Contacts of the helix formed by residues 709 - 720 (chain B) in PDB entry 1KT8
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 PRO 709 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A SER* 5.8 0.9 - - - +
106A ARG* 2.3 38.8 + - - +
107A LEU* 4.2 6.7 - - + -
198A VAL* 3.8 39.9 - - + -
203A LEU* 4.7 8.1 - - + -
705B GLY* 3.1 22.9 - - - +
706B ASN* 4.0 5.4 - - - +
707B TYR 3.4 3.1 - - - -
708B GLY* 1.4 87.4 - - - +
710B THR* 1.3 59.6 + - + +
713B VAL* 3.9 5.2 - - - +
727B TRP* 5.4 0.6 - - - -
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Residues in contact with THR 710 (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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155A VAL* 4.0 12.8 - - - +
692B ARG* 4.5 11.2 - - + -
706B ASN 3.5 22.4 - - - +
707B TYR* 2.7 32.4 + - + +
709B PRO* 1.3 74.1 - - + +
711B VAL* 1.3 58.3 + - - +
712B LEU 3.3 0.4 - - - -
713B VAL* 3.2 3.6 + - - +
714B GLN* 2.8 32.4 + - - +
727B TRP* 3.7 36.7 - - + +
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Residues in contact with VAL 711 (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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70A TYR* 6.2 0.2 - - + -
72A LEU* 4.2 17.0 - - + -
107A LEU 5.0 2.2 - - - +
108A CYS* 3.8 21.1 - - + -
155A VAL* 4.4 17.5 - - + +
156A SER* 3.7 11.4 - - - +
157A GLN* 3.5 32.3 - - + +
158A PRO* 5.6 0.2 - - + -
707B TYR 4.2 6.7 - - - +
708B GLY* 3.3 19.2 + - - +
710B THR* 1.3 77.1 + - - +
712B LEU* 1.3 63.4 + - - +
714B GLN* 3.2 8.0 + - + +
715B GLN* 3.0 25.4 + - + +
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Residues in contact with LEU 712 (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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105A MET 4.5 7.0 - - - +
106A ARG* 3.5 48.4 + - - +
108A CYS* 3.7 14.3 - - - -
709B PRO 4.2 1.4 + - - -
710B THR 3.3 0.2 - - - -
711B VAL* 1.3 78.2 - - - +
713B VAL* 1.3 62.8 + - - +
715B GLN* 3.3 21.2 + - + +
716B GLU* 3.0 21.3 + - - +
2001B GOL 3.5 35.4 - - - +
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Residues in contact with VAL 713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ARG* 4.2 1.1 - - - +
685B LEU* 5.1 0.3 - - - +
690B PHE* 3.6 35.0 - - + -
709B PRO 3.9 14.8 - - - +
710B THR 3.2 6.8 + - - +
712B LEU* 1.3 72.9 - - - +
714B GLN* 1.3 66.3 + - - +
716B GLU* 3.1 4.6 + - - +
717B ALA* 3.0 19.8 + - - +
725B VAL* 3.8 18.4 - - + -
727B TRP* 3.8 23.3 - - + -
2001B GOL 3.5 35.2 - - - -
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Residues in contact with GLN 714 (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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155A VAL 5.7 5.8 - - - +
710B THR* 2.8 18.3 + - - +
711B VAL* 3.6 6.7 - - - +
713B VAL* 1.3 76.2 - - - +
715B GLN* 1.3 66.0 + - + +
717B ALA* 3.0 14.1 + - - +
718B LEU* 3.1 30.2 + - + +
723B GLU 2.7 26.8 + - - -
724B GLN* 3.6 13.5 - - - +
725B VAL* 3.5 22.5 + - + +
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Residues in contact with GLN 715 (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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108A CYS* 3.7 22.1 - - - -
157A GLN* 2.5 40.5 + - + +
711B VAL* 3.0 19.0 + - + +
712B LEU* 3.5 17.6 - - + +
713B VAL 3.2 0.2 - - - -
714B GLN* 1.3 76.5 - - + +
716B GLU* 1.3 64.2 + - - +
718B LEU* 3.2 13.7 + - + +
719B LYS* 3.0 22.1 + - - +
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Residues in contact with GLU 716 (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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685B LEU* 4.5 3.6 - - + -
690B PHE* 4.1 22.2 - - + -
712B LEU* 3.0 14.1 + - + +
713B VAL* 3.1 12.3 + - - +
715B GLN* 1.3 77.4 - - - +
717B ALA* 1.3 62.7 + - - +
719B LYS* 3.2 39.6 + - - +
720B ARG* 2.9 40.1 + - + +
2001B GOL 4.1 14.1 + - - +
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Residues in contact with ALA 717 (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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685B LEU* 3.7 28.8 - - + +
713B VAL 3.0 4.8 + - - -
714B GLN* 3.0 15.8 + - - +
716B GLU* 1.3 76.1 - - - +
718B LEU* 1.3 62.2 + - - +
720B ARG* 3.2 8.0 + - - +
721B GLY 3.2 0.3 + - - -
722B CYS* 2.8 32.2 + - + +
724B GLN 4.2 6.7 - - - +
725B VAL* 3.8 25.6 - - + -
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Residues in contact with LEU 718 (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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714B GLN* 3.1 35.1 + - + +
715B GLN* 3.6 12.6 - - + +
717B ALA* 1.3 74.1 - - - +
719B LYS* 1.3 67.9 + - - +
721B GLY* 2.8 15.1 + - - -
722B CYS 3.2 18.4 - - - +
723B GLU* 4.2 8.3 - - + +
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Residues in contact with LYS 719 (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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715B GLN 3.0 14.3 + - - +
716B GLU* 3.2 36.7 + - - +
718B LEU* 1.3 77.1 - - - +
720B ARG* 1.3 81.8 + - - +
721B GLY 3.3 0.9 + - - -
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Residues in contact with ARG 720 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685B LEU* 4.4 21.5 - - + +
687B ASP* 5.3 6.9 + - - -
716B GLU* 2.9 41.6 + - + +
717B ALA* 3.9 6.1 - - - +
718B LEU 3.0 0.6 - - - -
719B LYS* 1.3 89.8 - - - +
721B GLY* 1.3 60.1 + - - +
722B CYS* 3.5 2.5 - - - +
822B ARG* 5.3 0.5 + - - -
824B LEU* 3.7 48.7 - - + +
827B ASP* 3.0 37.3 + - - +
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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