Contacts of the helix formed by residues 659 - 672 (chain B) in PDB entry 3K23
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 659 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610B TRP* 3.6 3.4 - - - -
614B ARG* 4.9 2.9 - - - +
657B GLN 3.7 2.4 + - - -
658B VAL* 1.3 79.5 - - - +
660B TYR* 1.3 56.5 + - - +
661B GLU* 4.2 5.4 + - - +
662B GLU* 2.9 34.2 + - - +
663B TYR* 2.7 32.4 + - - +
700B ALA 4.9 1.9 + - - -
704B ARG* 5.7 2.8 - - - +
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Residues in contact with TYR 660 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B GLU* 3.9 40.6 + - + -
540B GLU* 3.7 27.6 - - + +
610B TRP* 3.4 39.0 - + + -
614B ARG* 4.5 5.1 - - - +
659B SER* 1.3 72.3 - - - +
661B GLU* 1.3 61.2 + - + +
663B TYR* 3.0 13.4 + + - +
664B LEU* 2.8 55.6 + - + +
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Residues in contact with GLU 661 (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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533B VAL* 4.0 35.1 - - + +
534B SER* 6.0 0.3 - - - -
537B GLU* 4.8 13.2 - - - +
659B SER* 3.3 5.7 + - - +
660B TYR* 1.3 79.1 - - + +
662B GLU* 1.3 62.3 + - - +
664B LEU* 3.6 6.5 + - + +
665B CYS* 3.2 29.3 + - - -
700B ALA* 4.2 22.1 - - + +
703B LYS* 5.0 12.1 - - - +
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Residues in contact with GLU 662 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658B VAL* 4.1 6.5 - - + -
659B SER* 2.9 31.1 + - - +
661B GLU* 1.3 74.0 - - - +
663B TYR* 1.3 68.0 + - - +
665B CYS 3.3 1.2 + - - -
666B MET* 2.9 29.7 + - - +
697B LEU* 3.4 17.5 - - + +
700B ALA* 3.9 23.3 - - + +
701B ILE* 3.2 26.2 - - + +
704B ARG* 5.0 5.3 - - - +
714B ARG* 3.1 43.4 + - - -
718B LEU* 3.8 8.7 - - + -
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Residues in contact with TYR 663 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B JZN 4.8 0.9 + - - -
540B GLU* 3.0 21.4 + - - -
606B PHE* 3.6 35.2 - + - -
607B ALA* 3.7 14.0 - - - +
610B TRP* 3.4 54.4 - + + +
653B LEU* 5.2 0.7 - - + -
658B VAL* 3.7 8.3 - - + +
659B SER 2.7 17.4 + - - +
660B TYR* 3.2 23.3 - + - +
662B GLU* 1.3 72.9 - - - +
664B LEU* 1.3 86.2 + - + +
666B MET* 3.2 7.1 + - - +
667B LYS* 2.9 45.3 + - + +
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Residues in contact with LEU 664 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B VAL* 4.4 8.1 - - + +
536B LEU* 4.0 13.8 - - + +
537B GLU* 3.5 39.0 - - + +
540B GLU* 3.8 20.2 - - + +
577B TRP* 5.4 0.7 - - - -
660B TYR* 2.8 51.6 + - + +
661B GLU* 3.9 8.5 - - - +
663B TYR* 1.3 99.7 - - + +
665B CYS* 1.3 55.6 + - - +
667B LYS* 3.4 6.1 + - - +
668B THR* 2.8 32.6 + - - -
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Residues in contact with CYS 665 (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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533B VAL* 4.2 14.6 - - - -
536B LEU* 4.4 7.2 - - - -
661B GLU 3.2 16.0 + - - +
664B LEU* 1.3 76.8 - - - +
666B MET* 1.3 65.3 - - - +
668B THR* 3.3 9.5 + - - -
669B LEU* 3.1 25.9 + - - +
693B TYR* 4.6 5.0 - - + +
696B GLU* 3.7 41.7 - - - -
697B LEU* 3.6 30.3 - - + +
700B ALA* 4.4 1.6 - - - -
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Residues in contact with MET 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606B PHE* 3.6 25.6 - - + -
653B LEU* 4.7 0.9 - - + -
658B VAL* 4.5 8.5 - - - -
662B GLU 2.9 26.5 + - - +
663B TYR 3.2 4.0 + - - +
665B CYS* 1.3 73.1 - - - +
667B LYS* 1.3 65.6 + - - +
669B LEU* 2.8 15.0 + - - +
670B LEU* 2.9 15.0 + - - +
697B LEU* 3.9 19.3 - - + -
718B LEU* 3.5 44.4 - - + +
721B LEU* 3.9 17.5 - - + -
722B LEU* 3.3 39.6 - - + +
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Residues in contact with LYS 667 (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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2B JZN 3.4 32.3 + - - +
540B GLU* 3.4 30.2 + - - -
541B PRO* 4.8 0.4 - - - +
577B TRP* 3.8 32.5 - - + +
603B LEU* 3.6 27.6 - - + +
606B PHE* 4.0 16.7 - - + -
607B ALA* 4.6 6.7 - - + -
663B TYR* 2.9 43.3 + - + +
664B LEU* 3.7 7.4 - - - +
666B MET* 1.3 74.7 - - - +
668B THR* 1.3 62.6 + - - +
670B LEU* 3.2 12.8 + - + +
671B LEU 3.2 9.4 + - - -
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Residues in contact with THR 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B LEU* 3.2 19.7 - - + +
577B TRP* 4.1 12.5 - - - -
581B ILE* 3.9 24.2 - - + -
664B LEU 2.8 17.4 + - - -
665B CYS 3.5 8.1 - - - -
666B MET 3.1 0.4 - - - -
667B LYS* 1.3 76.2 - - - +
669B LEU* 1.3 62.6 + - - +
671B LEU* 3.5 5.6 - - + +
672B LEU* 3.4 23.9 + - + +
693B TYR* 3.9 39.3 - - + -
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Residues in contact with LEU 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665B CYS 3.1 11.3 + - - +
666B MET 2.8 9.5 + - - +
668B THR* 1.3 74.7 - - - +
670B LEU* 1.3 56.7 + - - +
671B LEU 3.1 1.6 - - - -
672B LEU* 2.7 45.1 + - + +
673B SER* 3.1 4.9 + - - -
690B ARG* 3.6 26.3 + - + +
693B TYR* 3.5 43.7 - - + +
694B ILE* 4.1 9.2 - - + -
697B LEU* 4.9 11.7 - - + -
715B PHE* 6.6 0.2 - - + -
719B THR* 6.4 0.2 - - + -
722B LEU* 3.8 17.7 - - + -
774B PHE* 4.2 23.3 - - + -
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Residues in contact with LEU 670 (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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599B SER* 3.4 13.9 - - - -
602B TYR* 3.7 38.9 - - + +
603B LEU* 4.6 4.7 - - + -
606B PHE* 3.4 49.8 - - + -
666B MET 2.9 11.8 + - - +
667B LYS* 3.2 8.9 + - + +
669B LEU* 1.3 75.3 - - - +
671B LEU* 1.3 59.4 + - - +
673B SER* 2.8 27.1 + - - +
722B LEU* 4.1 25.1 - - + +
725B MET* 3.8 22.9 - - + -
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Residues in contact with LEU 671 (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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577B TRP* 3.2 40.2 - - + -
578B ALA* 4.0 10.1 - - + -
581B ILE* 3.7 18.2 - - + -
584B PHE* 4.6 14.4 - - + -
595B LEU* 4.0 30.2 - - + +
596B LEU* 4.2 21.1 - - + -
599B SER* 3.5 24.9 + - - +
603B LEU* 4.1 4.3 - - + +
667B LYS 3.2 4.9 + - - -
668B THR* 3.5 10.8 - - + +
669B LEU 3.1 0.4 - - - -
670B LEU* 1.3 78.4 - - - +
672B LEU* 1.3 66.3 + - + +
673B SER 3.5 1.3 + - - -
674B SER 5.2 0.7 + - - +
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Residues in contact with LEU 672 (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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584B PHE* 5.0 8.7 - - + -
587B LEU* 5.2 2.2 - - + -
595B LEU* 4.3 12.1 - - + -
668B THR* 3.4 19.1 - - + +
669B LEU* 2.7 24.5 + - + +
671B LEU* 1.3 82.0 - - + +
673B SER* 1.3 55.0 + - - -
674B SER 3.6 2.2 - - - -
686B PHE* 3.5 37.4 - - + -
689B ILE* 4.0 22.4 - - + -
690B ARG* 3.1 52.7 + - + +
693B TYR* 4.2 10.3 - - + -
772B LEU* 3.5 1.2 - - - +
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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