44.6 - - + +
448C GLN* 3.7 20.9 - - + +
318O GLN 3.3 14.8 + - - +
319O GLN* 3.1 20.0 - - - +
321O GLU* 1.3 76.0 - - - +
323O ALA* 1.3 64.0 + - - +
325O GLN* 3.1 23.4 - - - +
326O GLU* 3.7 9.2 + - - +
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Residues in contact with ALA 323 (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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416C PHE* 3.1 42.6 - - + -
304O ALA* 4.0 4.4 - - - +
307O LEU* 5.0 0.4 - - + -
308O ALA* 3.3 29.8 - - - +
311O HIS* 4.8 0.2 - - + -
319O GLN 3.1 7.6 + - - +
320O ALA* 3.4 0.9 + - - +
322O LEU* 1.3 75.3 - - - +
324O LEU* 1.3 67.4 + - - +
325O GLN 3.0 2.5 - - - -
326O GLU* 3.0 15.8 + - - +
327O ALA* 3.2 10.0 + - - +
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Residues in contact with LEU 324 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305O LEU* 4.4 16.6 - - + -
308O ALA* 3.4 17.7 - - + +
320O ALA 2.8 19.3 + - - +
321O GLU* 3.8 5.4 - - - +
322O LEU 3.2 0.4 - - - -
323O ALA* 1.3 76.0 - - - +
325O GLN* 1.3 59.4 + - - +
327O ALA* 3.2 13.3 - - + +
328O ILE* 2.9 32.8 + - + +
343O CYS* 4.0 16.2 - - + +
346O TRP* 4.3 9.2 - - + -
347O LEU* 3.7 39.7 - - + +
350O LEU* 3.8 17.7 - - + -
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Residues in contact with GLN 325 (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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1096A PRO* 5.1 10.5 - - - +
1154A ASP* 4.8 7.3 - - - +
321O GLU 3.3 13.2 + - - +
322O LEU* 3.1 17.4 + - - +
324O LEU* 1.3 76.7 - - - +
326O GLU* 1.3 64.5 + - - +
328O ILE* 3.9 21.9 - - - +
329O ARG* 3.2 46.1 + - - +
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Residues in contact with GLU 326 (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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414C MET* 3.0 32.7 - - + +
415C PRO* 3.1 9.9 - - - +
416C PHE* 2.7 53.2 + - + +
417C TYR 3.9 3.1 - - - +
446C LEU* 3.9 4.3 - - - +
304O ALA* 3.8 14.6 - - + -
322O LEU 3.7 5.7 + - - +
323O ALA 3.0 8.8 + - - +
325O GLN* 1.3 76.0 - - - +
327O ALA* 1.3 65.2 - - - +
329O ARG* 3.0 30.9 + - - +
330O ILE* 3.0 23.3 + - - +
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Residues in contact with ALA 327 (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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301O ARG 4.4 4.6 - - - +
304O ALA* 3.7 13.0 - - - +
305O LEU* 3.4 37.9 - - + +
323O ALA 3.2 5.3 + - - +
324O LEU* 3.2 21.3 - - + +
326O GLU* 1.3 79.5 - - - +
328O ILE* 1.3 62.5 + - - +
330O ILE* 3.7 4.0 + - - +
331O ALA* 3.2 25.6 + - - +
343O CYS* 4.1 6.6 - - - -
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Residues in contact with ILE 328 (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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1096A PRO* 3.8 25.8 - - + +
1097A THR* 3.4 20.0 - - - +
1154A ASP* 4.6 4.5 - - - +
324O LEU* 2.9 19.6 + - + +
325O GLN* 3.9 32.5 - - - +
326O GLU 3.4 0.2 - - - -
327O ALA* 1.3 72.7 - - - +
329O ARG* 1.3 57.7 + - - +
331O ALA* 3.6 2.3 + - - +
332O GLN* 2.9 46.6 + - - +
340O LEU* 3.7 20.6 - - + +
343O CYS* 3.9 19.5 - - + -
347O LEU* 4.1 17.9 - - + -
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Residues in contact with ARG 329 (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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1154A ASP* 3.4 39.9 + - - +
1156A ALA* 3.4 23.0 - - + +
413C LYS* 3.3 31.8 + - - +
415C PRO* 5.1 4.4 - - - +
325O GLN* 3.2 34.1 + - - +
326O GLU* 3.0 27.8 + - - +
328O ILE* 1.3 77.6 - - - +
330O ILE* 1.3 73.4 + - + +
332O GLN 3.4 1.6 + - - -
333O GLU* 3.4 27.9 + - - +
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Residues in contact with ILE 330 (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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412C LEU* 3.8 15.5 - - + +
414C MET* 3.3 48.0 - - + -
296O TYR* 4.1 19.0 - - + -
300O LEU* 3.8 13.5 - - + +
301O ARG* 4.3 11.5 - - + +
304O ALA* 3.7 10.1 - - + -
326O GLU 3.0 26.0 + - - +
327O ALA* 4.1 5.4 - - - +
329O ARG* 1.3 75.9 - - + +
331O ALA* 1.3 63.0 + - - +
333O GLU* 3.2 22.5 + - - +
334O SER* 3.3 22.5 + - - -
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Residues in contact with ALA 331 (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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301O ARG* 4.3 8.6 - - + +
327O ALA 3.2 20.6 + - - +
328O ILE 3.6 6.1 - - - +
329O ARG 3.3 0.2 - - - -
330O ILE* 1.3 76.6 - - - +
332O GLN* 1.3 55.4 + - - +
334O SER 3.5 1.0 + - - -
335O ASN 3.0 15.6 + - - -
336O ASP* 3.0 27.5 + - - +
339O CYS* 3.7 25.4 - - - -
340O LEU* 3.9 20.4 - - + -
343O CYS* 4.9 0.9 - - - -
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Residues in contact with GLN 332 (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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1096A PRO 3.8 18.7 + - - +
1154A ASP* 3.4 32.7 + - - -
1156A ALA* 3.6 18.1 - - + +
1157A TRP* 3.4 33.9 - - - +
1159A VAL* 5.2 4.7 - - - +
1160A TYR* 3.4 25.5 + - + +
328O ILE* 2.9 29.9 + - - +
329O ARG* 3.8 4.9 - - - +
330O ILE 3.3 0.4 - - - -
331O ALA* 1.3 73.0 - - - +
333O GLU* 1.3 61.2 + - - +
334O SER 3.2 0.7 - - - -
335O ASN* 2.9 25.9 + - - +
340O LEU* 4.2 13.0 - - + -
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Residues in contact with GLU 333 (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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1156A ALA* 3.7 16.0 - - + +
1159A VAL* 5.7 8.9 - - + +
412C LEU 4.1 0.3 - - - +
413C LYS* 3.7 22.4 - - - +
296O TYR* 3.7 30.4 + - + +
329O ARG* 3.4 33.9 + - - +
330O ILE* 3.2 29.9 + - - +
332O GLN* 1.3 77.5 - - - +
334O SER* 1.3 57.1 + - - +
335O ASN* 4.7 3.3 - - - +
96R SER* 4.8 6.8 - - - +
99R ASN 4.4 12.0 - - - +
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Residues in contact with SER 334 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293O GLU* 3.6 25.8 + - - +
294O GLU 4.1 5.0 + - - -
295O GLY* 4.5 4.1 - - - -
296O TYR* 4.3 16.6 + - - +
301O ARG* 3.1 44.8 + - - +
330O ILE 3.3 8.6 + - - -
331O ALA 3.9 7.0 - - - -
332O GLN 3.2 0.2 - - - -
333O GLU* 1.3 73.6 - - - +
335O ASN* 1.3 76.4 + - - +
336O ASP* 3.3 2.4 + - - -
99R ASN 5.9 0.9 - - - -
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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