Contacts of the strand formed by residues 718 - 728 (chain A) in PDB entry 4KHW
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 718 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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490A LEU* 4.3 6.4 + - - +
493A GLN* 2.9 41.5 + - + +
494A ARG* 3.6 19.2 - - - +
497A GLU* 3.7 22.0 - - + -
714A ASP* 3.2 6.7 + - - -
715A MET 3.0 28.7 + - - -
716A GLU 4.6 0.5 + - - -
717A GLY* 1.3 77.4 - - - +
719A ARG* 1.3 60.2 + - - +
720A TYR* 3.4 26.5 + - + -
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Residues in contact with ARG 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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494A ARG* 5.6 0.2 - - - +
497A GLU* 3.7 17.1 - - - +
501A GLU* 5.1 2.4 - - - +
645A ASN* 2.7 40.8 + - - +
648A VAL* 3.5 23.7 - - - +
649A ASP* 2.7 34.7 + - - -
652A ASP* 3.6 25.9 + - - +
713A TRP* 3.8 13.7 - - - -
714A ASP* 2.7 23.5 + - - +
717A GLY 3.7 3.6 + - - +
718A THR* 1.3 69.5 - - - +
720A TYR* 1.3 71.2 + - - +
721A ALA* 3.6 1.4 + - - -
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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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493A GLN* 4.1 11.6 + - + -
497A GLU* 3.4 21.3 - - - +
501A GLU* 4.5 1.0 - - - +
712A VAL* 3.8 24.2 - - + -
713A TRP* 3.2 28.5 + - - +
715A MET* 3.2 39.0 - - + +
718A THR* 3.5 22.4 - - + -
719A ARG* 1.3 81.0 - - - +
721A ALA* 1.3 63.4 + - - +
722A GLU* 3.2 21.2 - - - +
723A PRO* 4.7 0.9 - - + -
724A LYS* 3.8 27.9 - - + +
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Residues in contact with ALA 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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497A GLU* 2.9 17.1 + - - +
500A LYS* 4.2 16.4 - - + -
501A GLU* 3.3 36.3 - - + +
504A HIS* 4.4 13.3 - - + -
713A TRP* 5.8 1.1 - - - -
719A ARG 3.6 1.4 + - - -
720A TYR* 1.3 71.9 - - - +
722A GLU* 1.3 72.0 + - + +
723A PRO* 4.7 1.3 - - - +
1009A NA 2.8 23.1 - - - -
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Residues in contact with GLU 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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504A HIS* 4.7 15.9 + - - +
720A TYR* 3.2 19.4 - - - +
721A ALA* 1.3 88.5 - - + +
723A PRO* 1.3 85.9 - - + +
724A LYS* 3.4 2.6 + - - +
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Residues in contact with PRO 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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692A PRO* 5.7 0.9 - - + -
711A ASN* 3.5 18.8 - - - +
712A VAL 3.5 10.3 - - - +
713A TRP* 3.6 47.1 - - + -
720A TYR* 4.7 2.0 - - + -
721A ALA 4.7 0.4 - - - +
722A GLU* 1.3 100.5 - - + +
724A LYS* 1.3 59.9 - - - +
725A LEU* 4.2 1.2 + - - +
754A GLN* 3.4 25.2 + - - +
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Residues in contact with LYS 724 (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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712A VAL* 3.0 35.2 + - + +
720A TYR* 3.8 34.0 - - + +
722A GLU 3.4 2.4 + - - +
723A PRO* 1.3 74.1 - - - +
725A LEU* 1.3 76.2 + - - +
726A LYS* 6.2 0.4 - - + -
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Residues in contact with LEU 725 (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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710A LEU 3.4 2.5 - - - +
711A ASN* 3.6 23.3 - - - +
723A PRO 4.2 0.9 + - - +
724A LYS* 1.3 81.9 - - - +
726A LYS* 1.3 60.6 + - - +
727A ILE* 3.6 21.1 + - + +
746A LYS* 3.9 38.7 + - + +
749A ILE* 4.5 1.1 - - + -
750A ARG* 3.6 44.2 - - + +
753A LEU* 4.2 22.2 - - + -
754A GLN* 4.3 6.5 - - - +
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Residues in contact with LYS 726 (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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626A TYR* 3.6 24.7 - - - +
686A GLU* 4.8 10.5 + - - -
687A ALA* 4.9 3.8 - - + -
708A TYR* 4.0 11.7 - - + +
709A ALA* 3.4 2.8 - - - -
710A LEU* 2.8 39.8 + - + +
712A VAL* 3.6 21.5 - - + -
715A MET* 3.9 27.6 - - + +
724A LYS* 3.4 2.2 + - + +
725A LEU* 1.3 70.6 - - - +
727A ILE* 1.3 58.4 + - - +
728A MET* 3.9 30.3 + - + +
115P C 5.6 0.8 + - - -
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Residues in contact with ILE 727 (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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708A TYR 3.5 2.9 - - - +
709A ALA* 4.0 10.8 - - + -
710A LEU 5.1 0.4 - - - +
725A LEU* 3.6 28.8 + - + +
726A LYS* 1.3 76.0 - - - +
728A MET* 1.3 72.2 + - - +
730A LEU* 3.6 33.0 - - + -
732A THR* 3.3 26.0 - - - +
733A GLN* 3.2 33.2 - - + +
746A LYS* 4.3 14.4 - - + -
749A ILE* 3.8 26.5 - - + -
114P C 4.1 0.5 + - - -
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Residues in contact with MET 728 (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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706A LYS 3.7 2.0 - - - +
707A ARG* 3.3 1.4 - - - -
708A TYR* 2.8 79.3 + - + +
726A LYS* 3.9 30.7 - - + +
727A ILE* 1.3 84.9 - - - +
729A GLY* 1.3 58.1 + - - +
730A LEU 2.8 12.1 + - - -
114P C 3.3 30.7 - - - +
115P C 3.1 26.0 - - - +
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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