Contacts of the strand formed by residues 650 - 660 (chain A) in PDB entry 1R5O
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 THR 650 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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568A GLU* 2.9 28.7 + - - +
646A ARG* 3.8 6.3 - - - +
647A ASP* 2.9 33.7 + - + +
648A GLN 5.2 1.6 - - - +
649A GLY* 1.3 79.1 - - - +
651A THR* 1.3 66.1 + - - +
652A VAL* 3.2 5.8 - - + +
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Residues in contact with THR 651 (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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223A ASN* 5.3 8.8 + - - +
567A LEU* 3.6 22.2 - - + +
568A GLU* 3.5 25.6 - - + +
644A THR* 5.3 3.5 - - - -
645A LEU 3.8 6.2 + - - -
646A ARG* 3.4 35.7 - - - +
650A THR* 1.3 80.0 + - - +
652A VAL* 1.3 62.5 + - - +
653A ALA 4.3 2.9 + - - -
654A VAL* 5.4 0.7 - - - +
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Residues in contact with VAL 652 (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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566A ILE* 3.4 6.7 - - + +
567A LEU* 2.5 37.8 + - - -
568A GLU* 4.5 5.2 - - + +
570A PRO* 4.3 21.5 - - + -
577A TYR* 3.5 26.2 - - + +
579A CYS* 6.1 1.3 - - + -
645A LEU* 2.9 11.1 + - + +
647A ASP* 3.2 28.3 - - + +
650A THR* 3.2 15.9 - - + +
651A THR* 1.3 83.6 + - - +
653A ALA* 1.3 61.6 + - + +
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Residues in contact with ALA 653 (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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564A ILE* 3.8 20.2 - - + -
565A ALA 3.0 18.8 - - - +
566A ILE* 3.8 5.6 - - + -
567A LEU* 3.5 7.7 - - - +
592A PHE* 5.8 0.2 - - + -
644A THR* 3.6 1.7 - - - -
645A LEU* 3.0 39.6 + - + +
651A THR* 4.3 1.2 + - - -
652A VAL* 1.3 82.1 - - + +
654A VAL* 1.3 73.9 + - - +
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Residues in contact with VAL 654 (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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224A GLU* 3.1 28.7 - - - +
226A ASP* 5.4 11.2 - - + +
230A LEU* 5.5 7.2 - - + -
233A MET* 3.6 15.3 - - + +
234A TYR* 4.0 11.4 - - + +
564A ILE* 4.5 1.6 - - - -
565A ALA* 2.8 42.8 + - + +
567A LEU* 4.1 17.9 - - + -
643A PHE* 3.6 8.1 - - - +
644A THR* 3.7 7.4 - - + +
651A THR* 5.4 1.1 - - - +
653A ALA* 1.3 85.6 - - - +
655A GLY* 1.3 58.7 + - - +
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Residues in contact with GLY 655 (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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233A MET* 3.8 3.8 - - - -
234A TYR* 3.1 11.0 + - - -
563A GLN 2.9 15.7 - - - -
564A ILE* 4.2 0.4 - - - -
642A ARG 3.7 0.5 - - - -
643A PHE* 2.8 52.7 + - - +
654A VAL* 1.3 76.0 - - - +
656A LYS* 1.3 60.8 + - - -
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Residues in contact with LYS 656 (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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232A ASP 5.4 0.2 + - - -
233A MET* 3.0 46.9 + - + +
234A TYR* 3.8 13.0 - - + -
563A GLN* 3.1 54.0 + - + +
603A ASN* 5.7 2.6 - - - +
634A PHE* 3.9 29.7 - - + -
641A GLY 3.1 11.4 - - - +
643A PHE* 3.8 2.7 - - - -
655A GLY* 1.3 73.8 - - - -
657A VAL* 1.3 62.7 + - - +
658A VAL* 3.5 10.5 + - - +
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Residues in contact with VAL 657 (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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560A PHE* 4.0 10.3 - - + -
561A ILE 3.5 12.3 - - - +
562A ALA* 3.7 7.9 - - - -
583A ILE* 4.8 1.8 - - + -
631A MET* 4.3 10.1 - - + -
632A GLU 3.3 9.0 - - - +
633A ARG* 3.6 1.8 - - - -
634A PHE* 3.2 24.9 + - - +
635A GLU 5.0 0.3 + - - -
640A MET 4.4 1.8 - - - +
641A GLY* 2.9 35.9 + - - +
643A PHE* 3.5 16.0 - - + -
656A LYS* 1.3 69.8 - - - +
658A VAL* 1.3 61.5 - - - +
659A LYS* 4.0 6.5 - - - +
660A ILE* 3.5 30.3 - - + -
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Residues in contact with VAL 658 (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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561A ILE* 3.1 39.3 + - + -
562A ALA* 3.8 7.6 - - - +
563A GLN* 4.6 17.3 - - + +
620A ILE* 5.4 2.5 - - + -
633A ARG* 3.2 27.2 + - - +
635A GLU* 4.8 4.7 - - - +
656A LYS* 3.5 14.0 + - - +
657A VAL* 1.3 75.3 - - - +
659A LYS* 1.3 63.5 + - + +
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Residues in contact with LYS 659 (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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560A PHE* 3.4 4.5 - - - +
561A ILE* 2.8 61.6 + - + +
633A ARG* 4.4 9.2 - - - +
657A VAL* 3.7 1.2 - - - +
658A VAL* 1.3 85.2 - - + +
660A ILE* 1.3 74.3 + - - +
661A LEU* 5.2 12.1 - - + +
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Residues in contact with ILE 660 (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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555A HIS* 4.6 26.0 - - + -
556A ALA 5.7 0.4 - - - +
557A THR* 4.0 20.2 - - + +
560A PHE* 4.2 2.2 - - + -
631A MET* 3.4 44.4 - - + +
632A GLU* 4.4 2.2 - - - +
633A ARG* 4.4 21.3 - - + +
657A VAL* 3.5 23.6 - - + -
659A LYS* 1.3 82.3 - - - +
661A LEU* 1.3 67.7 + - - +
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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