Contacts of the helix formed by residues 569 - 573 (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 SER 569 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B TYR* 4.9 3.3 + - - -
335B ASP 5.2 0.2 + - - -
336B ASN* 3.4 27.1 + - - -
562B MET* 3.7 12.7 - - - +
567B LYS* 3.3 2.0 - - - +
568B ASN* 1.3 81.7 - - - +
570B ILE* 1.3 66.4 + - - +
571B LYS* 3.3 19.2 + - - +
572B ASP* 3.2 32.1 + - - +
573B VAL 4.2 0.2 + - - -
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Residues in contact with ILE 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B ILE* 6.2 0.2 - - + -
335B ASP 4.0 6.7 - - - +
336B ASN 2.7 27.1 + - - +
337B THR 4.4 9.9 - - - +
338B HIS 4.1 1.8 - - - +
339B ASN* 3.9 34.5 - - + +
342B PHE* 4.9 7.2 - - + -
558B ASP* 3.5 35.9 - - + -
559B ARG* 5.0 4.3 - - + +
562B MET* 3.5 18.0 - - - -
569B SER* 1.3 68.8 + - - +
571B LYS* 1.3 66.7 + - + +
572B ASP 3.0 6.5 + - - -
573B VAL* 3.2 13.3 + - + +
574B ILE* 3.2 24.9 + - + +
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Residues in contact with LYS 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B TYR* 3.7 27.0 - - + -
237B ARG* 3.4 10.9 + - - -
339B ASN* 5.8 0.4 - - - +
569B SER* 3.1 13.1 + - - +
570B ILE* 1.3 85.5 - - + +
572B ASP* 1.3 59.8 + - - +
573B VAL 3.5 0.2 - - - -
574B ILE* 3.3 17.9 - - - +
577B PRO* 3.9 22.5 - - + +
579B MET* 6.3 0.4 - - + -
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Residues in contact with ASP 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ARG* 3.8 15.6 + - - -
234B TYR* 2.4 35.7 + - - -
237B ARG* 4.3 3.7 + - - +
250B THR* 4.3 6.1 - - - +
251B PHE* 3.1 23.0 - - - -
567B LYS* 3.7 34.9 - - + +
568B ASN 4.3 2.1 + - - -
569B SER* 3.4 25.4 + - - +
570B ILE 3.0 1.0 - - - -
571B LYS* 1.3 79.3 - - - +
573B VAL* 1.3 59.0 + - - +
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Residues in contact with VAL 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B THR* 4.2 6.7 - - + -
251B PHE* 3.2 13.3 - - - -
254B ARG* 2.7 41.6 + - - +
558B ASP* 3.3 26.5 - - - +
561B THR* 3.7 19.5 - - + -
562B MET* 3.8 19.3 - - + +
565B THR* 3.4 26.0 - - - +
567B LYS* 4.1 8.7 - - + -
570B ILE* 3.3 15.3 - - + +
572B ASP* 1.3 76.3 - - - +
574B ILE* 1.3 56.0 + - - +
575B LEU 4.0 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