Contacts of the helix formed by residues 300 - 315 (chain A) in PDB entry 2DFS
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 ASP 300 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A GLY 4.1 1.4 + - - -
299A ILE* 1.3 73.1 - - - +
301A ASP* 1.4 60.8 + - - +
302A ALA* 3.0 15.1 + - - +
303A LYS* 2.5 70.2 + - + +
304A GLU* 3.1 24.8 + - - +
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Residues in contact with ASP 301 (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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257A ARG* 2.7 47.8 + - - -
260A HIS* 5.1 1.0 + - - +
263A TYR* 3.9 16.8 - - - +
264A GLN* 3.5 28.2 - - - +
267A ALA* 3.9 18.1 - - + +
294A PRO 4.1 2.9 - - - +
295A VAL* 4.6 8.3 - - - +
296A ILE 4.9 1.1 + - - -
299A ILE* 3.6 18.8 + - - +
300A ASP* 1.4 71.7 + - - +
302A ALA* 1.4 55.4 + - - +
304A GLU* 3.6 2.1 + - - +
305A MET 3.0 21.3 + - - -
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Residues in contact with ALA 302 (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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267A ALA* 3.9 26.3 - - + +
268A SER* 3.9 15.5 + - - +
271A LEU* 6.1 2.2 - - + -
300A ASP* 3.0 11.0 + - - +
301A ASP* 1.4 75.6 - - - +
303A LYS* 1.3 64.7 + - - +
305A MET* 3.2 5.5 + - - +
306A VAL* 3.1 25.0 + - - +
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Residues in contact with LYS 303 (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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300A ASP* 2.5 54.2 + - + +
302A ALA* 1.3 71.1 - - + +
304A GLU* 1.3 64.4 - - - +
306A VAL* 3.1 13.1 + - + +
307A ASN* 3.0 25.8 + - - +
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Residues in contact with GLU 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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201A PRO* 5.8 0.2 - - - +
264A GLN* 3.3 17.9 - - + +
299A ILE* 4.2 18.4 - - + -
300A ASP 3.1 16.4 + - - +
301A ASP* 3.9 5.6 - - - +
303A LYS* 1.3 83.0 - - - +
305A MET* 1.3 50.2 + - - +
307A ASN* 2.9 34.1 + - - +
308A THR* 2.7 36.6 + - - -
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Residues in contact with MET 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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261A ILE* 3.8 17.0 - - + -
264A GLN* 3.5 24.1 - - + +
265A LEU* 3.9 17.9 - - + -
268A SER* 3.5 23.3 - - - +
274A PHE* 3.9 20.0 - - + -
301A ASP 3.0 13.4 + - - +
302A ALA 3.2 9.8 + - - +
304A GLU* 1.3 72.6 - - - +
306A VAL* 1.4 60.4 + - + +
308A THR* 3.6 5.3 - - - -
309A ARG* 2.9 43.8 + - - +
326A PHE* 3.6 37.2 - - + -
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Residues in contact with VAL 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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271A LEU* 6.1 5.8 - - + -
302A ALA 3.1 14.6 + - - +
303A LYS* 3.1 14.0 + - + +
305A MET* 1.4 73.7 - - + +
307A ASN* 1.3 58.2 + - - +
309A ARG* 3.8 10.3 - - - +
310A GLN* 3.0 57.4 + - + +
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Residues in contact with ASN 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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201A PRO* 4.3 21.7 - - - +
303A LYS 3.0 12.0 + - - +
304A GLU* 2.9 31.6 + - - +
306A VAL* 1.3 76.4 - - - +
308A THR* 1.4 55.3 + - - +
310A GLN* 3.3 9.5 + - - +
311A ALA* 3.0 28.6 + - - +
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Residues in contact with THR 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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201A PRO* 4.3 18.2 + - - +
202A ILE* 4.6 7.1 - - + +
205A SER* 3.8 20.2 - - - +
261A ILE* 4.2 14.4 - - + -
264A GLN* 3.0 15.7 + - - -
304A GLU 2.7 27.5 + - - -
305A MET* 3.6 11.4 - - - -
307A ASN* 1.4 72.3 - - - +
309A ARG* 1.3 61.1 + - - +
311A ALA* 3.4 7.3 + - - +
312A CYS* 3.2 30.3 + - - -
326A PHE* 5.4 4.5 - - + -
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Residues in contact with ARG 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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271A LEU* 4.8 6.7 - - - +
273A GLU* 2.6 40.9 + - - +
274A PHE* 3.5 25.3 - - - -
305A MET* 2.9 34.7 + - + +
306A VAL* 3.8 9.0 - - - +
308A THR* 1.3 75.8 - - - +
310A GLN* 1.3 63.3 + - + +
312A CYS* 3.3 2.8 + - - -
313A THR* 3.0 25.6 + - - -
319A ASP* 5.7 3.4 + - - -
322A GLN* 3.5 19.7 + - - +
323A MET* 5.4 4.6 - - - -
326A PHE* 3.8 25.5 - - + -
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Residues in contact with GLN 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 VAL* 3.0 42.0 + - + +
307A ASN* 3.3 10.2 + - - +
309A ARG* 1.3 75.2 - - + +
311A ALA* 1.3 55.7 + - - +
313A THR* 3.3 10.2 + - - -
314A LEU* 3.0 34.6 + - + +
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Residues in contact with ALA 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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198A ALA* 3.4 24.6 - - + +
201A PRO* 3.7 15.9 - - + -
202A ILE* 3.8 10.3 - - + +
307A ASN* 3.0 16.9 + - - +
308A THR 3.6 6.3 - - - +
310A GLN* 1.3 76.2 - - - +
312A CYS* 1.3 59.7 + - - +
314A LEU* 3.3 14.7 + - + +
315A LEU* 3.1 27.4 + - - +
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Residues in contact with CYS 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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202A ILE* 4.0 28.3 - - - -
308A THR* 3.2 25.4 + - - -
309A ARG* 3.5 2.2 - - - +
311A ALA* 1.3 73.7 - - - +
313A THR* 1.4 60.5 + - - +
315A LEU* 3.4 2.1 + - - -
316A GLY 3.2 5.2 + - - -
317A ILE* 3.0 47.2 + - + +
322A GLN* 3.5 31.2 - - + +
325A ILE* 5.2 7.9 - - - -
326A PHE* 5.4 5.6 - - - -
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Residues in contact with THR 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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309A ARG 3.0 10.4 + - - -
310A GLN* 3.3 13.0 + - - -
312A CYS* 1.4 74.9 - - - +
314A LEU* 1.4 63.0 + - + +
316A GLY* 3.3 11.6 + - - -
317A ILE 4.6 3.8 - - - +
319A ASP* 4.3 12.0 + - - +
322A GLN* 3.1 21.8 + - - +
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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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195A LYS* 5.9 2.6 - - - +
198A ALA* 4.2 25.4 - - + -
310A GLN* 3.0 22.5 + - + +
311A ALA* 3.3 12.3 + - + +
313A THR* 1.4 77.4 - - + +
315A LEU* 1.3 61.9 + - + +
316A GLY 3.3 2.5 + - - -
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Residues in contact with LEU 315 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A LYS* 3.7 33.9 - - + +
198A ALA* 4.2 4.0 - - + -
199A SER* 3.7 38.6 - - - +
202A ILE* 3.8 20.0 - - + -
311A ALA 3.1 12.3 + - - +
312A CYS 3.4 2.4 + - - +
313A THR 3.4 0.4 - - - -
314A LEU* 1.3 80.9 - - + +
316A GLY* 1.3 60.3 + - - +
317A ILE* 3.4 11.0 + - + +
418A HIS 4.5 6.1 - - - +
419A VAL* 4.1 17.0 - - + +
422A ALA* 3.4 38.6 - - + +
423A LEU* 5.9 2.0 - - + -
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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