Contacts of the helix formed by residues 449 - 462 (chain B) in PDB entry 6R7Z
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 449 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445B GLN* 3.8 5.3 + - - -
448B GLU* 1.3 83.7 - - - +
450B PHE* 1.3 57.0 + - - +
452B PRO* 3.5 6.4 - - - +
453B TYR* 2.7 38.3 + - - +
532B SER* 4.2 28.3 - - - -
536B LYS* 6.0 4.3 - - - -
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Residues in contact with PHE 450 (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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445B GLN* 3.2 20.9 + - + +
446B ILE* 3.6 8.0 + - + -
449B SER* 1.3 77.1 - - - +
451B LEU* 1.3 63.7 + - - +
453B TYR* 3.3 6.7 + - - +
454B TRP* 3.2 21.5 + - - +
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Residues in contact with LEU 451 (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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446B ILE* 3.1 21.7 + - + +
447B MET* 5.1 2.0 - - - -
450B PHE* 1.3 77.6 - - - +
452B PRO* 1.3 63.1 - - + +
454B TRP* 3.5 8.2 + - - +
455B LEU* 3.2 21.8 + - - +
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Residues in contact with PRO 452 (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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446B ILE 3.7 6.1 - - - +
447B MET 3.9 9.6 - - - +
448B GLU 3.3 20.6 - - - +
449B SER* 3.5 15.7 - - - +
451B LEU* 1.3 89.4 - - + +
453B TYR* 1.3 53.3 + - - +
455B LEU* 3.6 7.0 - - + +
456B GLN* 2.7 35.4 + - - +
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Residues in contact with TYR 453 (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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449B SER* 2.7 24.5 + - - +
450B PHE* 3.3 7.4 + - - +
452B PRO* 1.3 70.2 - - - +
454B TRP* 1.3 61.3 + - - +
456B GLN* 3.6 7.7 - - - +
457B ARG* 2.7 28.8 + - - +
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Residues in contact with TRP 454 (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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450B PHE 3.2 13.2 + - - +
451B LEU* 3.5 9.2 + - - +
453B TYR* 1.3 76.1 - - - +
455B LEU* 1.3 61.0 + - + +
457B ARG* 3.1 11.9 + - + +
458B LYS* 2.7 48.9 + - + +
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Residues in contact with LEU 455 (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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451B LEU 3.2 15.2 + - - +
452B PRO* 3.7 7.9 - - + +
454B TRP* 1.3 85.1 - - + +
456B GLN* 1.3 57.6 + - - +
458B LYS* 3.6 8.0 - - - +
459B HIS* 2.7 30.5 + - - +
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Residues in contact with GLN 456 (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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452B PRO 2.7 21.8 + - - +
453B TYR* 3.6 9.0 - - - +
454B TRP 3.2 0.2 - - - -
455B LEU* 1.3 70.9 - - - +
457B ARG* 1.3 56.3 + - - +
459B HIS* 3.7 6.2 - - - +
460B GLY* 2.7 30.7 + - - -
539B ARG 5.2 9.6 - - - +
540B VAL* 5.2 12.6 - - + -
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Residues in contact with ARG 457 (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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453B TYR 2.7 20.8 + - - +
454B TRP* 3.4 15.3 - - + +
456B GLN* 1.3 73.2 - - - +
458B LYS* 1.3 57.8 + - - +
460B GLY* 4.9 0.9 - - - -
461B VAL* 2.8 31.4 + - - +
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Residues in contact with LYS 458 (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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454B TRP* 2.7 40.7 + - + +
455B LEU* 3.6 9.9 - - - +
457B ARG* 1.3 73.2 - - - +
459B HIS* 1.3 57.2 + - - +
461B VAL* 3.4 5.4 + - - +
462B ARG* 3.0 29.3 + - - +
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Residues in contact with HIS 459 (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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455B LEU 2.7 21.0 + - - +
456B GLN* 3.9 6.7 - - - +
458B LYS* 1.3 74.6 - - - +
460B GLY* 1.3 57.8 + - - +
462B ARG* 3.1 27.6 + - - +
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Residues in contact with GLY 460 (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 2.7 21.9 + - - -
457B ARG* 3.8 1.8 - - - -
459B HIS* 1.3 72.2 - - - +
461B VAL* 1.3 64.7 + - - +
462B ARG 3.3 6.6 - - - +
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Residues in contact with VAL 461 (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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457B ARG 2.8 21.7 + - - +
458B LYS* 3.8 5.8 - - - +
460B GLY* 1.3 73.0 - - - +
462B ARG* 1.3 61.8 + - - +
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Residues in contact with ARG 462 (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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458B LYS 3.0 18.2 + - - +
459B HIS* 3.1 21.6 - - - +
460B GLY 3.3 6.8 - - - +
461B VAL* 1.3 81.9 - - - +
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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