Contacts of the helix formed by residues 296 - 306 (chain A) in PDB entry 5DO7
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 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A PRO 4.4 7.3 + - - -
254A SER* 3.5 22.8 + - - +
295A SER* 1.3 73.6 + - - +
297A PRO* 1.4 71.3 - - - +
298A PHE* 3.5 6.8 + - - +
299A ASP* 2.8 44.2 + - + +
300A PHE* 2.8 11.0 + - - -
273B ARG* 4.4 3.6 - - - +
274B SER* 3.0 13.4 + - - +
312B PRO 2.8 17.6 + - - -
313B ARG* 3.5 38.7 - - - +
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Residues in contact with PRO 297 (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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254A SER* 4.8 1.1 - - - +
257A PHE* 3.5 39.0 - - + -
281A LEU* 4.2 5.2 - - + -
291A CYS* 4.1 26.0 - - + -
292A PRO 5.5 1.3 - - - +
295A SER* 4.0 3.1 - - - +
296A ASN* 1.4 83.8 - - - +
298A PHE* 1.3 59.1 + - - +
300A PHE* 4.6 2.7 - - + -
301A TYR* 2.8 33.3 + - + -
311B CYS* 4.7 12.6 - - - +
312B PRO* 3.3 32.8 - - + +
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Residues in contact with PHE 298 (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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83A CYS* 3.8 22.7 - - - -
85A LEU* 3.6 38.1 - - + +
249A ILE* 4.7 3.8 - - + -
252A PRO* 2.7 49.8 - - + -
253A ARG 4.1 11.0 - - - +
256A LEU* 6.5 0.4 - - + -
257A PHE* 3.8 36.7 - + + -
260A PHE* 4.8 6.1 - + - -
263A ILE* 3.6 32.2 - - + +
265A ILE* 5.7 2.6 - - - +
280A MET* 5.2 2.5 - - - +
296A ASN* 2.9 9.2 + - - +
297A PRO* 1.3 82.2 - - - +
299A ASP* 1.3 63.1 - - + +
301A TYR* 4.4 3.7 - - - +
302A MET* 4.1 6.1 + - - +
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Residues in contact with ASP 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 5.3 0.4 - - - -
251A GLN* 6.1 0.2 - - - +
252A PRO 5.7 1.1 - - - +
295A SER 4.9 1.4 - - - +
296A ASN* 2.8 33.1 + - + +
298A PHE* 1.3 77.6 - - + +
300A PHE* 1.3 67.8 + - - +
302A MET* 2.8 39.5 + - - +
303A ASP* 3.3 4.5 + - - +
273B ARG* 2.7 64.9 + - - +
274B SER 4.4 2.3 + - - -
275B ASP* 5.0 1.0 + - - -
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Residues in contact with PHE 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A TYR* 4.1 17.0 - - + -
290A PRO 4.2 6.1 - - - -
291A CYS* 3.2 35.2 - - + -
292A PRO* 4.2 10.8 - - + -
295A SER* 3.6 35.5 + - - +
296A ASN 2.8 13.4 + - - +
297A PRO 4.2 2.2 - - - +
299A ASP* 1.3 71.1 - - - +
301A TYR* 1.3 88.8 + + - +
303A ASP* 2.8 34.7 + - + +
304A LEU* 3.4 29.2 + - + +
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Residues in contact with TYR 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 PHE* 4.7 0.2 - + - -
265A ILE* 5.6 3.8 - - + -
280A MET* 3.4 36.8 - - + -
281A LEU* 3.4 34.7 + - + +
284A PHE* 3.2 55.2 - + + -
285A ASN* 3.7 12.6 + - - -
289A TYR 4.4 5.4 - - - -
291A CYS* 3.3 37.7 - - + -
297A PRO* 2.8 26.0 + - + +
298A PHE 4.4 3.4 - - - +
300A PHE* 1.3 87.0 - + - +
302A MET* 1.3 59.8 + - - +
304A LEU* 3.4 5.2 + - - +
305A THR* 3.0 28.8 + - + +
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Residues in contact with MET 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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85A LEU* 3.6 43.7 - - + -
86A GLY 4.0 3.8 - - - +
87A SER* 3.6 34.8 - - - +
88A SER* 4.5 3.4 - - - +
250A HIS 5.3 5.2 - - - +
251A GLN* 6.5 1.3 - - - -
265A ILE* 5.4 2.6 - - + +
298A PHE 4.1 2.3 + - - +
299A ASP* 2.8 35.1 + - - +
301A TYR* 1.3 69.8 - - - +
303A ASP* 1.3 74.0 + - - +
305A THR* 2.1 32.7 + - - +
306A SER* 3.0 14.1 + - - +
273B ARG* 5.1 7.0 - - - -
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Residues in contact with ASP 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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299A ASP* 4.1 6.7 - - - +
300A PHE* 2.8 26.6 + - + +
302A MET* 1.3 82.3 - - - +
304A LEU* 1.3 64.4 + - + +
306A SER* 3.3 21.2 + - - +
321A ARG* 4.6 4.6 + - - -
245B SER* 3.4 11.3 + - - -
246B PHE* 5.7 2.9 - - - -
249B HIS* 5.4 0.8 - - - -
273B ARG* 2.9 25.2 + - - -
275B ASP* 3.2 30.1 - - - +
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Residues in contact with LEU 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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284A PHE* 3.7 21.1 - - + -
289A TYR* 3.4 50.0 - - + -
300A PHE* 3.4 26.6 + - + +
301A TYR* 3.7 8.7 - - - +
302A MET 3.2 0.4 - - - -
303A ASP* 1.3 81.5 - - + +
305A THR* 1.3 61.6 + - - +
306A SER* 3.3 3.5 + - - +
321A ARG* 3.9 42.3 + - - +
322A VAL* 4.5 7.8 - - - +
325A ILE* 5.2 4.9 - - + +
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Residues in contact with THR 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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85A LEU* 5.2 0.2 - - - +
87A SER* 4.5 5.2 + - - -
265A ILE* 3.6 38.4 - - + +
267A SER* 3.5 9.5 + - - -
272A ILE* 3.8 13.9 - - + +
284A PHE* 4.4 17.5 - - + -
301A TYR* 3.0 26.1 + - + +
302A MET* 2.1 43.0 + - - +
304A LEU* 1.3 73.3 - - - +
306A SER* 1.3 55.4 + - - -
322A VAL* 3.0 26.9 - - - +
325A ILE* 5.7 4.0 - - + -
329A TYR* 5.4 0.2 - - - +
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Residues in contact with SER 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A SER* 3.1 35.7 - - - -
88A SER 5.5 0.2 + - - -
267A SER* 4.1 4.5 - - - -
268A PHE* 4.9 2.5 - - - -
302A MET* 3.0 16.4 + - - +
303A ASP* 3.3 14.7 + - - +
304A LEU 3.2 4.0 - - - +
305A THR* 1.3 76.9 - - - +
307A VAL* 1.3 69.3 + - - +
308A ASP* 3.7 3.5 + - - +
318A THR* 5.1 2.4 - - - -
321A ARG* 5.6 1.9 + - - -
322A VAL* 5.3 0.4 - - - -
244B ASP* 5.6 1.7 + - - -
246B PHE* 4.7 9.4 - - - -
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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
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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