Contacts of the helix formed by residues 297 - 310 (chain A) in PDB entry 7C17
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 LYS 297 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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562 T 3.7 14.6 + - + +
572 A 5.8 6.1 - - - +
296A GLY* 1.3 76.3 - - - +
298A LYS* 1.3 66.6 + - + +
299A SER 3.6 0.9 - - - -
300A LEU* 3.9 4.9 + - - +
301A THR* 3.4 22.2 + - - +
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Residues in contact with LYS 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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552 T 3.4 53.8 + - - +
562 T 2.9 20.2 + - + +
297A LYS* 1.3 74.7 - - + +
299A SER* 1.3 71.1 + - - +
301A THR* 2.6 30.5 + - - +
302A GLU* 3.4 6.3 + - + +
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Residues in contact with SER 299 (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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552 T 5.5 0.4 - - - -
562 T 3.1 9.1 + - - -
263A THR* 5.8 1.6 - - - -
265A ARG* 5.7 4.9 - - - -
266A SER* 4.2 14.4 - - - -
294A ASN 3.0 25.5 + - - -
295A LEU* 3.3 13.5 - - - -
297A LYS 3.6 0.2 - - - -
298A LYS* 1.3 80.1 - - - +
300A LEU* 1.3 58.8 + - - +
301A THR 3.3 0.2 - - - -
302A GLU* 3.3 16.1 + - - +
303A ILE* 2.9 33.2 + - - +
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Residues in contact with LEU 300 (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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286A GLU* 6.0 4.3 - - + -
289A LEU* 5.5 9.2 - - + -
295A LEU* 4.2 17.1 + - + +
296A GLY 4.3 7.0 - - - +
297A LYS* 3.9 10.0 + - - +
298A LYS 3.2 0.4 - - - -
299A SER* 1.3 80.1 + - - +
301A THR* 1.3 58.6 + - + +
303A ILE* 3.3 12.8 + - - +
304A LYS* 2.9 27.5 + - - +
314A LEU* 3.8 14.4 - - + +
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Residues in contact with THR 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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297A LYS 3.4 19.3 - - - +
298A LYS* 2.6 20.8 + - - +
300A LEU* 1.3 77.4 - - + +
302A GLU* 1.3 56.3 + - - +
304A LYS* 3.4 8.6 + - - +
305A ASP* 2.9 29.0 + - - +
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Residues in contact with GLU 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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261A GLU 5.3 0.7 - - - +
262A LEU* 3.4 25.3 - - - +
263A THR* 3.3 38.9 + - + +
266A SER* 5.6 1.7 - - - -
298A LYS* 3.4 5.7 + - + +
299A SER* 3.3 21.8 + - - +
300A LEU 3.3 0.8 - - - -
301A THR* 1.3 80.0 + - - +
303A ILE* 1.3 59.3 + - - +
305A ASP* 3.3 9.5 + - + +
306A VAL* 2.9 36.6 + - - +
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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
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262A LEU* 4.1 26.5 - - + -
266A SER* 3.4 26.7 - - - +
270A LEU* 4.7 8.5 - - + -
289A LEU* 4.9 16.6 - - + -
295A LEU* 5.5 3.4 - - + -
299A SER 2.9 20.8 + - - +
300A LEU* 3.3 9.4 + - - +
302A GLU* 1.3 76.7 - - - +
304A LYS* 1.3 56.8 + - - +
306A VAL* 3.3 10.2 - - + +
307A LEU* 2.9 35.5 + - + +
314A LEU* 3.8 24.9 - - + -
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Residues in contact with LYS 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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286A GLU* 5.3 3.8 + - - -
300A LEU 2.9 16.9 + - - +
301A THR* 3.7 8.7 - - - +
303A ILE* 1.3 76.9 - - - +
305A ASP* 1.3 57.9 + - - +
307A LEU* 3.4 3.6 + - - +
308A ALA* 2.9 28.8 + - - +
312A LEU 4.8 0.7 - - - +
313A SER* 5.2 7.6 - - - -
314A LEU* 3.8 46.7 - - + +
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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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301A THR 2.9 16.6 + - - +
302A GLU* 3.6 11.8 - - + +
303A ILE 3.3 0.2 - - - -
304A LYS* 1.3 78.7 - - - +
306A VAL* 1.3 60.8 + - - +
308A ALA* 3.3 7.5 + - - +
309A SER* 2.9 26.9 + - - -
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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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260A LEU* 3.3 45.5 - - + +
261A GLU 5.1 3.6 - - - +
262A LEU* 3.8 24.2 - - + -
302A GLU* 2.9 23.0 + - - +
303A ILE* 3.3 15.9 - - + +
305A ASP* 1.3 77.0 - - - +
307A LEU* 1.3 63.9 + - + +
309A SER* 3.5 20.1 + - - +
310A ARG* 3.6 14.4 + - + +
603F ARG* 6.5 0.4 - - - -
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Residues in contact with LEU 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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260A LEU* 4.4 22.7 - - + -
278A ILE* 5.2 4.0 - - + -
281A LEU* 5.2 6.7 - - + +
282A VAL* 4.3 14.1 - - + -
303A ILE* 2.9 25.7 + - + +
304A LYS 3.7 4.5 - - - +
306A VAL* 1.3 79.2 - - + +
308A ALA* 1.3 53.8 + - - +
310A ARG* 3.2 5.3 + - + +
311A GLY 3.1 7.3 + - - -
312A LEU* 2.7 64.9 + - + +
313A SER* 3.7 25.8 - - - +
314A LEU* 3.8 24.2 - - + +
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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 LYS 2.9 18.1 + - - +
305A ASP* 3.3 8.9 + - - +
307A LEU* 1.3 73.8 - - - +
309A SER* 1.3 63.4 + - - +
311A GLY* 3.3 11.4 + - - +
312A LEU 3.3 10.7 + - - +
313A SER* 6.3 0.4 - - - -
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Residues in contact with SER 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ASP* 2.9 14.8 + - - -
306A VAL* 3.6 18.4 - - - +
307A LEU 3.2 0.6 - - - -
308A ALA* 1.3 77.9 - - - +
310A ARG* 1.3 70.6 + - - +
311A GLY 3.4 0.2 - - - -
603F ARG* 5.3 6.6 + - - -
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Residues in contact with ARG 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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252A ILE* 4.7 24.0 - - + +
255A ARG* 3.4 27.5 - - - +
259A ASP* 3.0 31.8 + - - +
260A LEU* 3.8 42.5 + - + +
278A ILE* 5.9 0.8 - - + +
306A VAL* 3.6 7.6 + - - +
307A LEU* 3.2 8.7 + - - +
309A SER* 1.3 88.6 + - - +
311A GLY* 1.3 59.4 + - - +
312A LEU* 3.4 13.4 + - + +
602F SER* 4.6 5.7 + - - -
603F ARG* 3.9 29.6 - - - +
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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