Contacts of the helix formed by residues 300 - 311 (chain f) in PDB entry 5T0J
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 CYS 300 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270f ILE* 5.5 2.7 - - - -
297f ARG* 3.4 37.1 - - + +
298f ASN 3.5 3.3 + - - +
299f GLU* 1.3 78.6 - - - +
301f ASP* 1.3 62.6 + - - +
302f PRO* 4.0 10.1 - - + -
303f ALA* 3.6 26.2 - - - -
304f LEU* 3.6 14.0 + - - +
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Residues in contact with ASP 301 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299f GLU 3.3 3.5 + - - +
300f CYS* 1.3 69.4 - - - +
302f PRO* 1.3 67.4 - - - +
304f LEU* 2.8 12.0 + - + +
305f ALA* 2.6 38.4 + - + +
330f TYR* 3.6 23.8 - - + +
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Residues in contact with PRO 302 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275f TYR* 6.0 2.2 - - - +
300f CYS* 3.6 13.2 - - + -
301f ASP* 1.3 101.1 - - - +
303f ALA* 1.3 62.3 + - - +
305f ALA* 3.2 9.4 + - + +
306f LEU* 3.1 22.2 + - - +
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Residues in contact with ALA 303 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270f ILE* 5.8 4.3 - - + -
274f LEU* 6.3 1.6 - - + -
275f TYR* 6.1 0.7 - - - +
293f ASN* 2.8 37.9 + - - +
297f ARG* 4.8 0.9 - - + -
300f CYS* 3.6 20.6 - - - +
301f ASP 3.3 0.6 - - - -
302f PRO* 1.3 80.1 - - - +
304f LEU* 1.3 59.8 + - - +
306f LEU* 3.7 8.5 + - - +
307f LEU* 3.4 17.0 + - - +
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Residues in contact with LEU 304 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293f ASN* 3.6 7.1 - - - +
297f ARG 5.2 0.9 - - - +
300f CYS 3.6 13.0 + - - +
301f ASP* 2.8 12.3 + - + +
303f ALA* 1.3 78.3 - - - +
305f ALA* 1.3 67.7 + - + +
307f LEU* 3.3 8.1 + - + +
308f SER* 3.2 24.2 + - - +
325f GLY 3.9 2.5 - - - +
326f LEU* 3.3 56.5 - - + +
329f ALA* 3.7 22.0 - - + -
330f TYR* 3.8 27.6 - - + +
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Residues in contact with ALA 305 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301f ASP* 2.6 19.2 + - + +
302f PRO* 3.2 9.8 + - + +
304f LEU* 1.3 77.0 - - + +
306f LEU* 1.3 60.3 + - - +
308f SER* 3.2 8.0 + - - -
309f ASP* 3.0 32.1 + - - +
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Residues in contact with LEU 306 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278f GLU* 3.8 29.2 - - + +
302f PRO 3.1 15.2 + - - +
303f ALA* 4.0 8.5 - - - +
304f LEU 3.3 0.2 - - - -
305f ALA* 1.3 72.3 - - - +
307f LEU* 1.3 74.5 + - + +
309f ASP* 4.0 4.7 - - - +
310f TYR* 3.1 32.5 + - + +
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Residues in contact with LEU 307 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289f CYS 5.1 6.5 - - - +
290f GLY* 4.5 8.1 - - - +
293f ASN* 3.3 39.3 - - + +
294f SER 4.8 0.9 - - - +
303f ALA 3.4 10.0 + - - +
304f LEU* 3.3 12.3 + - + +
305f ALA 3.3 0.6 - - - -
306f LEU* 1.3 84.7 - - + +
308f SER* 1.3 65.0 + - - +
310f TYR* 3.1 8.2 + - + +
311f VAL* 3.0 27.1 + - + +
318f MET* 5.6 4.3 - - + -
322f SER* 3.2 45.8 - - - +
325f GLY* 4.9 7.6 - - - -
326f LEU* 6.1 0.4 - - - -
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Residues in contact with SER 308 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304f LEU* 3.2 12.0 + - - +
305f ALA* 3.2 13.7 + - - -
307f LEU* 1.3 79.4 - - - +
309f ASP* 1.3 63.4 + - - +
311f VAL* 3.4 14.6 - - - +
312f LEU* 3.2 28.3 - - - +
322f SER* 4.9 0.7 - - - -
323f ILE* 6.2 0.4 - - - -
326f LEU* 5.2 18.4 - - - -
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Residues in contact with ASP 309 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305f ALA 3.0 19.5 + - - +
306f LEU* 4.0 4.9 - - - +
308f SER* 1.3 80.3 + - - +
310f TYR* 1.3 61.4 + - - +
312f LEU* 3.7 21.4 + - - +
313f HIS 4.8 0.3 + - - -
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Residues in contact with TYR 310 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282f LYS* 3.2 38.5 - - + +
286f LEU* 3.3 18.4 - - - +
306f LEU* 3.1 24.0 + - + +
307f LEU* 3.1 7.6 + - + +
309f ASP* 1.3 75.4 - - - +
311f VAL* 1.3 73.7 + - + +
312f LEU 3.1 5.9 + - - -
313f HIS* 3.2 25.4 + + + +
315f SER* 5.7 4.4 - - - -
318f MET* 3.6 36.8 - - + +
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Residues in contact with VAL 311 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307f LEU 3.0 13.2 + - - +
308f SER* 3.4 18.2 - - - +
310f TYR* 1.3 90.0 - - + +
312f LEU* 1.3 63.1 + - + +
313f HIS 3.0 6.5 - - - -
314f ASN* 3.1 13.0 + - - +
318f MET* 4.7 2.0 - - + +
319f ARG* 3.3 44.3 + - + +
322f SER* 3.3 33.7 - - - +
323f ILE* 4.3 16.6 - - + -
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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