Contacts of the helix formed by residues 309 - 319 (chain E) in PDB entry 2V90
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 GLY 309 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265E GLU* 3.6 9.0 - - - -
273E PRO* 4.2 7.2 - - - +
275E GLN* 3.4 1.1 - - - -
307E GLY 4.1 1.0 + - - -
308E LEU* 1.3 79.2 - - - +
310E HIS* 1.3 57.3 + - - -
311E GLU 3.6 2.0 - - - -
312E GLU* 3.7 7.2 + - - +
313E THR* 2.7 36.9 + - - -
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Residues in contact with HIS 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C ASP 4.4 0.4 - - - -
335C ARG* 3.5 46.8 + - + +
337C THR* 3.0 27.4 + - - -
263E LEU* 3.2 41.4 - - + +
265E GLU* 3.1 17.4 + - - +
275E GLN* 2.9 23.7 + - - +
309E GLY* 1.3 69.1 - - - +
311E GLU* 1.3 82.3 + - + +
313E THR* 3.1 3.8 + - - -
314E VAL* 2.8 42.7 + - + +
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Residues in contact with GLU 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LYS* 4.9 5.7 + - - -
334C ASP 3.6 14.4 - - - +
335C ARG* 5.5 4.4 - - - +
337C THR* 5.1 2.7 + - - -
310E HIS* 1.3 100.5 - - + +
312E GLU* 1.3 57.5 + - - +
314E VAL* 3.4 12.0 + - - +
315E SER* 2.8 32.6 + - - -
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Residues in contact with GLU 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308E LEU* 3.2 38.3 - - + +
309E GLY* 3.7 7.5 + - - +
310E HIS 3.3 0.6 - - - -
311E GLU* 1.3 79.4 - - - +
313E THR* 1.3 59.0 + - - +
315E SER* 2.9 20.5 + - - -
316E ARG* 3.1 43.2 + - - +
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Residues in contact with THR 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263E LEU* 4.0 11.4 - - + -
275E GLN* 3.7 19.9 - - + +
297E LEU* 3.8 29.2 - - + -
300E VAL* 4.7 0.9 - - + -
305E VAL* 4.2 15.5 - - + +
308E LEU* 3.6 21.8 - - - +
309E GLY 2.7 23.5 + - - -
310E HIS 3.1 3.8 + - - -
312E GLU* 1.3 74.4 - - - +
314E VAL* 1.3 64.2 + - - +
316E ARG* 3.3 6.0 + - - +
317E ILE* 3.1 22.7 + - + +
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Residues in contact with VAL 314 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C THR* 4.0 24.2 - - + +
339C VAL* 4.5 8.3 - - + -
263E LEU* 4.2 9.9 - - + -
310E HIS* 2.8 51.7 + - + +
311E GLU* 3.8 12.6 - - - +
313E THR* 1.3 73.8 - - - +
315E SER* 1.3 57.3 + - - +
317E ILE* 3.3 8.9 + - - +
318E GLN* 2.9 51.8 + - + +
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Residues in contact with SER 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311E GLU 2.8 19.2 + - - -
312E GLU* 2.9 23.9 + - - -
314E VAL* 1.3 76.1 - - - +
316E ARG* 1.3 52.4 + - - +
318E GLN* 3.6 12.0 - - - +
319E GLY* 2.6 34.3 + - - -
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Residues in contact with ARG 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300E VAL* 3.6 18.2 + - + +
303E GLU* 3.6 40.4 + - - +
304E SER 4.7 6.2 + - - -
305E VAL* 4.0 11.6 - - - +
308E LEU* 3.6 25.6 - - - +
312E GLU* 3.1 41.4 + - - +
313E THR* 3.5 8.1 - - - +
314E VAL 3.2 0.2 - - - -
315E SER* 1.3 79.9 - - - +
317E ILE* 1.3 61.2 + - - +
319E GLY* 3.6 5.4 + - - +
320E GLN* 3.5 22.0 + - - +
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Residues in contact with ILE 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339C VAL* 4.6 17.5 - - + -
259E PHE* 4.0 30.9 - - + -
261E PHE* 4.2 17.5 - - + -
263E LEU* 4.0 16.6 - - + -
297E LEU* 4.0 21.8 - - + -
300E VAL* 3.8 23.1 - - + -
313E THR 3.1 15.0 + - - +
314E VAL* 3.6 9.0 - - - +
316E ARG* 1.3 76.5 - - - +
318E GLN* 1.3 63.3 + - + +
320E GLN* 3.3 18.0 + - - +
321E GLY 4.0 5.9 + - - +
324E VAL* 4.5 7.9 - - + +
326E LEU* 4.2 6.7 - - + -
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Residues in contact with GLN 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337C THR* 5.5 2.6 - - - +
339C VAL* 5.1 9.3 - - + +
254E LYS* 5.5 6.9 + - - +
259E PHE* 6.3 0.2 - - - -
314E VAL* 2.9 39.7 + - + +
315E SER* 3.7 10.7 - - - +
317E ILE* 1.3 80.2 - - + +
319E GLY* 1.3 60.7 + - - +
320E GLN 3.1 1.8 + - - -
321E GLY* 3.2 13.8 + - - +
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Residues in contact with GLY 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315E SER 2.6 21.8 + - - -
316E ARG* 3.9 3.8 - - - -
317E ILE 3.3 0.6 - - - -
318E GLN* 1.3 71.9 - - - +
320E GLN* 1.3 65.7 + - - +
321E GLY 3.5 0.4 + - - -
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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