Contacts of the helix formed by residues 300 - 313 (chain A) in PDB entry 3CYV
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 PRO 300 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A TYR 4.6 0.4 - - - +
299A ALA* 1.3 89.6 - - + +
301A PRO* 1.3 78.5 - - + +
302A ALA* 3.2 5.6 - - + +
303A ARG* 2.7 27.1 + - + +
304A ILE 3.2 6.4 + - - -
337A HIS* 4.5 1.8 - - + -
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Residues in contact with PRO 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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299A ALA 3.7 0.4 - - - -
300A PRO* 1.3 82.0 - - + +
302A ALA* 1.3 66.1 + - - +
304A ILE* 2.9 21.9 + - + +
305A GLU* 3.0 20.2 + - - +
337A HIS* 3.4 25.4 - - + +
340A VAL* 3.8 30.3 - - + -
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Residues in contact with ALA 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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300A PRO* 3.0 6.9 + - + +
301A PRO* 1.3 77.4 - - - +
303A ARG* 1.3 61.4 + - - +
305A GLU* 3.5 13.8 + - - +
306A GLU* 3.4 22.1 + - - +
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Residues in contact with ARG 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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296A MET* 3.6 18.5 - - - +
299A ALA* 3.7 22.7 - - + -
300A PRO* 2.7 25.4 + - + +
302A ALA* 1.3 71.9 - - - +
304A ILE* 1.3 65.3 + - - +
306A GLU* 2.9 67.3 + - - +
307A GLU* 2.8 33.0 + - - +
310A THR* 5.5 1.0 + - - -
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Residues in contact with ILE 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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292A MET* 4.7 6.7 - - + -
296A MET* 3.4 22.0 - - + +
297A LEU* 3.8 24.9 - - + +
299A ALA* 3.5 19.3 - - + +
300A PRO 3.8 5.8 - - - +
301A PRO* 2.9 17.0 + - + +
303A ARG* 1.3 75.0 - - - +
305A GLU* 1.3 57.6 + - + +
307A GLU* 2.7 31.6 + - - +
308A VAL* 3.1 9.3 + - + +
337A HIS* 4.0 21.8 - - + +
340A VAL* 5.1 2.7 - - + -
341A PHE* 4.0 39.3 - - + +
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Residues in contact with GLU 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 PRO* 3.0 16.9 + - - +
302A ALA* 3.6 14.5 - - - +
304A ILE* 1.3 76.3 - - - +
306A GLU* 1.3 56.8 + - - +
308A VAL* 3.1 6.1 + - - +
309A ALA* 3.0 26.2 + - - +
340A VAL* 3.9 22.3 - - + +
344A ALA* 3.8 23.1 - - + +
347A ARG* 3.4 29.3 + - - -
348A LEU* 3.8 12.5 - - + +
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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 ALA 3.4 7.5 + - - +
303A ARG* 2.9 59.0 + - - +
304A ILE 3.1 1.0 - - - -
305A GLU* 1.3 78.7 - - - +
307A GLU* 1.3 56.7 + - - +
308A VAL 3.3 0.2 - - - -
309A ALA* 3.8 10.1 - - + +
310A THR* 2.9 31.3 + - - +
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Residues in contact with GLU 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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292A MET* 3.8 17.4 - - + +
293A ASP* 5.6 2.4 + - - +
296A MET* 3.6 25.7 - - + +
303A ARG* 2.8 39.6 + - - +
304A ILE 2.7 16.3 + - - +
306A GLU* 1.3 71.7 - - - +
308A VAL* 1.3 59.2 + - - +
309A ALA 3.3 0.2 - - - -
310A THR* 4.1 10.5 + - - +
311A ILE* 2.9 56.3 + - + +
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Residues in contact with VAL 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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292A MET* 5.2 1.1 - - - -
304A ILE* 3.1 12.0 + - + +
305A GLU* 3.3 7.6 - - - +
307A GLU* 1.3 78.6 - - - +
309A ALA* 1.3 52.3 + - - +
311A ILE 3.6 0.3 - - - -
312A LEU* 2.7 49.8 + - + +
323A PHE* 3.7 10.1 - - + -
341A PHE* 3.9 29.6 - - + -
344A ALA* 3.5 48.0 - - + +
345A VAL* 3.5 21.3 - - + +
348A LEU* 4.6 1.1 - - + -
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Residues in contact with ALA 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 GLU 3.0 15.3 + - - +
306A GLU* 3.8 10.1 - - + +
308A VAL* 1.3 75.0 - - - +
310A THR* 1.3 65.7 + - - +
312A LEU* 3.4 10.7 + - - +
313A ALA* 3.1 21.8 + - - +
348A LEU* 4.2 15.7 - - + +
352A TYR* 4.4 3.8 + - - -
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Residues in contact with THR 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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275A ILE* 5.7 3.9 - - + +
303A ARG* 5.5 0.5 + - - -
306A GLU* 2.9 24.8 + - - +
307A GLU* 3.7 17.1 + - - +
308A VAL 3.3 0.2 - - - -
309A ALA* 1.3 75.0 - - - +
311A ILE* 1.3 58.2 + - + +
313A ALA* 2.6 39.1 + - - +
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Residues in contact with ILE 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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275A ILE* 3.8 31.8 - - + +
291A ASN* 4.1 18.6 - - + +
292A MET* 3.5 44.4 - - + +
307A GLU* 2.9 40.8 + - + +
310A THR* 1.3 76.2 - - + +
312A LEU* 1.3 56.3 + - - +
313A ALA 2.6 15.2 - - - +
315A PHE* 4.0 11.3 + - - +
321A HIS* 4.8 5.9 - - + +
323A PHE* 3.5 29.4 - - + -
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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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21A THR* 3.9 12.1 - - - +
308A VAL* 2.7 46.1 + - + +
309A ALA* 3.7 5.8 - - - +
310A THR 3.2 0.2 - - - -
311A ILE* 1.3 73.4 - - - +
313A ALA* 1.3 52.5 + - - +
315A PHE* 5.0 1.1 - - - -
316A GLY* 2.5 39.7 + - - +
321A HIS* 4.4 8.5 - - - +
323A PHE* 4.2 17.7 - - + -
345A VAL* 4.1 2.0 - - + +
348A LEU* 3.4 32.1 - - + +
349A SER* 3.4 30.1 - - - +
352A TYR* 3.6 17.6 - - + -
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Residues in contact with ALA 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ILE* 5.1 2.6 - - - +
309A ALA 3.1 9.3 + - - +
310A THR* 2.6 24.7 + - - +
311A ILE* 2.6 13.7 - - - +
312A LEU* 1.3 73.6 - - - +
314A GLY* 1.3 59.9 + - - +
315A PHE 2.8 5.8 - - - +
316A GLY* 4.2 1.3 - - - +
317A HIS* 6.3 0.7 - - - -
352A TYR* 3.5 21.7 + - + +
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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