Contacts of the strand formed by residues 563 - 568 (chain B) in PDB entry 1LRX
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 PRO 563 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520B ARG* 3.9 4.2 - - - +
534B THR* 3.0 27.4 + - + -
535B ASP 3.0 32.6 + - - +
536B TRP* 3.6 7.6 - - + -
540B ALA* 3.7 9.0 - - + -
541B LYS 4.2 0.2 - - - +
559B ASN* 4.9 0.2 - - + -
561B GLN 3.1 8.9 - - - +
562B TRP* 1.3 79.5 - - - +
564B ASN* 1.3 64.6 + - - +
565B GLY 3.5 2.5 - - - -
577B TRP* 3.2 45.1 - - + -
578B VAL 3.4 9.9 - - - +
579B ASP* 4.5 2.0 - - - +
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Residues in contact with ASN 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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520B ARG* 3.4 47.8 - - + +
521B ALA* 4.4 2.6 - - - +
536B TRP* 3.7 9.9 - - - +
562B TRP* 3.1 27.1 + - - +
563B PRO* 1.3 80.6 - - - +
565B GLY* 1.3 57.2 + - - +
578B VAL 3.1 7.3 + - - -
580B SER* 3.6 21.3 + - - -
609B PHE* 3.1 47.5 - - + +
610B SER* 3.1 6.1 + - - -
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Residues in contact with GLY 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B ALA* 3.6 12.6 - - - +
534B THR* 4.1 1.9 + - - -
563B PRO 3.5 3.4 + - - -
564B ASN* 1.3 80.6 - - - +
566B ILE* 1.3 61.1 + - - -
576B TYR 3.5 1.0 - - - +
577B TRP* 3.1 5.2 - - - +
578B VAL* 2.9 42.0 + - - +
610B SER* 3.8 10.1 - - - -
611B LEU* 3.9 4.8 - - - +
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Residues in contact with ILE 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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521B ALA* 3.4 35.3 - - - +
522B ILE 4.0 2.9 - - - +
523B VAL* 3.3 16.7 + - + +
532B TYR* 3.7 40.8 - - + +
533B TRP 3.9 0.9 - - - +
534B THR* 3.4 13.9 - - + +
542B ILE* 3.6 27.1 - - + -
565B GLY* 1.3 75.0 - - - +
567B THR* 1.3 71.1 + - - +
575B LEU* 3.7 18.8 - - + -
576B TYR 3.1 12.1 - - - +
577B TRP* 4.5 0.4 - - + -
611B LEU 3.9 2.7 + - - -
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Residues in contact with THR 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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523B VAL* 3.7 18.8 - - + +
566B ILE* 1.3 77.3 + - - +
568B LEU* 1.3 68.1 + - - +
575B LEU* 4.6 0.4 - - - -
576B TYR* 3.0 26.6 + - - +
611B LEU 2.7 27.1 + - - -
612B ALA* 4.0 5.3 - - + +
613B VAL* 3.3 42.9 - - - +
653B VAL* 5.8 3.8 - - - +
656B HIS* 6.4 2.2 - - + -
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Residues in contact with LEU 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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523B VAL* 3.7 16.8 - - + +
524B VAL 3.7 8.3 - - - +
525B ASP* 3.6 33.7 - - - +
526B PRO* 5.0 3.6 - - + -
532B TYR* 3.3 44.9 - - + +
567B THR* 1.3 80.4 - - - +
569B ASP* 1.3 69.0 + - - +
572B SER* 4.8 0.2 - - - -
573B GLY 4.8 9.2 - - - +
574B ARG 3.5 14.6 - - - +
575B LEU* 3.6 23.6 - - + +
613B VAL* 3.0 26.6 - - - +
614B PHE* 5.6 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