Contacts of the strand formed by residues 564 - 570 (chain B) in PDB entry 3P1X
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 GLN 564 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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560B GLU* 3.3 3.7 - - - +
561B VAL 2.8 36.9 + - - +
562B ASP* 3.1 20.4 - - - +
563B GLY* 1.3 79.9 - - - +
565B LYS* 1.3 63.4 + - - +
566B PHE* 3.4 19.6 - - + -
587B LYS* 4.6 13.3 - - - +
588B LEU* 3.4 31.4 - - - +
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Residues in contact with LYS 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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558B GLU* 3.9 37.1 + - + +
559B VAL 3.6 1.6 - - - -
560B GLU* 2.9 46.2 - - + -
563B GLY 5.8 0.9 - - - +
564B GLN* 1.3 74.2 - - - +
566B PHE* 1.3 71.9 + - - +
567B GLN* 5.5 1.3 - - + -
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Residues in contact with PHE 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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558B GLU* 3.2 2.9 - - - -
559B VAL* 2.8 40.9 + - + +
561B VAL* 3.9 6.7 - - + -
564B GLN* 3.4 39.5 - - + -
565B LYS* 1.3 79.3 - - - +
567B GLN* 1.3 61.8 + - - +
580B ALA* 3.7 20.5 - - - +
583B ALA* 3.9 9.2 - - + -
584B ALA* 3.6 28.3 - - + +
587B LYS* 3.7 29.4 - - + -
588B LEU* 3.6 37.9 - - + -
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Residues in contact with GLN 567 (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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544B ILE* 3.9 30.3 - - - +
556B VAL* 4.1 14.4 - - + +
557B MSE 3.0 9.9 - - - +
558B GLU* 3.3 26.8 + - + +
565B LYS* 5.5 1.1 - - + -
566B PHE* 1.3 79.9 - - - +
568B GLY* 1.3 59.9 + - - +
579B TYR* 3.9 4.3 - - - +
580B ALA* 3.6 10.1 - - - -
583B ALA* 4.0 9.5 - - - +
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Residues in contact with GLY 568 (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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556B VAL* 3.4 4.4 - - - -
557B MSE 2.8 32.2 + - - -
567B GLN* 1.3 76.4 - - - +
569B ALA* 1.3 60.7 + - - -
576B ALA* 3.3 23.3 - - - +
579B TYR* 3.5 7.4 - - - -
580B ALA* 3.4 10.7 - - - +
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Residues in contact with ALA 569 (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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555B PHE 3.1 12.6 - - - +
556B VAL* 4.0 14.8 - - + -
568B GLY* 1.3 75.0 - - - +
570B GLY* 1.3 58.8 + - - +
576B ALA* 3.9 5.8 - - - -
579B TYR* 3.5 26.9 - - - +
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Residues in contact with GLY 570 (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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553B LYS 4.6 0.4 - - - -
554B ARG* 3.7 3.0 - - - +
555B PHE* 2.9 32.6 + - - +
569B ALA* 1.3 77.4 - - - +
571B SER* 1.3 60.6 + - - -
572B ASN 3.1 7.9 + - - -
575B VAL* 3.6 16.4 - - - -
576B ALA* 4.0 1.8 - - - +
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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