Contacts of the helix formed by residues 557 - 566 (chain B) in PDB entry 4YCV
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 557 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B ARG* 4.9 7.0 - - - +
257B ILE* 5.1 9.6 - - + -
258B ILE* 3.8 34.8 - - + -
261B LEU* 3.6 30.7 - - + -
325B ILE* 5.1 3.6 - - + -
343B THR* 3.2 32.7 + - + +
344B SER* 4.2 1.3 - - - -
345B CYS* 4.1 11.7 - - + +
364B PHE* 6.3 0.4 - - + -
555B LEU* 3.9 13.7 - - + +
556B GLY* 1.3 70.9 - - - -
558B ASP* 1.3 59.5 + - - +
560B ILE* 3.4 8.2 + - + +
561B THR* 2.7 45.9 + - - +
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Residues in contact with ASP 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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254B ARG* 2.7 43.7 + - - +
342B PHE* 3.3 15.8 - - - +
343B THR 3.0 32.4 + - - +
556B GLY* 4.5 0.7 - - - -
557B ILE* 1.3 77.4 + - - +
559B ARG* 1.3 57.5 + - - +
561B THR* 3.4 1.3 + - - -
562B MET* 2.9 25.3 + - - +
570B ILE* 3.5 27.1 - - + -
573B VAL* 3.3 12.6 - - + +
574B ILE* 3.8 10.4 - - - +
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Residues in contact with ARG 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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337B THR* 3.1 29.7 + - + +
338B HIS* 2.9 42.0 + - - -
499B LYS* 4.6 7.1 - - - +
500B GLU* 2.6 67.7 + - - +
501B VAL* 4.7 4.9 - - + -
556B GLY* 4.2 13.8 + - - +
557B ILE 3.3 0.4 - - - -
558B ASP* 1.3 74.2 - - + +
560B ILE* 1.3 66.7 + - - +
562B MET* 2.8 28.5 + - - +
563B PHE* 3.0 29.0 + - + -
570B ILE* 5.2 4.9 - - + -
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Residues in contact with ILE 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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257B ILE* 5.0 9.2 - - + -
364B PHE* 4.6 7.2 - - + -
365B PHE* 3.5 36.3 - - + -
368B LEU* 4.8 7.9 - - + -
496B ILE* 5.3 2.2 - - + -
501B VAL* 3.5 24.2 - - + -
555B LEU* 4.4 17.0 - - + -
556B GLY 3.1 20.6 - - - +
557B ILE* 3.4 10.2 + - + +
559B ARG* 1.3 75.1 - - - +
561B THR* 1.3 58.2 + - - +
563B PHE* 3.1 10.0 + - - +
564B LEU* 2.9 48.2 + - + +
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Residues in contact with THR 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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250B THR* 4.9 0.7 - - + +
254B ARG* 3.6 40.8 - - + +
257B ILE* 4.6 12.2 - - + +
557B ILE* 2.7 34.1 + - - +
558B ASP* 3.5 8.2 - - - -
559B ARG 3.1 0.2 - - - -
560B ILE* 1.3 73.2 - - - +
562B MET* 1.3 54.6 - - - +
564B LEU* 4.6 4.0 - - - +
565B THR* 2.2 51.1 + - + +
573B VAL* 3.7 20.9 - - + -
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Residues in contact with MET 562 (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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336B ASN 4.2 5.2 - - - +
337B THR* 4.6 14.4 - - + -
380B TYR* 3.8 7.8 - - - +
558B ASP 2.9 16.2 + - - +
559B ARG* 2.8 25.1 + - - +
561B THR* 1.3 75.9 - - - +
563B PHE* 1.3 60.7 + - + +
565B THR* 3.4 4.7 + - - -
566B ASN* 2.7 31.5 + - - -
567B LYS* 3.0 32.7 + - + +
568B ASN 3.7 20.0 - - - +
569B SER 3.7 14.4 - - - +
570B ILE* 3.5 26.5 - - - +
573B VAL* 3.8 13.0 - - + +
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Residues in contact with PHE 563 (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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337B THR* 5.7 2.9 - - + -
378B ILE* 3.6 15.7 - - + +
379B SER 5.5 0.9 - - - +
380B TYR* 3.7 51.5 - + + +
392B ILE* 5.0 1.8 - - + -
394B PHE* 5.7 0.4 - - + -
496B ILE* 3.3 47.6 - - + -
497B CYS* 3.6 21.8 - - + -
499B LYS* 3.7 16.4 - - + -
501B VAL* 4.1 13.0 - - + -
559B ARG* 3.0 41.9 + - + -
560B ILE* 3.7 9.0 - - - +
562B MET* 1.3 87.2 - - + +
564B LEU* 1.3 67.3 + - + +
566B ASN* 3.9 2.1 + - - +
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Residues in contact with LEU 564 (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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253B THR* 5.1 1.5 - - + +
257B ILE* 3.4 33.0 - - + -
365B PHE* 6.1 0.9 - - + -
368B LEU* 3.7 20.0 - - + -
369B VAL* 4.3 16.2 - - + -
372B LEU* 3.7 15.5 - - + -
373B PHE* 3.0 38.2 - - + -
378B ILE* 3.6 23.9 - - + +
394B PHE* 4.5 10.5 - - + -
560B ILE* 2.9 26.3 + - + +
561B THR* 4.3 1.8 - - - +
563B PHE* 1.3 82.3 - - + +
565B THR* 1.3 63.4 + - + +
566B ASN* 3.4 1.1 + - - +
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Residues in contact with THR 565 (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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249B HIS* 6.2 0.2 - - - +
250B THR* 3.8 29.0 + - + +
253B THR* 3.5 37.7 - - + +
561B THR* 2.2 39.6 + - + +
562B MET 3.4 2.6 + - - -
564B LEU* 1.3 76.1 - - - +
566B ASN* 1.3 72.1 + - - +
567B LYS* 3.4 14.0 + - - +
573B VAL* 3.4 14.0 - - - +
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Residues in contact with ASN 566 (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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379B SER* 3.3 26.6 + - - +
380B TYR* 3.8 11.4 - - - -
381B ASN* 3.0 39.9 + - - +
562B MET 2.7 8.0 + - - -
563B PHE 3.9 1.6 + - - +
564B LEU 3.4 4.3 - - - +
565B THR* 1.3 82.6 - - - +
567B LYS* 1.3 68.8 + - - +
568B ASN* 4.9 3.3 - - - +
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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