Contacts of the strand formed by residues 598 - 604 (chain B) 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 PHE 598 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565B HIS* 3.8 22.2 - + + -
589B MET* 3.9 21.8 - - + -
592B ASP* 4.0 23.1 + - + -
593B ILE* 3.6 33.1 + - + +
596B HIS* 3.2 8.7 - - - +
597B LYS* 1.3 84.2 - - + +
599B ILE* 1.3 62.9 + - - +
600B GLU 3.2 11.2 - - - +
601B ALA* 4.2 8.7 - - + -
610B GLY* 3.6 22.0 - - - -
611B THR 3.2 23.3 - - - +
612B SER* 3.4 21.5 - - - -
613B VAL* 4.2 2.8 - - - +
637B ARG* 3.9 11.3 - - - +
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Residues in contact with ILE 599 (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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598B PHE* 1.3 72.7 - - - +
600B GLU* 1.3 60.0 + - + +
611B THR* 3.0 33.5 + - + +
612B SER 4.7 0.4 - - - +
613B VAL* 3.8 28.0 - - + +
616B VAL* 4.0 5.8 - - + -
628B LEU* 4.0 25.1 - - + -
630B VAL* 4.2 9.0 - - + -
634B ALA* 3.5 18.5 - - + -
637B ARG* 2.4 47.6 + - + -
638B LEU* 3.7 33.0 - - + +
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Residues in contact with GLU 600 (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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598B PHE* 3.2 5.3 - - - +
599B ILE* 1.3 92.2 - - + +
601B ALA* 1.3 68.0 + - - +
610B GLY* 3.1 2.7 - - - -
611B THR* 3.0 24.2 + - - +
630B VAL* 3.3 17.3 - - + +
631B SER* 2.7 41.2 + - - +
634B ALA* 4.3 3.3 + - + +
637B ARG* 3.6 10.5 + - - +
2C TYR* 2.6 38.5 + - - +
6C THR* 3.8 23.0 + - + +
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Residues in contact with ALA 601 (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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593B ILE* 3.8 38.6 - - + -
598B PHE* 4.2 7.2 - - + -
600B GLU* 1.3 81.4 - - - +
602B GLY* 1.3 59.5 + - - +
609B TYR 3.1 13.0 - - - +
610B GLY* 4.0 2.0 - - - -
637B ARG* 5.0 5.4 + - - +
5C ALA 5.0 0.2 - - - +
6C THR* 4.4 8.0 - - - +
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Residues in contact with GLY 602 (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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593B ILE* 5.5 1.0 - - - +
601B ALA* 1.3 76.8 - - - +
603B GLN* 1.3 60.3 + - - -
608B LEU* 3.4 8.2 - - - +
609B TYR* 2.9 31.1 + - - +
5C ALA* 3.6 21.8 - - - +
6C THR* 4.3 1.8 - - - +
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Residues in contact with GLN 603 (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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586B ARG* 2.7 35.9 + - - +
602B GLY* 1.3 75.6 - - - -
604B TYR* 1.3 63.6 + - - +
606B SER* 3.5 21.1 - - - +
607B HIS 3.3 11.4 - - - +
608B LEU* 4.0 8.9 - - + +
4C LYS 4.5 1.6 - - - +
5C ALA* 3.5 16.5 + - - +
8C PRO* 6.0 0.9 - - - +
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Residues in contact with TYR 604 (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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681A GLU* 2.6 42.5 + - - +
682A GLN* 5.5 2.7 - - + +
603B GLN* 1.3 75.4 - - - +
605B ASN* 1.3 98.1 + - + +
606B SER 3.1 1.8 - - - -
607B HIS* 2.8 22.2 + - - +
609B TYR* 3.8 12.9 + - + -
1C SEP 3.8 37.2 - - - +
4C LYS* 3.6 34.2 + - + -
5C ALA* 3.5 21.7 - - + +
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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