Contacts of the strand formed by residues 717 - 723 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ILE 4.6 0.2 - - - +
134B LEU* 3.5 15.1 - - - +
694B LEU* 3.7 16.4 - - + -
696B VAL* 3.7 18.2 - - + -
710B CYS* 3.6 33.4 - - + -
711B ASN 2.7 21.5 + - - -
712B ASP* 3.7 6.3 - - - +
714B SER* 2.9 19.0 + - - +
716B GLU* 1.3 83.2 - - + +
718B ARG* 1.3 67.1 + - - +
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Residues in contact with ARG 718 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ILE 4.0 4.7 - - - -
134B LEU* 3.8 13.4 - - + +
313B LEU* 4.2 10.8 - - + -
392B ASP* 5.0 3.6 + - - -
394B PHE* 3.3 58.5 - - - +
694B LEU* 4.1 9.2 - - - +
715B TRP 5.1 3.6 + - - +
716B GLU 5.0 3.7 + - - +
717B THR* 1.3 81.4 - - - +
719B PHE* 1.3 61.3 + - - +
720B TYR* 3.7 36.4 + - + -
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Residues in contact with PHE 719 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B VAL* 4.7 0.9 - - + -
132B GLY* 3.1 14.3 - - - -
133B ILE* 3.0 54.4 + - + +
313B LEU* 4.1 4.3 - - - +
681B PRO* 4.1 23.6 - - + -
693B PHE* 3.8 46.7 - + + -
694B LEU* 3.7 20.2 - - + -
718B ARG* 1.3 73.5 - - - +
720B TYR* 1.3 73.0 + - - +
721B TRP* 4.4 12.6 - + + -
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Residues in contact with TYR 720 (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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131B GLN* 3.6 10.3 - - + -
312B HIS* 6.2 0.9 - - + -
313B LEU* 3.5 36.6 - - + +
394B PHE* 4.1 5.5 - - - -
718B ARG* 3.7 45.0 + - + -
719B PHE* 1.3 88.2 - - - +
721B TRP* 1.3 62.1 + - - +
722B HIS* 4.3 0.9 - - + -
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Residues in contact with TRP 721 (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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116B ALA* 3.9 19.5 - - + -
117B ASP* 4.1 16.8 - - - -
130B ALA 5.6 0.7 - - - -
131B GLN* 2.8 39.5 + - + +
647B ASP* 5.4 0.9 - - - -
678B GLY* 4.7 7.1 - - - -
679B ALA* 3.0 28.5 + - - +
680B ASN* 3.6 33.7 - - + -
681B PRO* 3.4 23.8 - - + -
719B PHE* 4.4 10.3 - + + -
720B TYR* 1.3 75.8 - - - +
722B HIS* 1.3 74.8 + - - +
723B LYS 4.3 9.8 + - - -
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Residues in contact with HIS 722 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B GLN* 6.1 0.4 - - - -
720B TYR* 4.3 1.0 + - + -
721B TRP* 1.3 89.3 + - - +
723B LYS 1.3 51.2 + - - +
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Residues in contact with LYS 723 (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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721B TRP* 4.2 16.6 + - - -
722B HIS* 1.3 72.1 + - - +
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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
------------------------------------------------------------
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