Contacts of the helix formed by residues 475 - 487 (chain B) in PDB entry 6R7X
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 ASP 475 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B LEU* 5.6 1.5 - - - +
473B ASP 3.7 3.4 + - - -
474B ILE* 1.3 75.6 - - - +
476B ALA* 1.3 64.9 + - - +
477B THR* 3.3 5.4 + - - +
478B LEU* 3.7 12.9 + - + +
479B TYR* 3.7 7.1 + - - +
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Residues in contact with ALA 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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467B VAL* 4.6 13.5 - - + -
470B LEU* 6.2 2.0 - - + -
474B ILE* 3.0 17.6 + - + +
475B ASP* 1.3 71.0 - - - +
477B THR* 1.3 58.8 + - - +
480B GLU* 2.6 52.8 + - + +
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Residues in contact with THR 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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176B SER* 5.6 5.4 - - - +
475B ASP* 3.3 3.2 - - - +
476B ALA* 1.3 77.7 + - - +
478B LEU* 1.3 56.5 + - - +
480B GLU* 4.3 8.8 - - - +
481B GLN* 3.4 27.6 + - - +
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Residues in contact with LEU 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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17B PRO* 3.8 22.7 - - + -
53B ARG* 3.7 29.2 - - - +
55B LEU* 4.6 9.0 - - + +
71B LEU* 3.8 13.5 - - + -
173B LEU* 4.1 20.2 - - + -
475B ASP* 3.7 10.0 + - + +
476B ALA 3.2 0.2 - - - -
477B THR* 1.3 78.9 - - - +
479B TYR* 1.3 60.6 + - - +
480B GLU 3.3 1.1 - - - -
481B GLN* 3.3 7.8 + - - +
482B VAL* 2.9 38.0 + - + +
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Residues in contact with TYR 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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55B LEU* 3.6 30.5 - - + +
56B LEU* 3.8 25.4 - - + -
59B TYR* 5.9 0.2 - + - -
63B THR* 3.7 26.4 - - + +
66B ASN* 3.3 26.3 + - + +
466B LYS* 3.8 10.3 + - - -
467B VAL* 4.6 17.0 - - + -
470B LEU* 4.8 9.0 - - + -
474B ILE* 3.8 39.9 - - + -
475B ASP 3.7 3.7 + - - +
476B ALA* 5.6 0.2 - - - -
478B LEU* 1.3 78.6 - - - +
480B GLU* 1.3 61.6 + - + +
482B VAL* 3.4 1.4 + - - +
483B ILE* 2.9 58.3 + - + +
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Residues in contact with GLU 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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463B VAL* 4.7 5.9 - - + +
464B LYS* 3.2 43.8 + - + +
467B VAL* 4.0 33.7 - - + +
468B GLN* 6.1 0.7 - - - +
476B ALA* 2.6 28.8 + - - +
477B THR* 4.3 10.0 - - - +
479B TYR* 1.3 80.7 - - - +
481B GLN* 1.3 61.6 + - - +
483B ILE* 3.5 2.3 + - - +
484B LEU* 2.9 28.7 + - + +
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Residues in contact with GLN 481 (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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173B LEU* 4.1 20.3 - - + +
174B HIS* 2.5 34.2 + - - +
176B SER* 5.0 13.3 + - - +
477B THR* 3.4 24.0 + - - +
478B LEU* 3.3 11.1 + - - +
479B TYR 3.3 0.2 - - - -
480B GLU* 1.3 82.7 + - - +
482B VAL* 1.3 56.2 + - - +
484B LEU* 3.4 6.6 + - - +
485B GLU* 2.9 51.6 + - + +
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Residues in contact with VAL 482 (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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20B VAL* 4.0 20.6 - - + -
55B LEU* 3.8 36.8 - - + -
69B LEU* 3.9 21.5 - - + -
71B LEU* 4.2 4.5 - - + -
171B PHE* 4.5 2.4 - - + -
173B LEU* 4.0 29.2 - - + -
478B LEU* 2.9 23.0 + - + +
479B TYR 3.9 3.4 - - - +
481B GLN* 1.3 76.3 - - + +
483B ILE* 1.3 58.2 + - - +
485B GLU* 3.7 1.6 - - - +
486B LYS* 2.9 29.3 + - - +
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Residues in contact with ILE 483 (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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55B LEU* 5.1 0.2 - - + -
66B ASN* 3.3 36.6 - - + +
69B LEU* 3.7 22.2 - - + -
463B VAL* 4.1 20.1 - - + +
466B LYS* 5.2 8.3 - - + +
467B VAL* 5.0 6.3 - - + -
479B TYR* 2.9 44.0 + - + +
480B GLU* 3.9 5.2 - - - +
482B VAL* 1.3 75.7 - - - +
484B LEU* 1.3 62.5 + - - +
486B LYS* 3.5 19.0 + - - +
487B GLU* 3.9 21.8 + - - +
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Residues in contact with LEU 484 (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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456B GLN* 4.0 15.0 + - - +
459B HIS* 4.7 3.3 - - + -
460B GLY* 3.7 30.3 - - - +
463B VAL* 4.2 22.8 - - + +
464B LYS* 4.5 20.0 - - - +
480B GLU* 2.9 19.0 + - + +
481B GLN* 3.8 7.0 - - - +
483B ILE* 1.3 79.0 - - - +
485B GLU* 1.3 62.4 + - + +
486B LYS 3.4 0.5 + - - -
487B GLU* 3.6 10.4 + - - +
488B MET* 3.7 27.3 + - + +
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Residues in contact with GLU 485 (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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171B PHE* 3.9 16.0 - - + -
172B PRO 3.9 11.1 - - - +
173B LEU* 4.1 5.7 - - - +
174B HIS* 3.3 43.6 + - - +
481B GLN* 2.9 48.5 + - + +
482B VAL* 3.7 1.6 - - - +
484B LEU* 1.3 77.7 - - + +
486B LYS* 1.3 63.1 + - - +
487B GLU 3.3 0.4 - - - -
488B MET* 3.8 23.9 + - + -
542B LYS* 3.3 28.0 - - + +
543B ARG 4.7 2.4 + - - -
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Residues in contact with LYS 486 (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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22B GLU* 3.4 37.6 + - - +
66B ASN* 4.3 15.5 - - - +
68B ASN* 5.6 0.7 - - - +
69B LEU* 3.9 20.6 - - + -
169B GLN* 3.3 17.2 + - - +
171B PHE* 4.1 8.3 - - + -
482B VAL 2.9 17.7 + - - +
483B ILE* 3.7 25.1 - - - +
484B LEU 3.2 0.4 - - - -
485B GLU* 1.3 79.9 - - - +
487B GLU* 1.3 95.1 + - + +
488B MET 3.6 1.4 + - - +
542B LYS* 3.8 6.6 + - - -
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Residues in contact with GLU 487 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ASN* 5.7 0.2 + - - -
456B GLN* 4.6 3.8 - - - +
459B HIS* 2.5 50.0 + - + +
463B VAL* 3.9 12.1 - - - +
483B ILE* 3.9 15.1 + - - +
484B LEU 3.6 5.7 + - - +
485B GLU 3.3 0.4 - - - -
486B LYS* 1.3 106.7 + - + +
488B MET* 1.3 64.7 + - - +
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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