Contacts of the helix formed by residues 471 - 480 (chain B) in PDB entry 5M4G
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 THR 471 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B LEU* 4.2 14.6 - - + -
314B ARG* 4.3 17.0 - - - +
470B ARG* 1.3 79.1 - - - +
472B VAL* 1.3 64.9 + - - +
473B GLU* 3.7 20.5 + - - +
474B GLU* 2.9 42.1 + - - +
475B ILE* 2.9 22.7 + - - +
488B PRO* 5.5 0.3 - - - +
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Residues in contact with VAL 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B PHE* 3.6 45.5 - - + -
303B LYS* 4.2 22.0 - - + +
306B TYR* 4.2 8.2 - - + -
307B GLU* 3.7 32.0 + - + +
310B LEU* 5.3 0.8 - - - +
470B ARG 3.8 0.6 + - - -
471B THR* 1.3 72.7 - - - +
473B GLU* 1.3 71.1 + - + +
475B ILE* 3.3 1.2 + - - +
476B GLU* 2.9 46.9 + - - +
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Residues in contact with GLU 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B LYS* 5.0 3.3 + - - -
307B GLU* 4.7 5.7 - - - +
471B THR* 3.7 15.8 + - - +
472B VAL* 1.3 96.5 + - + +
474B GLU* 1.3 56.1 + - - +
476B GLU* 3.4 6.5 + - - +
477B ALA* 2.9 31.4 + - - +
488B PRO* 3.6 28.4 - - + +
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Residues in contact with GLU 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ARG* 5.1 2.5 + - - -
468B VAL 4.8 0.7 - - - +
469B PRO* 3.5 19.2 - - + +
470B ARG* 2.9 23.0 + - - +
471B THR* 2.9 40.1 + - - +
473B GLU* 1.3 75.8 - - - +
475B ILE* 1.3 57.2 + - - +
477B ALA* 3.4 2.8 + - - +
478B CYS* 2.9 28.4 + - - +
488B PRO* 4.0 25.0 - - + +
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Residues in contact with ILE 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B MET* 4.5 8.3 - - - -
291B SER 3.7 12.8 - - - +
292B PHE* 3.6 25.1 - - + -
293B PRO* 4.4 0.2 - - + -
298B PHE* 3.8 19.7 - - + -
306B TYR* 3.2 36.8 - - + +
469B PRO* 3.7 25.8 - - + +
470B ARG 3.6 7.4 - - - +
471B THR 2.9 13.7 + - - +
472B VAL 3.7 3.4 - - - +
474B GLU* 1.3 72.7 - - - +
476B GLU* 1.3 67.8 + - - +
478B CYS* 3.2 4.0 + - - +
479B MET* 2.9 34.0 + - + +
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Residues in contact with GLU 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B GLY 3.4 24.3 - - - +
297B LYS* 3.5 22.7 + - + +
298B PHE* 2.9 45.1 + - + +
472B VAL* 2.9 29.9 + - - +
473B GLU* 3.9 5.6 - - - +
475B ILE* 1.3 75.9 - - + +
477B ALA* 1.3 62.3 + - - +
479B MET* 3.4 3.3 + - - +
480B ALA* 3.0 24.6 + - - +
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Residues in contact with ALA 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473B GLU 2.9 18.4 + - - +
474B GLU 3.6 4.5 - - - +
476B GLU* 1.3 76.2 - - - +
478B CYS* 1.3 66.1 + - - +
480B ALA* 3.2 8.7 + - - -
482B CYS* 3.1 47.0 + - + -
486B PHE* 4.2 8.3 - - + -
488B PRO* 3.9 18.6 - - + -
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Residues in contact with CYS 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B ARG* 3.8 38.6 - - - +
210B MET* 3.8 17.3 - - + -
211B LYS* 3.4 25.3 - - - +
469B PRO* 3.7 24.0 - - + -
474B GLU 2.9 17.8 + - - +
475B ILE* 3.6 4.9 - - - +
477B ALA* 1.3 76.2 - - - +
479B MET* 1.3 58.8 + - - +
481B GLY* 2.9 16.3 + - - -
482B CYS* 4.2 8.0 + - - +
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Residues in contact with MET 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B MET* 3.5 35.3 - - + +
211B LYS 4.3 11.8 - - - +
213B VAL* 4.6 8.5 - - + +
292B PHE* 3.7 33.7 - - + -
293B PRO* 3.2 30.1 - - - +
294B ALA 3.8 13.2 - - - +
295B ASN 4.8 0.2 - - - -
296B GLY* 3.7 24.0 - - - -
475B ILE* 2.9 26.6 + - + +
476B GLU 4.0 3.8 - - - +
478B CYS* 1.3 77.1 - - - +
480B ALA* 1.3 57.1 + - - +
481B GLY* 3.1 4.1 + - - -
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Residues in contact with ALA 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476B GLU 3.0 17.7 + - - +
477B ALA* 3.6 7.9 - - - +
478B CYS 3.2 0.4 - - - -
479B MET* 1.3 75.0 - - - +
481B GLY* 1.3 59.7 + - - +
482B CYS* 3.4 8.9 + - - -
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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