Contacts of the helix formed by residues 792 - 802 (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 THR 792 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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732B ASP* 3.5 45.8 - - - +
733B HIS 3.8 4.3 - - - -
734B GLN* 4.4 2.2 - - + -
735B LEU* 3.5 5.1 - - - +
790B THR* 4.2 11.4 - - + -
791B ILE* 1.3 78.3 - - - +
793B MET* 1.3 63.7 + - - +
794B LYS* 3.7 8.8 + - - +
795B GLN* 3.0 40.9 + - - +
796B LEU* 3.0 21.0 + - - +
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Residues in contact with MET 793 (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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686B ALA* 5.0 0.9 - - - -
726B LEU* 4.6 7.0 - - - -
728B LEU* 3.8 18.2 - - + -
732B ASP 4.2 0.6 + - - -
733B HIS* 3.1 26.2 + - + +
735B LEU* 3.5 21.7 - - + +
792B THR* 1.3 71.6 - - - +
794B LYS* 1.3 63.5 + - - +
796B LEU* 3.1 17.2 + - + +
797B LEU* 2.9 32.5 + - + +
823B ILE* 4.7 4.3 - - + -
825B TYR* 3.5 61.5 - - + +
830B LEU* 3.7 22.7 - - + -
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Residues in contact with LYS 794 (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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732B ASP 5.1 2.5 + - - +
792B THR* 3.1 9.7 - - - +
793B MET* 1.3 81.2 - - - +
795B GLN* 1.3 65.0 + - + +
797B LEU* 3.4 11.1 + - - +
798B ARG* 3.3 20.9 + - + +
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Residues in contact with GLN 795 (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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747B TRP* 4.1 18.5 - - + -
749B HIS* 4.4 13.1 + - - -
750B GLU* 4.0 27.9 + - - +
789B ARG* 5.5 5.7 + - - +
790B THR 3.4 9.2 + - - +
791B ILE* 3.4 12.3 - - - +
792B THR* 3.0 44.8 + - - +
794B LYS* 1.3 78.7 - - + +
796B LEU* 1.3 61.9 + - - +
798B ARG* 3.6 4.8 + - - +
799B ALA* 3.2 24.8 + - - +
804B ARG* 5.0 0.2 + - - -
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Residues in contact with LEU 796 (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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735B LEU* 4.3 13.5 - - + -
745B VAL* 4.8 13.0 - - + -
747B TRP* 4.3 15.4 - - + -
791B ILE* 5.3 2.7 - - + -
792B THR 3.0 12.9 + - - +
793B MET* 3.1 30.9 + - + +
795B GLN* 1.3 77.0 - - - +
797B LEU* 1.3 63.0 + - - +
799B ALA* 3.4 1.7 + - - +
800B LEU* 3.0 45.7 + - + +
805B VAL* 4.1 20.0 - - + -
808B VAL* 5.0 11.4 - - + -
823B ILE* 4.0 27.1 - - + -
830B LEU* 5.0 1.3 - - + -
832B ILE* 4.9 1.8 - - + -
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Residues in contact with LEU 797 (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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793B MET* 2.9 25.1 + - + +
794B LYS* 3.7 9.2 - - - +
795B GLN 3.4 0.2 - - - -
796B LEU* 1.3 76.8 - - - +
798B ARG* 1.3 63.4 + - - +
800B LEU* 3.5 9.5 + - + +
801B GLU* 3.4 26.3 + - - +
825B TYR* 4.0 26.7 - - + -
830B LEU* 3.6 43.3 - - + -
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Residues in contact with ARG 798 (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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750B GLU* 3.8 39.0 + - - +
794B LYS* 3.3 11.4 + - + +
795B GLN* 3.9 8.3 - - - +
797B LEU* 1.3 75.0 - - - +
799B ALA* 1.3 67.6 + - - +
801B GLU* 3.1 21.6 + - + +
802B GLU* 3.2 47.5 + - + +
804B ARG* 3.8 7.9 - - - +
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Residues in contact with ALA 799 (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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747B TRP* 3.7 17.0 - - + -
795B GLN 3.2 16.3 + - - +
796B LEU 3.8 1.1 - - - +
798B ARG* 1.3 78.2 - - - +
800B LEU* 1.3 62.2 + - - +
802B GLU 3.1 2.4 + - - -
803B GLY 3.1 4.0 + - - -
804B ARG* 2.8 56.9 + - + +
805B VAL* 3.7 20.0 - - + -
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Residues in contact with LEU 800 (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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796B LEU* 3.0 36.9 + - + +
797B LEU* 3.7 11.9 - - + +
798B ARG 3.2 0.4 - - - -
799B ALA* 1.3 76.1 - - - +
801B GLU* 1.3 60.8 + - + +
803B GLY* 3.2 12.1 + - - -
805B VAL* 3.4 32.3 - - + +
830B LEU* 4.4 18.2 - - + -
831B HIS 4.2 5.6 - - - +
832B ILE* 3.8 25.6 - - + -
833B PRO* 3.9 27.9 - - + +
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Residues in contact with GLU 801 (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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797B LEU* 3.4 16.5 + - - +
798B ARG* 3.1 15.4 + - + +
800B LEU* 1.3 76.5 - - + +
802B GLU* 1.3 62.2 + - + +
803B GLY 2.9 7.3 + - - -
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Residues in contact with GLU 802 (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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798B ARG* 3.2 46.6 + - + +
799B ALA 3.1 2.0 + - - -
801B GLU* 1.3 82.0 - - + +
803B GLY* 1.3 63.3 + - - +
804B ARG* 3.0 41.1 + - - +
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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
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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