Contacts of the helix formed by residues 532 - 546 (chain 8) in PDB entry 6FF7
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 GLY 532 (chain 8).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5288 ILE 4.3 0.8 + - - -
5298 LYS 3.9 8.4 + - - -
5308 ARG 3.7 1.4 - - - -
5318 THR* 1.3 77.5 - - - +
5338 ILE* 1.3 62.3 + - - +
5348 GLN* 3.3 3.3 + - - -
5358 GLU* 4.0 8.4 + - - +
5368 MET* 3.7 21.3 + - - +
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Residues in contact with ILE 533 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5288 ILE 4.8 4.5 + - - +
5318 THR* 3.3 9.8 - - - +
5328 GLY* 1.3 78.1 - - - +
5348 GLN* 1.3 59.2 + - - +
5368 MET* 3.9 4.0 - - - +
5378 ARG* 2.9 31.4 + - - +
1130u PRO* 4.4 27.6 - - + -
1131u ALA* 5.2 4.9 - - + +
1134u ASN* 5.8 3.1 - - + -
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Residues in contact with GLN 534 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5288 ILE 5.5 1.4 + - - +
5298 LYS* 5.6 12.5 - - + +
5328 GLY* 3.3 1.2 - - - -
5338 ILE* 1.3 77.0 - - - +
5358 GLU* 1.3 61.3 + - - +
5378 ARG* 3.4 4.7 + - - +
5388 GLU* 2.9 31.1 + - - +
1134u ASN* 5.6 7.4 - - + -
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Residues in contact with GLU 535 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5328 GLY* 4.0 9.4 + - - +
5338 ILE 3.5 0.2 - - - -
5348 GLN* 1.3 78.9 - - - +
5368 MET* 1.3 58.3 + - - +
5388 GLU* 3.5 5.3 + - - +
5398 ALA* 2.9 30.2 + - - +
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Residues in contact with MET 536 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5328 GLY 3.7 16.5 + - - +
5338 ILE* 3.6 4.7 + - - +
5348 GLN 3.3 0.4 - - - -
5358 GLU* 1.3 78.5 - - - +
5378 ARG* 1.3 57.6 + - - +
5398 ALA* 3.4 6.3 + - - +
5408 LEU* 2.9 30.5 + - - +
5638 LYS 5.8 0.9 - - - +
5648 ILE* 4.9 20.2 - - + -
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Residues in contact with ARG 537 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5338 ILE 2.9 21.7 + - - +
5348 GLN* 3.8 4.7 - - - +
5358 GLU 3.3 0.2 - - - -
5368 MET* 1.3 77.7 - - - +
5388 GLU* 1.3 57.1 + - - +
5408 LEU* 3.4 4.4 + - - +
5418 GLN* 2.9 29.3 + - - +
1131u ALA* 6.2 4.0 - - + -
1134u ASN* 5.0 13.5 - - + -
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Residues in contact with GLU 538 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5348 GLN 2.9 18.0 + - - +
5358 GLU* 4.0 5.2 - - - +
5378 ARG* 1.3 76.1 - - - +
5398 ALA* 1.3 56.6 + - - +
5418 GLN* 3.4 6.3 + - - +
5428 GLU* 2.9 30.5 + - - +
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Residues in contact with ALA 539 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5358 GLU 2.9 19.0 + - - +
5368 MET* 3.7 7.9 - - - +
5388 GLU* 1.3 76.6 - - - +
5408 LEU* 1.3 57.1 + - - +
5428 GLU* 3.3 6.2 + - - +
5438 LYS* 2.9 28.4 + - - +
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Residues in contact with LEU 540 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5368 MET 2.9 18.2 + - - +
5378 ARG* 4.0 5.2 - - - +
5398 ALA* 1.3 74.3 - - - +
5418 GLN* 1.3 60.4 + - - +
5438 LYS* 3.4 8.1 + - - +
5448 GLU* 2.9 29.3 + - - +
5638 LYS* 6.0 5.6 - - + -
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Residues in contact with GLN 541 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5378 ARG 2.9 18.4 + - - +
5388 GLU* 3.8 7.0 - - - +
5408 LEU* 1.3 76.2 - - - +
5428 GLU* 1.3 57.8 + - - +
5448 GLU* 3.2 6.6 + - - +
5458 GLU* 2.9 31.2 + - - +
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Residues in contact with GLU 542 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5388 GLU 2.9 18.3 + - - +
5398 ALA* 3.8 6.5 - - - +
5418 GLN* 1.3 76.5 - - - +
5438 LYS* 1.3 61.2 + - - +
5458 GLU* 3.9 5.7 + - - +
5468 GLN* 3.8 17.2 + - - +
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Residues in contact with LYS 543 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5398 ALA 2.9 17.2 + - - +
5408 LEU* 3.7 8.5 - - - +
5418 GLN 3.2 0.2 - - - -
5428 GLU* 1.3 77.5 - - - +
5448 GLU* 1.3 60.4 + - - +
5468 GLN* 3.6 12.7 + - - +
5478 LYS* 3.8 9.7 + - - +
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Residues in contact with GLU 544 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5408 LEU 2.9 18.2 + - - +
5418 GLN* 3.2 7.6 + - - +
5438 LYS* 1.3 75.5 - - - +
5458 GLU* 1.3 63.9 + - - +
5468 GLN 3.2 0.7 - - - -
5478 LYS* 3.3 21.8 + - - +
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Residues in contact with GLU 545 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5418 GLN 2.9 16.3 + - - +
5428 GLU* 3.9 6.7 + - - +
5438 LYS 3.4 0.2 - - - -
5448 GLU* 1.3 76.5 - - - +
5468 GLN* 1.3 60.3 + - - +
5478 LYS 3.3 4.4 + - - +
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Residues in contact with GLN 546 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5428 GLU 3.8 10.9 + - - +
5438 LYS* 3.6 10.0 + - - +
5448 GLU 3.2 0.8 - - - -
5458 GLU* 1.3 77.6 - - - +
5478 LYS* 1.3 62.7 + - - +
5488 THR* 3.8 1.2 + - - -
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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