Contacts of the helix formed by residues 613 - 628 (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 ASP 613 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504B SER* 3.6 16.1 + - - +
505B PHE* 4.8 0.7 - - - -
506B LYS* 6.0 1.6 - - - +
612B PHE* 1.3 76.7 - - - +
614B LYS* 1.3 65.6 + - - +
615B LEU* 2.6 38.1 + - - +
616B GLU* 3.0 42.2 + - + +
617B LEU 3.1 10.2 + - - -
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Residues in contact with LYS 614 (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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594B TRP* 4.5 18.9 + - - +
597B MET* 3.8 29.8 - - + +
598B ASP* 2.7 34.9 + - - +
601B LEU* 5.1 12.5 - - + +
612B PHE* 3.5 16.8 + - + -
613B ASP* 1.3 73.4 + - - +
615B LEU* 1.3 83.5 + - + +
617B LEU* 3.4 2.4 + - - +
618B LEU* 2.9 28.4 + - - +
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Residues in contact with LEU 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594B TRP* 4.2 25.1 - - + +
613B ASP* 2.6 16.4 + - - +
614B LYS* 1.3 91.8 - - + +
616B GLU* 1.3 60.0 + - + +
618B LEU* 3.7 12.7 - - + +
619B GLU* 2.8 29.6 + - - +
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Residues in contact with GLU 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B PHE* 3.2 31.0 - - + +
506B LYS* 4.0 17.2 - - + +
507B ALA* 2.7 40.6 + - - +
508B ALA 4.6 0.2 + - - -
613B ASP* 3.0 34.8 + - + +
615B LEU* 1.3 74.8 - - - +
617B LEU* 1.3 68.0 + - - +
619B GLU* 3.1 5.1 + - - +
620B CYS* 2.9 29.7 + - - -
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Residues in contact with LEU 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B PHE* 4.0 18.7 - - + -
539B LEU* 3.9 25.4 - - + -
597B MET* 3.6 20.4 - - + -
600B MET* 3.9 24.5 - - + -
612B PHE* 3.6 31.4 - - + -
613B ASP 3.1 9.6 + - - +
614B LYS 3.9 6.1 - - - +
616B GLU* 1.3 80.3 - - - +
618B LEU* 1.3 63.5 + - - +
620B CYS 3.2 1.8 + - - +
621B ILE* 2.9 38.7 + - + +
644B PRO* 5.1 0.9 - - + -
663B LEU* 4.1 14.8 - - + -
665B VAL* 4.7 1.1 - - + -
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Residues in contact with LEU 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B MET* 4.9 5.6 - - + -
590B LEU* 3.9 10.5 - - + -
593B PRO* 3.7 27.6 - - + -
594B TRP* 3.7 35.2 - - + +
597B MET* 4.2 13.2 - - + -
614B LYS 2.9 17.8 + - - +
615B LEU* 3.7 14.6 - - + +
616B GLU 3.1 0.2 - - - -
617B LEU* 1.3 78.8 - - - +
619B GLU* 1.3 56.1 + - - +
621B ILE* 3.2 5.1 + - + +
622B ARG* 2.8 25.3 + - - +
863B PHE* 3.6 37.0 - - + -
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Residues in contact with GLU 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B ALA* 3.7 23.1 - - + -
510B LEU* 5.6 0.2 - - + -
615B LEU 2.8 17.4 + - - +
616B GLU* 3.1 4.7 + - - +
618B LEU* 1.3 78.5 - - - +
620B CYS* 1.3 56.1 + - - +
622B ARG* 2.4 52.0 + - - +
623B ARG* 2.7 43.5 + - + +
863B PHE* 4.8 4.8 - - - -
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Residues in contact with CYS 620 (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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505B PHE* 3.9 14.4 - - - -
507B ALA* 4.0 10.1 - - - -
510B LEU* 3.4 32.3 - - + -
539B LEU* 3.8 21.6 - - + +
551B PRO* 3.8 15.5 - - - -
553B ILE* 4.4 2.9 - - - +
616B GLU 2.9 21.3 + - - +
617B LEU* 3.7 4.5 - - - +
619B GLU* 1.3 76.3 - - - +
621B ILE* 1.3 58.9 + - - +
623B ARG* 3.3 9.0 + - - +
624B LEU* 2.9 27.5 + - - +
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Residues in contact with ILE 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B LEU* 4.7 1.8 - - + -
578B MET* 3.8 27.1 - - + -
590B LEU* 4.4 4.9 - - + -
597B MET* 3.9 19.1 - - + -
617B LEU* 2.9 36.7 + - + +
618B LEU* 3.6 5.8 - - - +
620B CYS* 1.3 74.3 - - - +
622B ARG* 1.3 66.1 + - - +
624B LEU* 3.2 5.5 + - + +
625B ILE* 2.8 50.2 + - + +
642B VAL* 4.0 13.9 - - + -
644B PRO* 4.1 16.8 - - + -
665B VAL* 4.2 16.2 - - + -
667B LEU* 5.7 0.2 - - + -
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Residues in contact with ARG 622 (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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590B LEU* 5.3 2.0 - - - -
618B LEU* 2.8 14.1 + - - +
619B GLU* 2.4 53.9 + - - +
621B ILE* 1.3 79.4 - - - +
623B ARG* 1.3 79.8 + - - +
625B ILE* 3.3 5.3 + - - +
626B GLU* 2.6 58.4 + - - +
863B PHE* 3.8 21.5 - - + -
864B PRO 4.0 7.0 - - - -
865B VAL* 2.6 44.3 + - - +
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Residues in contact with ARG 623 (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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510B LEU* 4.0 31.4 - - + +
512B LEU* 3.7 31.4 - - - +
553B ILE* 3.8 11.8 - - + +
619B GLU* 2.7 34.0 + - - +
620B CYS* 3.7 6.5 - - - +
621B ILE 3.2 0.2 - - - -
622B ARG* 1.3 96.7 - - - +
624B LEU* 1.3 63.0 + - - +
626B GLU* 3.2 38.6 + - - +
627B VAL* 3.2 18.7 + - - +
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Residues in contact with LEU 624 (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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537B HIS* 4.0 7.6 - - + -
538B MET* 3.5 36.6 - - - +
539B LEU* 3.9 6.5 - - + +
553B ILE* 3.5 28.4 - - + +
620B CYS 2.9 17.2 + - - +
621B ILE* 3.6 6.1 - - + +
623B ARG* 1.3 76.1 - - - +
625B ILE* 1.3 65.2 + - + +
626B GLU 3.0 0.9 + - - -
627B VAL* 3.0 15.5 + - - +
628B ASP* 3.2 10.3 + - - +
665B VAL* 3.8 30.3 - - + +
667B LEU* 3.5 38.4 - - + -
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Residues in contact with ILE 625 (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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580B ALA* 4.2 3.1 - - + -
588B VAL* 4.3 16.6 - - + -
590B LEU* 3.8 25.8 - - + -
621B ILE* 2.8 33.3 + - + +
622B ARG* 3.9 4.3 - - - +
624B LEU* 1.3 75.7 - - + +
626B GLU* 1.3 60.8 + - - +
628B ASP* 3.3 1.8 + - - +
629B LYS* 3.0 20.3 + - - +
632B VAL* 4.3 12.8 - - + -
640B LEU* 3.8 23.8 - - + -
642B VAL* 3.7 27.6 - - + -
667B LEU* 4.3 15.7 - - + -
865B VAL 4.4 8.1 - - - +
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Residues in contact with GLU 626 (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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622B ARG* 2.6 43.0 + - - +
623B ARG* 3.2 33.4 + - - +
624B LEU 3.0 0.4 - - - -
625B ILE* 1.3 75.5 - - - +
627B VAL* 1.3 69.5 + - + +
629B LYS* 3.1 35.2 + - - +
865B VAL* 5.1 11.6 + - + +
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Residues in contact with VAL 627 (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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512B LEU* 4.4 13.2 - - + -
514B MET* 3.8 36.8 - - + -
537B HIS* 3.9 30.5 - - + +
553B ILE* 4.5 5.2 - - + -
623B ARG* 3.4 20.6 - - - +
624B LEU* 3.0 8.0 + - - +
626B GLU* 1.3 81.8 - - + +
628B ASP* 1.3 59.3 + - - +
629B LYS 3.5 1.7 + - - -
630B ASP* 4.3 7.8 - - - +
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Residues in contact with ASP 628 (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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535B THR* 2.4 30.6 + - + +
536B ASP* 4.0 2.8 - - - +
537B HIS* 3.2 41.2 + - - +
624B LEU* 3.2 10.2 + - - +
625B ILE* 3.3 5.1 + - - +
626B GLU 3.2 0.6 - - - -
627B VAL* 1.3 82.9 - - - +
629B LYS* 1.3 54.3 + - - -
630B ASP* 3.1 4.0 - - - -
631B TRP* 2.7 54.4 + - + +
632B VAL* 3.7 4.7 + - - +
640B LEU* 5.3 1.4 - - + +
667B LEU* 4.2 13.7 - - + +
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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
------------------------------------------------------------
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