Contacts of the strand formed by residues 668 - 675 (chain J) in PDB entry 1O19
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 668 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121J LEU* 6.2 0.6 - - - +
165J PHE* 4.5 21.4 - + - -
169J ASP* 4.7 5.3 + - - -
171J GLU* 4.2 16.0 + - - +
172J ASN 2.7 14.6 + - - +
173J GLN* 2.6 28.5 + - - +
174J SER 3.2 15.9 + - - -
494J HIS* 3.6 20.2 + + - -
498J LEU* 5.3 4.0 - - - +
667J THR* 1.3 71.0 - - - +
669J PRO* 1.3 85.6 + - + +
670J HIS* 3.3 24.8 + + - -
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Residues in contact with PRO 669 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121J LEU* 5.5 2.8 - - - +
174J SER* 3.1 11.7 - - - +
176J LEU* 4.5 1.3 - - + -
490J PHE* 3.5 37.0 - - + -
494J HIS* 3.6 37.4 + - + +
667J THR 3.1 13.4 - - - +
668J HIS* 1.3 106.3 + - + +
670J HIS* 1.3 63.1 + - - +
671J PHE* 3.7 19.8 - - + -
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Residues in contact with HIS 670 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121J LEU* 6.2 2.0 - - - +
158J ILE* 4.5 18.5 + - + +
161J ASN* 5.2 2.9 - - + +
162J ALA* 4.1 13.8 - - + -
165J PHE* 3.9 23.2 - + - -
173J GLN* 3.2 34.2 + - + +
174J SER* 2.7 17.1 + - - +
175J ILE* 2.9 18.1 - - + -
176J LEU* 2.7 33.5 + - - +
668J HIS* 3.3 42.7 + + - -
669J PRO* 1.3 71.9 + - - +
671J PHE* 1.3 55.4 + - - +
672J VAL* 5.1 0.4 - - - -
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Residues in contact with PHE 671 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121J LEU* 3.7 20.0 + - + +
122J PHE* 3.7 22.4 - + + -
123J CYS* 3.5 18.6 + - - +
158J ILE* 4.4 4.4 - - - +
176J LEU* 3.9 26.0 - - + -
487J LEU 4.8 3.1 - - - -
490J PHE* 4.1 8.5 - + - -
491J PHE* 3.2 56.1 - + + -
494J HIS* 4.2 16.2 - + - -
669J PRO* 3.7 29.6 - - + -
670J HIS* 1.3 72.1 - - - +
672J VAL* 1.3 69.0 + - - +
673J ARG* 3.9 25.1 - - - +
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Residues in contact with VAL 672 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123J CYS* 3.8 17.3 - - + +
125J THR* 4.9 2.0 - - - +
155J ILE* 4.5 24.5 - - + -
158J ILE* 4.2 20.0 - - + -
175J ILE* 3.8 22.7 - - + -
176J LEU 2.8 20.9 + - - +
177J ILE* 3.4 22.2 - - + -
178J THR 3.3 12.6 + - - -
188J ASN* 5.5 0.2 - - - +
192J VAL* 6.4 1.1 - - + -
671J PHE* 1.3 78.6 - - - +
673J ARG* 1.3 67.7 + - - +
674J CYS* 4.5 12.3 - - - -
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Residues in contact with ARG 673 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122J PHE* 3.9 28.6 - - + -
123J CYS 3.3 11.6 + - - +
124J VAL* 3.4 5.3 - - - -
125J THR 3.0 24.3 + - - -
176J LEU* 3.0 36.4 + - - +
178J THR* 3.6 30.9 + - - +
484J ASN* 5.4 3.0 + - - -
487J LEU* 5.2 15.4 - - - +
488J GLN* 4.6 8.5 + - - -
491J PHE* 5.9 1.6 - - - +
671J PHE* 3.9 21.7 - - - -
672J VAL* 1.3 76.5 + - - +
674J CYS* 1.3 62.0 + - - +
675J ILE* 3.9 5.7 + - + +
698J ASN* 3.2 50.4 + - + +
700J VAL* 4.7 7.4 - - + -
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Residues in contact with CYS 674 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125J THR* 3.6 7.6 - - + +
177J ILE* 3.5 27.4 - - - -
178J THR 2.9 14.2 + - - +
179J GLY* 3.7 10.7 - - - -
183J ALA* 3.4 32.2 - - + +
185J LYS* 4.2 7.0 - - + -
188J ASN* 2.9 32.5 - - - +
672J VAL* 4.5 7.9 - - - -
673J ARG* 1.3 74.1 - - - +
675J ILE* 1.3 64.1 + - - +
694J GLN* 4.6 2.6 - - - +
698J ASN* 4.8 3.5 + - - -
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Residues in contact with ILE 675 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106J LEU* 5.4 2.0 - - + -
124J VAL* 3.0 34.3 - - + -
125J THR 2.5 18.3 + - - +
126J VAL* 3.6 22.7 - - + -
127J ASN* 3.1 28.8 + - - +
183J ALA* 3.9 7.2 - - - +
673J ARG* 3.9 9.2 - - + +
674J CYS* 1.3 76.8 - - - +
676J ILE* 1.3 70.7 + - - +
677J PRO* 3.5 0.8 - - + +
691J VAL* 4.3 17.5 - - + -
694J GLN* 4.1 16.8 - - + +
695J LEU* 4.7 12.1 - - + -
698J ASN* 3.7 23.6 - - - +
700J VAL* 5.7 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