Contacts of the helix formed by residues 303 - 317 (chain A) in PDB entry 3SFX
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 ARG 303 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A PHE* 2.8 45.6 + - + +
301A GLN* 3.3 44.4 + - + +
302A ASN* 1.3 74.0 - - - +
304A VAL* 1.3 59.0 + - - +
305A ASP 3.4 2.7 - - - -
306A ASP* 2.9 37.1 + - - +
307A ALA* 3.1 22.0 + - - +
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Residues in contact with VAL 304 (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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299A ILE* 5.1 13.0 - - + -
302A ASN* 3.1 17.6 + - - +
303A ARG* 1.3 73.2 - - - +
305A ASP* 1.3 72.4 + - - +
307A ALA* 3.4 6.8 + - - +
308A ALA* 2.9 30.2 + - - +
333A CYS* 3.5 37.6 - - + +
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Residues in contact with ASP 305 (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 ARG 3.4 0.4 - - - -
304A VAL* 1.3 86.1 - - - +
306A ASP* 1.3 63.0 + - - +
308A ALA* 3.4 7.2 + - - +
309A LYS* 3.1 42.9 + - - +
333A CYS 5.5 1.0 - - - +
334A ALA* 5.9 3.3 - - - +
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Residues in contact with ASP 306 (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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298A PHE* 3.5 25.4 - - + -
303A ARG* 2.9 46.9 + - + +
304A VAL 3.3 0.2 - - - -
305A ASP* 1.3 79.6 - - - +
307A ALA* 1.3 64.1 + - - +
309A LYS* 3.5 23.9 + - - +
310A VAL* 3.3 26.5 + - - +
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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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295A ALA* 3.5 25.2 - - - +
298A PHE* 3.7 9.3 - - + -
299A ILE* 3.6 22.9 - - + -
303A ARG 3.1 13.3 + - - +
304A VAL 3.7 7.0 - - - +
305A ASP 3.3 0.2 - - - -
306A ASP* 1.3 75.1 - - - +
308A ALA* 1.3 64.8 + - - +
310A VAL* 3.1 4.9 + - - +
311A PHE* 3.0 31.1 + - + -
333A CYS* 4.1 6.5 - - - -
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Residues in contact with ALA 308 (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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304A VAL 2.9 18.7 + - - +
305A ASP* 3.5 8.7 - - - +
307A ALA* 1.3 74.7 - - - +
309A LYS* 1.3 58.7 + - + +
311A PHE* 3.2 10.5 + - - +
312A GLU* 2.8 31.5 + - - +
330A ARG* 3.6 18.8 - - + +
333A CYS* 3.9 15.8 - - + -
334A ALA* 5.4 6.3 - - + -
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Residues in contact with LYS 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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305A ASP* 3.1 25.8 + - - +
306A ASP* 3.6 25.4 + - - +
307A ALA 3.3 0.2 - - - -
308A ALA* 1.3 76.8 - - + +
310A VAL* 1.3 61.5 + - + +
312A GLU* 3.6 8.3 + - - +
313A LYS* 3.2 27.0 + - - +
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Residues in contact with VAL 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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291A LEU* 3.3 50.5 - - + +
294A LEU* 4.1 12.6 - - + -
295A ALA* 3.9 10.1 - - + -
298A PHE* 3.9 20.9 - - + -
306A ASP 3.3 14.3 + - - +
307A ALA 3.1 7.4 + - - +
309A LYS* 1.3 75.2 - - + +
311A PHE* 1.3 61.6 + - - +
313A LYS* 3.2 8.1 + - + +
314A LEU* 3.0 28.1 + - + +
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Residues in contact with PHE 311 (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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292A GLU* 5.1 2.7 - - - -
295A ALA* 3.5 24.7 - - + -
296A ASP* 4.0 0.9 - - - -
299A ILE* 3.8 22.0 - - + -
307A ALA* 3.0 25.0 + - + -
308A ALA 3.6 5.2 - - - +
310A VAL* 1.3 74.8 - - - +
312A GLU* 1.3 58.4 + - - +
314A LEU* 3.3 8.3 + - + -
315A SER* 2.9 30.1 + - - -
326A TRP* 3.5 55.6 - + - +
329A ARG* 3.5 54.7 - - + -
330A ARG* 3.8 6.5 - - + +
333A CYS* 3.9 11.9 - - - -
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Residues in contact with GLU 312 (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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308A ALA 2.8 17.2 + - - +
309A LYS* 3.6 9.3 - - - +
310A VAL 3.2 0.2 - - - -
311A PHE* 1.3 77.2 - - - +
313A LYS* 1.3 72.9 + - - +
315A SER* 3.2 7.7 + - - -
316A SER* 2.9 49.8 + - - -
327A GLU* 5.7 0.7 - - - +
330A ARG* 4.2 23.7 - - - +
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Residues in contact with LYS 313 (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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291A LEU* 5.4 2.5 - - + -
309A LYS 3.2 13.4 + - - +
310A VAL* 3.2 12.6 + - - +
312A GLU* 1.3 86.9 + - - +
314A LEU* 1.3 60.2 + - - +
316A SER* 4.1 2.9 - - - +
317A GLU* 2.9 57.6 + - - +
318A TYR* 2.9 41.2 + - + -
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Residues in contact with LEU 314 (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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288A PRO* 3.7 28.5 - - + +
291A LEU* 3.9 29.2 - - + -
292A GLU* 4.0 11.4 - - - +
310A VAL* 3.0 17.8 + - + +
311A PHE* 3.3 15.7 + - + +
313A LYS* 1.3 75.8 - - - +
315A SER* 1.3 62.7 + - - +
318A TYR* 3.6 4.6 + - + +
319A ASP* 2.8 55.0 + - + +
326A TRP* 3.6 42.6 - - + +
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Residues in contact with SER 315 (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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311A PHE 2.9 17.3 + - - -
312A GLU* 3.4 8.5 - - - -
314A LEU* 1.3 78.1 - - - +
316A SER* 1.3 61.2 + - - +
320A GLN* 3.8 9.0 - - - +
323A ALA* 2.7 51.8 + - - +
326A TRP* 3.6 12.1 - - - +
327A GLU* 3.9 16.0 + - - +
5B PHE* 4.0 9.2 - - - -
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Residues in contact with SER 316 (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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312A GLU* 2.9 41.2 + - - -
313A LYS* 4.1 2.1 + - - -
315A SER* 1.3 74.5 - - - +
317A GLU* 1.3 74.0 + - - +
320A GLN* 3.2 21.5 + - - +
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Residues in contact with GLU 317 (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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313A LYS* 2.9 44.2 + - + +
315A SER 3.6 0.8 - - - -
316A SER* 1.3 89.6 + - - +
318A TYR* 1.3 90.8 + - + +
319A ASP 3.6 2.0 - - - -
320A GLN* 3.3 22.2 + - - +
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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