Contacts of the strand formed by residues 729 - 736 (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 SER 729 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647A ASP* 5.4 1.3 - - - -
648A ARG 4.4 0.8 + - - -
677A VAL* 3.6 4.5 - - - +
678A GLY 2.6 41.7 + - - +
679A ALA* 4.7 2.2 - - - -
721A TRP* 2.3 47.3 + - - -
722A HIS 3.0 10.8 + - - -
723A LYS* 4.4 0.7 - - - -
724A GLY* 4.1 1.8 - - - +
727A GLY 3.8 4.1 + - - -
728A LEU* 1.3 81.6 - - - +
730A ASN* 1.3 67.7 + - - +
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Residues in contact with ASN 730 (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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659A LEU* 3.5 25.1 - - - +
675A ILE* 3.7 23.9 - - + +
676A PHE 3.4 5.4 - - - +
677A VAL* 4.8 0.2 - - - -
678A GLY 4.3 0.7 - - - -
720A TYR 4.0 0.2 - - - +
721A TRP* 3.4 8.2 - - - -
722A HIS* 3.0 42.8 + - + +
729A SER* 1.3 83.4 + - - +
731A ALA* 1.3 61.1 + - - +
732A THR* 4.1 5.2 - - - +
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Residues in contact with ALA 731 (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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675A ILE* 4.6 0.4 - - - -
676A PHE* 2.9 43.1 + - - +
678A GLY* 4.1 4.0 - - - +
719A PHE* 3.7 13.2 - - + -
720A TYR 3.5 4.7 - - - -
721A TRP* 4.7 3.1 - - + +
730A ASN* 1.3 74.4 - - - +
732A THR* 1.3 61.8 + - - +
750A TYR* 3.4 47.3 - - + +
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Residues in contact with THR 732 (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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673A GLU* 3.7 37.0 - - + +
674A VAL 3.5 5.4 - - - +
675A ILE* 3.8 19.9 - - + +
718A ARG 3.7 0.7 - - - +
719A PHE* 3.4 4.9 - - - -
720A TYR* 2.7 54.1 + - + +
722A HIS* 6.1 1.6 - - - +
730A ASN* 4.1 4.4 - - - +
731A ALA* 1.3 73.7 + - - +
733A VAL* 1.3 63.9 + - - +
734A GLU* 4.1 14.5 + - + +
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Residues in contact with VAL 733 (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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672A ALA 3.7 1.4 - - - +
673A GLU* 3.5 2.4 - - - -
674A VAL* 3.0 33.6 + - - +
676A PHE* 4.0 19.7 - - + -
694A LEU* 3.7 46.0 - - + -
696A VAL* 5.4 1.6 - - + -
717A THR* 5.4 0.2 - - - -
718A ARG 3.4 2.7 - - - +
719A PHE* 3.9 17.5 - - + -
732A THR* 1.3 75.5 - - - +
734A GLU* 1.3 68.3 + - - +
735A TRP 4.2 0.2 + - - -
748A ILE* 3.6 30.7 - - + +
749A ARG 4.6 1.6 - - - +
750A TYR* 4.8 3.1 - - + -
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Residues in contact with GLU 734 (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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671A VAL* 4.1 13.1 - - + +
672A ALA 3.3 2.9 - - - -
673A GLU* 3.4 33.2 - - + +
716A GLU 4.0 0.3 - - - +
717A THR* 3.3 7.3 - - - -
718A ARG* 2.8 48.3 + - + +
720A TYR* 3.7 31.6 + - + -
732A THR* 4.2 7.5 - - + +
733A VAL* 1.3 80.0 - - - +
735A TRP* 1.3 60.3 + - - +
736A HIS* 3.2 23.0 + - + -
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Residues in contact with TRP 735 (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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671A VAL* 3.4 1.1 - - - -
672A ALA* 2.7 40.3 + - + +
696A VAL* 3.8 32.1 - - + -
709A VAL* 5.6 3.6 - - + -
710A CYS* 3.9 8.6 - - - -
716A GLU* 3.8 20.3 + - + -
717A THR* 3.9 19.1 - - + +
733A VAL* 4.2 0.6 + - + -
734A GLU* 1.3 72.4 - - - +
736A HIS* 1.3 65.4 + - - +
737A ILE* 3.0 31.8 + - + +
738A PRO* 4.0 15.2 - - + +
741A ALA* 4.6 7.2 - - + -
746A TYR* 3.6 50.5 - + + -
748A ILE* 4.3 6.9 - - + +
775A PHE* 4.2 17.0 - + - -
777A VAL* 3.9 20.2 - - + -
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Residues in contact with HIS 736 (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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669A GLY 5.6 0.7 - - - +
670A GLU 3.8 4.9 - - - -
671A VAL* 3.3 31.3 - - + +
715A TRP 5.8 0.4 - - - +
716A GLU* 2.9 35.8 + - - +
718A ARG* 3.2 52.2 + - + -
734A GLU* 3.2 26.1 + - + -
735A TRP* 1.3 68.2 - - - +
737A ILE* 1.3 66.1 + - - +
738A PRO* 3.1 10.5 - - - +
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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