Contacts of the strand formed by residues 717 - 723 (chain A) in PDB entry 4WGK
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 717 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A ILE 4.6 0.3 - - - +
134A LEU* 3.5 14.7 - - - +
694A LEU* 3.8 13.9 - - + -
696A VAL* 3.7 17.9 - - + -
710A CYS* 3.6 30.7 - - + -
711A ASN 2.7 23.7 + - - +
712A ASP* 3.8 6.1 - - - +
714A SER* 3.0 16.6 + - - +
716A GLU* 1.3 80.8 - - - +
718A ARG* 1.3 70.0 + - - +
734A GLU 3.3 7.9 - - - +
735A TRP* 3.9 9.6 - - + -
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Residues in contact with ARG 718 (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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133A ILE 4.0 4.7 - - - -
134A LEU* 3.9 13.6 - - + +
313A LEU* 4.0 9.6 - - + -
392A ASP* 5.2 2.2 + - - -
394A PHE* 3.3 56.9 - - - +
694A LEU* 4.2 3.1 - - - -
715A TRP 5.2 3.8 + - - +
716A GLU 5.1 0.2 - - - +
717A THR* 1.3 80.1 - - - +
719A PHE* 1.3 60.7 - - - +
720A TYR* 3.7 33.7 + - + -
732A THR 3.7 0.3 - - - +
733A VAL* 3.4 5.7 - - - +
734A GLU* 2.8 44.9 + - + +
736A HIS* 3.2 46.5 + - + +
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Residues in contact with PHE 719 (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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115A VAL* 4.7 3.1 - - + -
132A GLY* 3.1 28.8 - - - -
133A ILE* 3.1 36.2 + - + +
313A LEU* 4.4 2.4 - - - +
681A PRO* 4.2 22.4 - - + -
693A PHE* 3.9 32.5 - + + -
694A LEU* 3.6 14.8 - - + -
718A ARG* 1.3 74.2 - - - +
720A TYR* 1.3 65.1 + - - +
721A TRP* 4.5 8.3 - - + -
731A ALA* 3.7 19.5 - - + -
732A THR 3.4 3.1 - - - -
733A VAL* 3.9 20.0 - - + -
750A TYR* 3.5 38.1 - + - -
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Residues in contact with TYR 720 (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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131A GLN* 3.4 16.4 - - + +
312A HIS* 6.2 0.7 - - + -
313A LEU* 3.4 39.6 - - + +
394A PHE* 4.5 3.5 - - - -
718A ARG* 3.7 33.4 + - + -
719A PHE* 1.3 79.7 - - - +
721A TRP* 1.3 62.7 + - - +
722A HIS* 4.3 0.4 + - + -
730A ASN 4.0 0.2 - - - +
731A ALA* 3.5 3.8 - - - +
732A THR* 2.7 57.3 + - + +
734A GLU* 3.7 35.5 + - + -
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Residues in contact with TRP 721 (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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116A ALA* 3.8 16.6 - - + -
117A ASP* 3.7 20.2 - - - -
130A ALA 5.7 0.9 - - - -
131A GLN* 2.8 37.4 + - - +
132A GLY* 5.3 0.4 - - - -
647A ASP* 5.4 0.7 - - - -
679A ALA 3.0 23.9 + - - -
680A ASN* 3.7 32.1 - - + -
681A PRO* 3.4 24.9 - - + -
719A PHE* 4.5 6.7 - + + -
720A TYR* 1.3 76.1 - - - +
722A HIS* 1.3 61.4 + - - +
723A LYS* 3.6 33.9 - - + -
729A SER* 2.3 37.3 + - - -
730A ASN 3.4 10.3 - - - -
731A ALA* 4.7 7.0 - - + -
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Residues in contact with HIS 722 (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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720A TYR* 4.3 0.4 - - + -
721A TRP* 1.3 74.8 - - - +
723A LYS* 1.3 85.5 + - - +
724A GLY* 5.2 1.7 - - - -
729A SER* 3.0 6.4 + - - -
730A ASN* 3.0 45.1 + - + +
732A THR* 6.1 1.1 - - - +
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Residues in contact with LYS 723 (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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117A ASP* 5.1 10.3 + - - +
642A ILE* 6.0 2.6 - - - +
645A ILE* 3.4 32.5 - - - +
680A ASN* 6.4 0.2 - - - +
721A TRP* 3.6 37.5 + - + -
722A HIS* 1.3 95.1 + - - +
724A GLY* 1.3 72.5 + - - +
727A GLY* 5.9 4.0 - - - +
728A LEU 4.2 5.2 - - - +
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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