Contacts of the helix formed by residues 563 - 574 (chain B) in PDB entry 1F89
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 563 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307B LEU* 4.1 1.8 - - - -
310B LYS* 3.3 32.9 + - + +
518B TYR* 3.2 12.2 + - - +
561B GLU* 3.3 6.9 + - + +
562B LEU* 1.3 72.1 - - - +
564B PRO* 1.3 74.6 - - - +
565B GLU* 2.6 49.4 + - - +
566B VAL* 3.3 27.0 + - + +
567B ILE* 3.5 13.0 + - - +
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Residues in contact with PRO 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B SER* 4.2 4.8 + - - +
303B ALA* 4.2 24.2 - - - +
304B SER 4.3 1.1 - - - +
305B LYS 5.7 0.4 - - - +
307B LEU* 3.3 38.6 - - + +
308B SER 4.6 0.9 - - - +
309B GLN* 3.8 20.4 - - - +
310B LYS* 3.6 17.3 - - + -
562B LEU 3.8 1.1 - - - +
563B ASP* 1.3 89.1 - - - +
565B GLU* 1.3 56.8 + - + +
567B ILE* 3.6 7.1 + - + +
568B GLU* 3.1 33.9 + - - +
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Residues in contact with GLU 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B SER* 3.0 46.2 + - - +
310B LYS* 5.9 0.6 + - - -
563B ASP* 2.6 28.0 + - - +
564B PRO* 1.3 71.6 - - + +
566B VAL* 1.3 55.2 + - + +
568B GLU* 3.8 0.2 - - - +
569B SER* 2.7 37.7 + - - -
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Residues in contact with VAL 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B TYR* 3.4 22.4 - - - +
542B ASP* 4.3 9.2 - - + +
543B PRO* 3.8 14.4 - - + -
563B ASP* 3.3 23.6 + - + +
565B GLU* 1.3 75.5 - - + +
567B ILE* 1.3 67.5 + - - +
569B SER* 3.8 3.5 - - - -
570B PHE* 3.1 52.3 + - + -
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Residues in contact with ILE 567 (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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306B ILE* 4.5 15.3 - - + -
307B LEU* 4.1 14.4 - - + -
487B PHE* 4.1 25.8 - - + +
516B GLN 3.9 9.9 - - - +
517B VAL* 5.3 1.1 - - - -
518B TYR* 3.5 27.6 - - + -
543B PRO* 3.4 27.4 - - + +
563B ASP 3.5 8.2 + - - +
564B PRO* 3.9 7.0 - - + +
566B VAL* 1.3 76.1 - - - +
568B GLU* 1.3 62.9 + - - +
570B PHE* 3.8 1.6 - - - +
571B ARG* 2.8 57.0 + - + +
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Residues in contact with GLU 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B SER* 3.3 32.5 + - - +
305B LYS* 4.0 24.0 - - + +
306B ILE* 5.0 10.5 + - - +
564B PRO* 3.1 21.2 + - - +
565B GLU 3.8 2.9 - - - +
567B ILE* 1.3 83.8 - - - +
569B SER* 1.3 66.2 + - - +
571B ARG* 2.8 28.5 + - - +
572B GLN* 2.9 30.9 + - + +
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Residues in contact with SER 569 (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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302B SER* 5.2 1.3 + - - -
565B GLU* 2.7 23.7 + - - -
566B VAL* 3.8 4.9 - - - -
568B GLU* 1.3 73.8 - - - +
570B PHE* 1.3 75.8 + - - +
572B GLN* 3.6 10.4 - - - +
573B ALA* 3.4 21.1 + - - +
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Residues in contact with PHE 570 (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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516B GLN* 3.1 15.7 - - + +
542B ASP* 4.4 2.9 - - - -
543B PRO* 4.6 9.6 - - + +
544B ARG* 3.4 64.6 - - + +
566B VAL* 3.1 40.2 + - + +
567B ILE 3.8 2.0 - - - +
569B SER* 1.3 92.1 - - - +
571B ARG* 1.3 60.0 + - - +
572B GLN 3.2 1.8 - - - -
573B ALA* 3.8 11.8 - - + +
574B VAL* 3.2 19.1 + - - +
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Residues in contact with ARG 571 (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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306B ILE* 3.3 31.0 - - - +
482B ALA 4.6 7.9 + - - -
486B ALA 4.2 5.1 + - - -
515B ASN 3.8 12.2 + - - -
516B GLN* 3.5 42.3 + - + +
517B VAL* 3.9 12.5 - - - +
567B ILE* 2.8 35.8 + - + +
568B GLU* 2.8 17.6 + - - +
570B PHE* 1.3 77.3 - - - +
572B GLN* 1.3 67.3 + - + +
574B VAL 4.1 0.2 - - - -
575B PRO* 3.4 23.4 - - - +
576B LEU* 3.4 45.9 - - + +
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Residues in contact with GLN 572 (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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568B GLU* 2.9 35.9 + - + +
569B SER* 3.6 10.3 - - - +
571B ARG* 1.3 81.6 - - - +
573B ALA* 1.3 65.3 + - - +
575B PRO* 3.6 9.2 - - - +
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Residues in contact with ALA 573 (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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569B SER 3.4 13.9 + - - +
570B PHE* 3.8 14.4 - - + +
572B GLN* 1.3 82.7 - - - +
574B VAL* 1.3 67.4 + - + +
575B PRO* 3.2 7.1 - - - +
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Residues in contact with VAL 574 (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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170A TYR* 4.2 14.1 - - + +
173A ARG* 3.6 45.3 - - + +
174A PHE* 6.2 0.4 - - + -
203A HIS* 5.4 8.1 - - + -
516B GLN* 2.7 37.3 + - - +
570B PHE 3.2 7.0 + - - +
571B ARG 3.5 3.9 - - - +
573B ALA* 1.3 87.2 - - + +
575B PRO* 1.3 66.9 - - - +
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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