Contacts of the strand formed by residues 625 - 628 (chain A) in PDB entry 5YPO
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 HIS 625 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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534A ALA* 3.9 8.9 - - + +
535A ARG* 2.7 42.9 + - + +
537A ILE* 3.8 8.7 - - + +
558A LYS* 2.9 18.0 + - + -
559A PHE* 3.3 42.7 - + + +
560A GLY 2.8 25.7 + - - +
619A VAL* 4.1 0.2 - - - -
623A GLY 6.1 0.2 - - - -
624A LYS* 1.3 69.0 - - - +
626A CYS* 1.3 63.0 + - - +
627A ILE 3.3 1.0 + - - -
646A ILE* 4.8 2.0 - - + -
708A ILE* 4.2 5.6 - - + +
712A SER* 3.0 35.6 + - - -
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Residues in contact with CYS 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534A ALA 5.1 0.2 + - - -
536A PRO* 3.5 21.0 - - + +
537A ILE 2.7 32.0 + - - +
560A GLY 3.3 7.0 - - - -
562A CYS* 3.8 22.0 - - - -
616A VAL* 4.3 13.2 - - + +
619A VAL* 3.7 28.5 - - + -
620A ALA* 5.1 2.2 - - + +
624A LYS 3.4 5.0 + - - +
625A HIS* 1.3 69.9 - - - +
627A ILE* 1.3 61.2 + - - +
628A LEU* 3.4 26.4 + - - +
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Residues in contact with ILE 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537A ILE* 3.7 22.0 - - + +
548A ASN* 3.6 38.6 - - + +
551A LEU* 3.7 22.2 - - + -
552A LEU* 4.0 24.2 - - + -
559A PHE* 3.6 42.2 - - + -
560A GLY 2.6 17.8 + - - +
561A SER* 4.1 12.5 - - - -
562A CYS* 4.8 1.6 + - - -
626A CYS* 1.3 68.6 - - - +
628A LEU* 1.3 63.8 + - - +
629A ASP* 3.9 1.6 + - + -
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Residues in contact with LEU 628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536A PRO* 4.1 17.9 - - + -
537A ILE 2.8 18.4 + - - +
538A ILE* 3.8 25.3 - - + +
539A ILE 4.6 3.5 + - - +
544A LYS* 5.2 0.2 + - - -
548A ASN* 3.9 12.6 + - - +
562A CYS* 3.9 16.6 - - - -
599A ILE* 4.3 12.6 - - + -
611A THR* 4.6 1.1 - - + -
616A VAL* 3.9 11.7 - - + -
626A CYS* 3.6 31.2 - - - +
627A ILE* 1.3 73.6 - - - +
629A ASP* 1.3 59.8 + - - +
630A VAL* 3.5 15.4 + - + -
638A LEU* 3.7 32.5 - - + -
-2D ARG* 5.9 0.9 - - - +
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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