Contacts of the helix formed by residues 301 - 313 (chain A) in PDB entry 5V8V
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 SER 301 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A GLY* 1.3 74.7 - - - +
302A THR* 1.3 63.9 + - - +
303A SER* 3.4 8.4 + - - -
304A SER* 3.0 30.8 + - - -
305A ILE* 2.9 21.8 + - - +
369A MET 4.2 4.4 + - - -
370A ASP* 3.6 14.4 - - - +
377A PRO* 5.1 15.3 - - - -
378A THR 4.6 8.2 + - - -
379A TRP* 5.3 2.2 - - - +
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Residues in contact with THR 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A GLY 3.7 1.0 + - - -
301A SER* 1.3 71.0 - - - +
303A SER* 1.3 63.9 + - - +
305A ILE* 4.1 0.2 - - - +
306A GLU* 2.9 28.9 + - + +
321A TYR* 5.8 2.9 - - - +
368A ALA* 3.7 22.9 - - + +
370A ASP* 2.3 38.1 + - - -
306B GLU* 5.8 4.7 - - - +
316B LYS* 4.3 18.0 - - + +
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Residues in contact with SER 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A SER* 3.2 8.2 + - - -
302A THR* 1.3 80.8 - - - +
304A SER* 1.3 63.5 + - - +
306A GLU* 3.4 5.3 + - - +
307A LYS* 3.2 31.1 + - - +
370A ASP* 5.0 0.2 + - - -
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Residues in contact with SER 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A LEU* 3.7 26.2 - - - +
283A CYS* 5.7 1.0 + - - +
301A SER* 3.0 23.3 + - - -
303A SER* 1.3 75.6 + - - +
305A ILE* 1.3 59.4 + - - +
307A LYS* 3.1 6.1 + - - +
308A LEU* 2.8 28.9 + - - +
379A TRP* 3.7 34.2 + - - -
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Residues in contact with ILE 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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300A GLY 3.5 30.5 - - - +
301A SER 2.9 19.8 + - - +
304A SER* 1.3 75.7 - - - +
306A GLU* 1.3 58.6 + - - +
308A LEU* 3.6 8.0 - - + +
309A MET* 2.8 40.1 + - + +
321A TYR* 3.6 32.5 - - + +
366A ILE* 3.8 24.2 - - + -
367A HIS 3.7 6.7 - - - +
368A ALA* 3.8 14.6 - - + +
379A TRP* 3.8 19.7 - - + -
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Residues in contact with GLU 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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302A THR* 2.9 23.9 + - + +
303A SER* 3.7 5.6 - - - +
305A ILE* 1.3 76.2 - - - +
307A LYS* 1.3 62.4 + - + +
309A MET* 4.0 2.8 - - - +
310A GLU* 3.1 26.1 + - - +
321A TYR* 4.6 11.1 + - - +
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Residues in contact with LYS 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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281A LEU* 5.5 3.3 - - + +
282A LEU* 4.1 26.6 - - + +
303A SER* 3.2 19.9 + - - +
304A SER 3.1 8.5 + - - +
306A GLU* 1.3 77.4 - - + +
308A LEU* 1.3 65.2 + - - +
310A GLU* 3.5 11.3 + - - +
311A ALA* 3.2 22.7 + - - +
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Residues in contact with LEU 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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274A VAL* 5.2 6.3 - - + -
276A VAL* 3.5 29.2 - - + -
281A LEU* 6.1 0.2 - - - -
282A LEU* 4.2 11.2 - - + +
304A SER 2.8 20.0 + - - +
305A ILE* 3.6 27.4 - - + +
307A LYS* 1.3 73.7 - - - +
309A MET* 1.3 62.9 + - + +
311A ALA* 3.4 5.7 + - - +
312A LEU* 3.1 33.3 + - + +
334A ILE* 4.0 32.5 - - + -
336A PHE* 6.5 0.2 - - + -
366A ILE* 3.9 17.7 - - + -
379A TRP* 4.6 12.3 - - + -
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Residues in contact with MET 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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305A ILE* 2.8 23.3 + - + +
306A GLU* 4.1 3.4 - - - +
308A LEU* 1.3 79.0 - - + +
310A GLU* 1.3 61.5 + - - +
312A LEU* 3.2 8.5 + - + +
313A GLY 2.8 23.7 + - - -
314A ALA* 2.9 25.5 + - + +
321A TYR* 3.3 54.5 - - + -
364A LEU* 3.6 28.3 - - + -
366A ILE* 3.5 45.1 - - + +
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Residues in contact with GLU 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 GLU 3.1 18.7 + - - +
307A LYS* 3.9 11.7 - - - +
308A LEU 3.4 0.2 - - - -
309A MET* 1.3 76.4 - - - +
311A ALA* 1.3 62.6 + - - +
313A GLY* 3.0 15.1 + - - +
314A ALA 5.3 1.6 - - - -
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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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276A VAL* 4.2 27.8 - - + +
281A LEU* 5.4 6.3 - - + -
307A LYS 3.2 12.5 + - - +
308A LEU 3.6 8.3 - - - +
310A GLU* 1.3 78.3 - - - +
312A LEU* 1.3 63.8 + - - +
313A GLY 3.5 0.5 + - - -
332A PRO* 5.1 3.5 - - - +
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Residues in contact with LEU 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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276A VAL* 3.8 11.9 - - + -
308A LEU* 3.1 28.2 + - + +
309A MET* 3.2 11.4 + - + +
311A ALA* 1.3 75.9 - - - +
313A GLY* 1.3 62.2 + - - +
314A ALA* 3.5 7.0 + - + +
323A VAL* 4.6 1.4 - - - +
331A LEU* 3.4 27.5 - - + +
332A PRO* 3.6 37.0 - - + +
334A ILE* 3.8 25.1 - - + -
350A TYR* 3.7 23.6 - - + +
364A LEU* 4.2 15.0 - - + -
366A ILE* 5.4 0.4 - - + -
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Residues in contact with GLY 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 MET 2.8 5.1 + - - -
310A GLU* 3.0 13.2 + - - -
311A ALA 3.2 0.6 + - - -
312A LEU* 1.3 78.9 - - - +
314A ALA* 1.3 60.9 + - - +
315A LYS* 4.0 8.6 + - - +
323A VAL* 4.3 7.0 - - - +
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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