Contacts of the strand formed by residues 554 - 561 (chain B) in PDB entry 5ZF6
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 ILE 554 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B ALA* 3.3 13.3 - - - +
235B ASN* 3.2 16.5 - - - -
236B ILE* 2.9 12.7 + - + +
238B GLN* 4.2 34.8 - - + +
241B PHE* 4.2 35.4 - - + -
547B ILE* 3.7 34.8 - - + -
548B ALA 3.5 10.1 - - - +
553B GLY* 1.3 74.1 - - - -
555B THR* 1.3 65.2 + - - +
556B ALA 4.0 7.9 - - - +
575B ILE* 4.9 1.1 - - + -
579B SER* 5.9 0.4 - - - -
582B LYS* 3.3 26.5 - - - +
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Residues in contact with THR 555 (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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232B SER* 3.3 4.2 - - - -
233B ALA* 2.8 33.9 + - - +
235B ASN* 4.0 18.2 - - + +
241B PHE* 6.3 0.2 - - - -
456B LYS 3.7 6.2 - - - +
457B ALA* 3.0 28.9 + - - +
460B PRO* 3.7 23.6 - - + -
461B VAL* 5.1 2.7 - - + -
506B VAL* 4.9 0.7 - - + -
548B ALA 3.0 5.4 + - - -
549B GLY* 3.2 24.2 + - - -
550B THR* 4.4 5.6 - - + +
554B ILE* 1.3 78.6 - - - +
556B ALA* 1.3 65.8 + - - +
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Residues in contact with ALA 556 (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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231B ALA* 3.3 12.8 - - - +
241B PHE* 6.3 0.2 - - - -
453B LEU* 4.2 14.1 - - + -
456B LYS* 4.0 11.0 - - + -
457B ALA* 3.8 31.6 - - + +
485B MET* 5.7 0.2 - - + -
546B LYS 4.7 0.2 - - - -
547B ILE* 3.3 8.5 - - - +
548B ALA* 2.9 26.8 + - + -
554B ILE* 3.9 2.8 - - - +
555B THR* 1.3 82.4 + - - +
557B LEU* 1.3 61.3 + - - +
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Residues in contact with LEU 557 (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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229B LEU* 4.0 31.6 - - + +
230B GLU* 3.4 5.2 - - - +
231B ALA* 2.7 41.4 + - + +
241B PHE* 3.5 39.3 - - + -
245B ILE* 4.6 1.6 - - + -
453B LEU* 4.6 2.6 - - - +
545B PHE* 3.6 41.7 - - + -
546B LYS 3.3 13.0 - - - +
547B ILE* 3.9 9.6 - - + -
556B ALA* 1.3 77.4 - - - +
558B GLN* 1.3 76.3 + - - +
559B ALA 4.1 0.7 - - - +
575B ILE* 5.2 0.2 - - + -
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Residues in contact with GLN 558 (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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136B ARG* 3.6 7.5 - - - +
229B LEU 3.4 4.3 - - - -
230B GLU* 2.9 37.2 + - - +
449B GLY 5.1 4.9 + - - -
453B LEU* 4.0 34.5 - - + +
544B ASP 3.1 5.7 - - - +
546B LYS* 2.7 56.6 + - + +
557B LEU* 1.3 74.4 - - - +
559B ALA* 1.3 58.7 + - - +
560B ASP* 3.4 18.4 - - - +
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Residues in contact with ALA 559 (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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136B ARG* 3.7 12.8 + - - -
228B MET* 4.3 4.3 - - - +
229B LEU* 2.7 40.4 + - + -
544B ASP 3.7 3.8 - - - -
545B PHE* 3.6 31.9 - - + -
557B LEU* 4.1 1.0 - - + +
558B GLN* 1.3 70.3 - - - +
560B ASP* 1.3 65.5 + - - +
561B ILE* 3.5 20.1 + - + -
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Residues in contact with ASP 560 (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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136B ARG* 2.7 45.4 + - - +
543B MET* 3.2 4.5 - - - -
544B ASP* 2.9 41.2 + - + +
546B LYS* 2.8 30.4 + - - -
558B GLN* 3.4 12.2 - - - +
559B ALA* 1.3 70.0 - - - +
561B ILE* 1.3 62.2 + - - +
562B LYS* 3.4 13.4 + - - +
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Residues in contact with ILE 561 (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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136B ARG 5.1 1.0 - - - +
140B PRO* 3.5 20.4 - - - +
226B ILE* 3.6 41.5 - - + +
227B VAL 3.5 21.6 + - - +
228B MET 4.4 0.4 - - - +
229B LEU* 5.0 1.3 - - + -
542B ASP 3.8 5.8 - - - +
543B MET* 4.0 9.6 - - + -
559B ALA* 3.5 24.8 + - + +
560B ASP* 1.3 73.1 - - - +
562B LYS* 1.3 62.5 + - - +
563B LEU 3.7 20.6 - - - +
565B GLY 4.6 0.4 - - - +
566B ILE* 3.8 39.5 - - + -
571B VAL* 5.1 0.2 - - + -
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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