Contacts of the helix formed by residues 294 - 311 (chain A) in PDB entry 5F0P
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 ASN 294 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A GLU* 3.0 26.5 + - - +
292A ASN 3.7 2.2 + - - +
293A VAL* 1.3 69.2 - - - +
295A VAL* 1.3 60.7 + - - +
296A LYS* 3.4 14.1 - - - +
297A ASN* 3.0 58.7 + - + +
298A ILE* 3.5 14.9 + - - +
346A ASP* 5.9 0.6 + - - -
507A EDO 3.5 28.3 + - - -
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Residues in contact with VAL 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A CYS* 3.9 29.4 - - + +
289A LEU* 5.0 1.3 - - + -
293A VAL* 2.9 23.1 + - + +
294A ASN* 1.3 70.1 - - - +
296A LYS* 1.3 65.6 + - - +
298A ILE* 3.2 10.1 + - + +
299A ILE* 3.1 26.9 + - + +
335A VAL* 3.3 32.5 - - + -
339A ARG* 3.7 37.2 - - + +
342A MET* 5.7 3.6 - - + -
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Residues in contact with LYS 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ASN* 3.4 10.8 - - - +
295A VAL* 1.3 77.5 - - - +
297A ASN* 1.3 75.3 + - - +
299A ILE* 3.4 1.4 + - - +
300A ILE* 3.0 52.4 + - + +
342A MET* 3.9 20.8 - - + +
346A ASP* 3.5 33.9 - - + +
349A SER* 3.9 19.1 + - - -
350A LEU* 4.1 17.2 - - + +
507A EDO 3.4 35.5 + - - -
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Residues in contact with ASN 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A GLU* 5.6 2.0 + - - -
264A GLU* 3.8 17.5 + - - +
294A ASN* 3.0 40.9 + - + +
295A VAL 3.3 0.2 - - - -
296A LYS* 1.3 99.2 + - - +
298A ILE* 1.3 63.7 + - - +
300A ILE* 4.2 7.6 - - - +
301A ALA* 3.1 25.3 + - - +
507A EDO 4.0 11.8 + - - -
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Residues in contact with ILE 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A GLU* 4.5 6.3 - - + +
263A MET* 3.9 13.9 - - + -
264A GLU* 4.1 20.9 - - + +
267A ILE* 3.4 17.2 - - + +
282A PHE* 3.6 35.9 - - + -
286A CYS* 3.8 12.1 - - - -
289A LEU* 3.7 29.2 - - + -
293A VAL* 3.8 18.8 - - + -
294A ASN 3.5 8.9 + - - +
295A VAL* 3.2 10.8 + - - +
297A ASN* 1.3 77.4 - - - +
299A ILE* 1.3 64.6 + - - +
301A ALA 3.3 2.3 + - - -
302A LEU* 3.2 17.0 + - - +
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Residues in contact with ILE 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A PHE* 5.9 0.2 - - - -
283A LEU* 4.0 17.7 - - + -
286A CYS* 4.6 6.1 - - + -
295A VAL* 3.1 21.9 + - + +
296A LYS 4.0 3.1 - - - +
298A ILE* 1.3 75.5 - - - +
300A ILE* 1.3 64.1 + - - +
302A LEU* 3.3 7.9 + - - +
303A ILE* 3.1 40.6 + - + +
328A PHE* 4.3 10.3 - - + -
332A VAL* 3.9 26.5 - - + -
335A VAL* 3.7 39.7 - - + -
350A LEU* 4.2 17.5 - - + -
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Residues in contact with ILE 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A LYS* 3.0 46.8 + - + +
297A ASN* 4.2 7.0 - - - +
299A ILE* 1.3 76.4 - - - +
301A ALA* 1.3 57.9 + - - +
303A ILE* 3.3 6.3 + - - +
304A ASP* 2.9 48.0 + - - +
349A SER* 4.0 20.2 - - - +
350A LEU* 4.3 4.9 - - + -
353A SER* 3.8 25.1 - - - +
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Residues in contact with ALA 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A GLU* 5.2 8.3 - - + -
267A ILE* 4.0 17.2 - - + +
297A ASN 3.1 19.9 + - - +
298A ILE* 3.3 5.6 + - - +
300A ILE* 1.3 78.0 - - - +
302A LEU* 1.3 57.6 + - - +
304A ASP* 3.6 9.8 + - - +
305A ARG* 3.1 27.5 + - - +
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Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ILE* 4.0 23.7 - - + +
275A HIS* 4.1 35.0 - - + +
279A LEU* 4.2 10.1 - - + -
282A PHE* 4.0 27.8 - - + -
283A LEU* 4.6 6.7 - - + -
298A ILE 3.2 11.0 + - - +
299A ILE* 3.6 9.2 - - - +
300A ILE 3.2 0.2 - - - -
301A ALA* 1.3 77.3 - - - +
303A ILE* 1.3 59.0 + - - +
305A ARG* 3.2 4.0 + - + +
306A LEU* 3.0 37.4 + - + +
328A PHE* 3.6 29.8 - - + -
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Residues in contact with ILE 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ILE* 3.1 24.3 + - + +
300A ILE* 3.8 4.9 - - - +
302A LEU* 1.3 77.7 - - - +
304A ASP* 1.3 60.8 + - - +
306A LEU* 3.2 8.3 + - - +
307A ALA* 2.9 29.0 + - + +
328A PHE* 3.5 40.2 - - + -
332A VAL* 5.2 0.9 - - + -
353A SER* 3.6 46.0 - - - +
354A LEU* 4.8 6.7 - - + +
356A ASN* 5.1 4.9 - - - +
357A LEU* 3.8 28.9 - - + +
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Residues in contact with ASP 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ILE* 2.9 39.5 + - - +
301A ALA* 3.7 9.0 - - - +
303A ILE* 1.3 77.3 - - - +
305A ARG* 1.3 61.0 + - - +
307A ALA* 3.5 7.0 + - - +
308A LEU* 3.4 27.8 + - - +
353A SER* 5.6 1.7 - - - -
356A ASN* 3.8 19.9 + - - -
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Residues in contact with ARG 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ILE* 3.2 31.6 + - + -
268A GLN* 3.2 23.8 + - - +
269A VAL 5.0 0.6 + - - -
270A PHE 3.3 25.1 + - - -
271A PRO* 3.8 3.4 - - - +
272A ASP* 2.7 54.8 + - - +
275A HIS* 4.0 3.9 - - - -
301A ALA 3.1 16.8 + - - +
302A LEU* 3.2 6.7 + - + +
304A ASP* 1.3 75.7 - - - +
306A LEU* 1.3 62.1 + - + +
308A LEU* 3.5 11.2 + - + +
309A PHE* 3.2 16.5 + - - +
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Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ASP* 3.7 21.8 - - + +
275A HIS* 4.5 10.5 - - + -
276A LEU* 3.9 28.5 - - + -
279A LEU* 4.2 10.5 - - + -
302A LEU* 3.0 23.8 + - + +
303A ILE* 3.2 5.8 + - - +
305A ARG* 1.3 73.2 - - - +
307A ALA* 1.3 59.2 + - - +
309A PHE* 3.4 7.0 + - + +
310A ALA* 3.1 26.5 + - - +
318A ILE* 4.2 4.6 - - + +
324A LEU* 4.2 18.8 - - + -
328A PHE* 3.7 35.4 - - + -
357A LEU* 4.9 7.6 - - + -
361A CYS* 4.2 4.5 - - - -
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Residues in contact with ALA 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A ILE* 2.9 18.6 + - + +
304A ASP* 3.6 9.6 - - - +
305A ARG 3.3 0.2 - - - -
306A LEU* 1.3 75.2 - - - +
308A LEU* 1.3 65.3 + - + +
309A PHE 3.1 0.2 - - - -
310A ALA* 3.1 13.5 + - - +
311A HIS* 3.3 18.2 + - - +
356A ASN* 5.2 7.2 - - - +
357A LEU* 5.8 0.4 - - - -
360A LYS* 4.0 33.4 - - + +
361A CYS* 4.5 11.4 - - - -
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Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ASP 3.4 14.9 + - - +
305A ARG* 3.5 11.0 + - + +
306A LEU 3.5 0.2 - - - -
307A ALA* 1.3 79.2 - - + +
309A PHE* 1.3 59.5 + - - +
311A HIS* 4.3 5.3 - - + +
312A ARG* 3.5 23.2 + - - +
360A LYS* 5.9 5.4 - - + +
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Residues in contact with PHE 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A ASP* 3.8 29.4 - - + +
273A GLU* 3.8 34.1 - - + -
276A LEU* 3.8 23.8 - - + -
305A ARG 3.2 13.3 + - - +
306A LEU* 3.5 11.7 - - + +
307A ALA 3.1 0.8 - - - -
308A LEU* 1.3 77.6 - - - +
310A ALA* 1.3 63.3 + - - +
311A HIS 3.6 0.3 + - - -
312A ARG* 3.6 20.9 + - + +
315A GLY* 5.9 1.6 - - - -
316A PRO* 4.2 15.3 - - + -
317A GLY* 3.5 34.7 - - - -
318A ILE* 4.2 11.4 - - + -
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Residues in contact with ALA 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A LEU 3.1 8.5 + - - +
307A ALA 3.1 9.1 + - - +
309A PHE* 1.3 79.0 - - - +
311A HIS* 1.3 61.6 + - - +
312A ARG 3.6 3.3 + - - +
317A GLY* 5.3 7.3 - - - -
318A ILE* 3.7 28.3 - - + -
360A LYS 3.7 20.9 - - - +
361A CYS* 4.1 9.0 - - - -
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Residues in contact with HIS 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ALA 3.3 10.6 + - - +
308A LEU* 4.5 4.5 - - + +
310A ALA* 1.3 78.3 - - + +
312A ARG* 1.3 61.9 + - - +
313A GLU* 3.5 4.5 + - - +
359A MET 5.1 0.8 + - - -
360A LYS* 3.1 56.0 + - + +
363A PRO* 5.2 6.4 - - + +
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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