Contacts of the helix formed by residues 310 - 323 (chain R) in PDB entry 6CMO
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 ASN 310 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351A CYS 5.3 1.5 + - - +
352A GLY* 3.5 28.9 - - - +
73R ASN* 5.3 2.2 + - - +
307R ILE 3.7 3.4 + - - +
308R MET 3.3 5.1 - - - +
309R MET* 1.3 83.3 - - + +
311R LYS* 1.3 74.5 + - - +
312R GLN* 3.2 38.1 + - - +
313R PHE* 3.3 39.1 + - + +
314R ARG* 3.2 19.9 + - - +
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Residues in contact with LYS 311 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A LYS* 4.0 11.7 + - - +
352A GLY* 3.6 25.7 + - - -
354A PHE* 2.7 42.3 + - - -
309R MET 3.5 5.9 + - - +
310R ASN* 1.3 75.7 + - - +
312R GLN* 1.3 77.2 + - + +
314R ARG* 3.6 28.6 - - - +
315R ASN* 2.9 45.1 + - - +
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Residues in contact with GLN 312 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A LYS 4.6 13.1 + - - -
350A ASP* 5.7 2.6 + - - +
352A GLY* 6.0 0.9 - - - -
68R LEU* 3.6 28.9 - - + +
73R ASN* 5.7 1.2 + - - -
310R ASN* 3.2 27.7 + - - +
311R LYS* 1.3 88.6 - - + +
313R PHE* 1.3 57.5 + - - +
315R ASN* 3.4 6.3 + - - +
316R CYS* 2.9 35.7 + - - -
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Residues in contact with PHE 313 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58R THR* 6.5 0.9 - - + -
61R VAL* 3.8 26.3 - - + +
68R LEU* 3.7 22.7 - - + -
73R ASN* 3.4 41.1 - - + -
76R LEU* 5.1 7.2 - - + -
307R ILE* 4.6 29.6 - - + +
310R ASN* 3.3 45.3 + - + +
312R GLN* 1.3 75.5 - - - +
314R ARG* 1.3 60.8 + - - +
316R CYS* 3.8 4.7 - - - +
317R MET* 2.9 32.6 + - - +
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Residues in contact with ARG 314 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308R MET* 4.9 13.4 - - - +
310R ASN 3.2 14.3 + - - +
311R LYS* 3.6 26.1 - - - +
312R GLN 3.2 0.4 - - - -
313R PHE* 1.3 77.4 - - - +
315R ASN* 1.3 72.3 + - - +
317R MET* 3.3 11.7 - - + +
318R LEU* 2.9 58.2 + - + +
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Residues in contact with ASN 315 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311R LYS* 2.9 35.4 + - - +
312R GLN* 3.8 7.3 - - - +
314R ARG* 1.3 92.1 + - - +
316R CYS* 1.3 57.2 + - - +
318R LEU* 4.1 6.7 - - - +
319R THR* 2.6 39.7 + - - +
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Residues in contact with CYS 316 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61R VAL* 4.7 8.1 - - + -
65R HIS* 4.6 27.8 + - + -
68R LEU* 3.7 29.6 - - + -
312R GLN* 2.9 24.6 + - - +
313R PHE* 3.9 6.7 - - - +
314R ARG 3.3 0.2 - - - -
315R ASN* 1.3 79.7 - - - +
317R MET* 1.3 51.3 + - - +
319R THR* 3.9 4.1 - - - -
320R THR* 2.4 39.1 + - - -
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Residues in contact with MET 317 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54R ILE* 6.3 5.2 - - + -
57R LEU* 4.9 24.8 - - + +
61R VAL* 5.0 8.9 - - + +
313R PHE 2.9 21.4 + - - +
314R ARG* 3.3 15.0 - - - +
316R CYS* 1.3 74.8 - - - +
318R LEU* 1.3 93.2 + - - +
320R THR* 3.6 6.2 - - - -
321R ILE* 2.9 35.8 + - + +
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Residues in contact with LEU 318 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314R ARG* 2.9 49.8 + - + +
315R ASN* 4.1 7.6 - - - +
317R MET* 1.3 90.1 - - - +
319R THR* 1.3 59.8 + - - +
321R ILE* 3.7 11.5 - - + +
322R CYS* 2.9 34.7 + - - +
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Residues in contact with THR 319 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65R HIS* 6.2 4.7 - - + -
315R ASN* 2.6 26.6 + - - +
316R CYS* 4.0 5.8 - - - -
318R LEU* 1.3 75.9 - - - +
320R THR* 1.3 61.2 + - - +
322R CYS* 4.5 3.6 - - - -
323R CYS* 3.2 39.7 + - - +
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Residues in contact with THR 320 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57R LEU* 4.5 18.2 - - + -
60R TYR* 3.6 33.4 - - + -
61R VAL* 4.8 3.8 - - + +
65R HIS* 3.9 17.2 + - - -
316R CYS 2.4 26.4 + - - -
317R MET* 3.6 8.2 - - - -
318R LEU 3.2 0.2 - - - -
319R THR* 1.3 79.9 - - - +
321R ILE* 1.3 61.8 + - + +
323R CYS* 3.6 15.6 - - - +
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Residues in contact with ILE 321 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57R LEU* 5.2 21.3 - - + -
317R MET* 2.9 25.3 + - + +
318R LEU* 3.7 18.8 - - + +
320R THR* 1.3 77.0 - - + +
322R CYS* 1.3 67.9 + - + +
323R CYS 3.4 3.3 + - - +
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Residues in contact with CYS 322 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318R LEU* 2.9 21.2 + - + +
319R THR* 4.3 3.8 - - - +
321R ILE* 1.3 81.8 - - + +
323R CYS* 1.3 64.6 + - - +
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Residues in contact with CYS 323 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319R THR* 3.2 35.6 + - - +
320R THR* 3.6 12.7 - - - +
321R ILE 3.4 3.8 - - - +
322R CYS* 1.3 84.6 - - - +
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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