Contacts of the helix formed by residues 659 - 673 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610C TRP* 3.7 0.7 - - - -
614C ARG* 4.9 2.0 - - - +
657C GLN 3.6 1.6 + - - -
658C VAL* 1.3 76.9 - - - +
660C TYR* 1.3 54.3 + - - +
661C GLU* 3.3 9.2 + - - +
662C GLU* 2.9 40.8 + - - +
663C TYR* 2.7 33.1 + - - +
700C ALA 4.8 2.8 + - - -
704C ARG* 3.9 21.8 - - - +
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Residues in contact with TYR 660 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766B ASN* 5.2 7.2 - - + -
537C GLU* 3.8 37.0 + - + +
540C GLU* 3.7 27.3 - - + +
610C TRP* 3.5 36.4 - + + -
614C ARG* 4.9 4.3 - - - +
659C SER* 1.3 74.0 - - - +
661C GLU* 1.3 59.8 + - + +
663C TYR* 3.4 20.2 - + - +
664C LEU* 3.2 40.4 + - + +
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Residues in contact with GLU 661 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766B ASN* 4.0 22.1 - - + +
533C VAL* 3.3 40.7 - - + +
537C GLU* 4.2 9.9 - - - +
659C SER* 3.1 7.7 + - - +
660C TYR* 1.3 79.4 - - + +
662C GLU* 1.3 67.4 + - - +
664C LEU* 3.5 5.2 + - - +
665C CYS* 3.2 26.0 + - - -
700C ALA* 4.1 18.3 - - + +
703C LYS* 5.1 10.5 - - - +
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Residues in contact with GLU 662 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658C VAL* 3.5 8.2 - - + -
659C SER* 2.9 39.7 + - - +
661C GLU* 1.3 75.9 - - - +
663C TYR* 1.3 65.4 + - - +
665C CYS* 2.9 15.6 + - - +
666C MET* 3.0 16.7 + - - +
697C LEU* 4.2 12.1 - - + -
700C ALA* 3.8 22.4 - - + +
701C ILE* 3.5 25.9 - - - +
704C ARG* 3.7 7.6 + - - -
714C ARG* 2.9 40.5 + - - -
718C LEU* 4.0 7.9 - - + -
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Residues in contact with TYR 663 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C JZN 4.1 1.7 + - - -
540C GLU* 4.0 7.1 + - + -
606C PHE* 3.3 43.7 - + - -
607C ALA* 3.6 19.8 + - - +
610C TRP* 3.1 62.3 - + + +
611C ARG* 6.0 0.3 - - - +
658C VAL* 3.7 8.1 - - + +
659C SER 2.7 20.2 + - - +
660C TYR* 3.4 21.8 - + - +
662C GLU* 1.3 72.6 - - - +
664C LEU* 1.3 87.1 + - + +
666C MET* 3.4 2.0 + - - -
667C LYS* 3.0 40.6 + - - +
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Residues in contact with LEU 664 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533C VAL* 4.2 4.5 - - + +
536C LEU* 3.7 20.6 - - + +
537C GLU* 3.6 45.1 - - + +
540C GLU* 3.1 30.3 - - - +
577C TRP* 5.3 0.3 - - - -
660C TYR* 3.2 27.2 + - + +
661C GLU* 3.9 7.4 - - - +
662C GLU 3.2 1.0 - - - -
663C TYR* 1.3 94.2 - - + +
665C CYS* 1.3 67.7 + - - +
667C LYS* 3.0 9.6 + - - +
668C THR* 3.0 26.2 + - - -
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Residues in contact with CYS 665 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533C VAL* 5.4 6.3 - - - -
536C LEU* 4.5 13.5 - - - -
661C GLU 3.2 16.6 - - - -
662C GLU 2.9 6.4 + - - +
664C LEU* 1.3 76.8 - - - +
666C MET* 1.3 65.3 + - - +
668C THR* 2.9 17.4 + - - +
669C LEU* 3.1 17.4 + - - +
693C TYR* 4.4 7.1 - - - +
696C GLU* 3.6 40.8 - - + -
697C LEU* 3.8 23.8 - - + +
700C ALA* 4.6 2.9 - - - -
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Residues in contact with MET 666 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606C PHE* 3.5 35.2 - - + -
653C LEU* 5.0 1.1 - - + -
658C VAL* 4.4 13.9 - - - -
662C GLU 3.0 13.2 + - - +
663C TYR 3.6 3.4 - - - +
665C CYS* 1.3 75.0 - - - +
667C LYS* 1.3 59.4 + - - +
669C LEU* 3.4 10.4 + - - +
670C LEU* 3.3 26.9 + - - +
697C LEU* 3.7 20.4 - - + +
718C LEU* 3.6 57.9 - - + +
721C LEU* 4.4 13.9 - - + -
722C LEU* 3.6 17.4 - - + +
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Residues in contact with LYS 667 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C JZN 4.4 14.5 + - + +
540C GLU* 3.0 41.0 + - - -
541C PRO* 4.5 1.8 - - - +
577C TRP* 3.5 30.9 - - + +
603C LEU* 3.2 44.4 - - + +
606C PHE* 3.9 14.6 - - + -
607C ALA* 4.6 7.0 - - + -
663C TYR* 3.0 41.5 + - + +
664C LEU* 3.0 10.5 + - - +
666C MET* 1.3 74.0 - - - +
668C THR* 1.3 65.9 + - - +
669C LEU 3.1 2.4 + - - -
670C LEU* 3.2 4.3 + - - +
671C LEU 3.2 5.5 + - - -
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Residues in contact with THR 668 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536C LEU* 3.5 22.5 - - - +
577C TRP* 3.6 16.1 - - + -
581C ILE* 4.0 17.0 - - + -
664C LEU 3.0 11.7 + - - -
665C CYS* 2.9 9.5 + - - -
667C LYS* 1.3 75.3 - - - +
669C LEU* 1.3 57.1 + - - +
671C LEU* 3.2 19.6 - - + +
672C LEU* 3.3 14.5 + - + +
693C TYR* 3.7 42.2 - - + -
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Residues in contact with LEU 669 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665C CYS 3.1 16.5 + - - +
666C MET* 3.6 11.7 - - - +
667C LYS 3.1 0.8 - - - -
668C THR* 1.3 72.3 - - - +
670C LEU* 1.3 52.8 + - - +
671C LEU 2.9 4.9 - - - -
672C LEU* 2.5 11.0 + - + +
673C SER* 2.5 39.2 + - - -
690C ARG* 3.8 22.0 - - + +
693C TYR* 3.9 13.9 - - + +
694C ILE* 3.8 33.7 - - + +
697C LEU* 4.3 15.7 - - + -
722C LEU* 3.5 32.3 - - + -
774C PHE* 4.7 11.4 - - + -
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Residues in contact with LEU 670 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599C SER* 3.5 9.0 - - - +
602C TYR* 3.4 34.2 - - + +
603C LEU* 4.2 7.6 - - + -
606C PHE* 3.5 44.4 - - + -
666C MET 3.3 14.6 + - - +
667C LYS 3.2 7.7 + - - +
669C LEU* 1.3 75.0 - - - +
671C LEU* 1.3 57.9 + - - +
673C SER* 3.0 21.0 + - - +
722C LEU* 3.6 22.0 - - + +
725C MET* 3.4 40.2 - - + -
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Residues in contact with LEU 671 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577C TRP* 3.8 25.4 - - + -
578C ALA* 4.3 9.2 - - + -
581C ILE* 4.3 11.9 - - + -
584C PHE* 4.1 21.5 - - + -
595C LEU* 3.6 27.5 - - + +
596C LEU* 4.4 12.8 - - + -
599C SER* 3.1 35.0 - - - +
603C LEU* 3.9 9.6 - - + +
667C LYS 3.2 7.9 + - - +
668C THR* 3.2 14.8 - - + +
669C LEU 2.9 0.2 - - - -
670C LEU* 1.3 78.3 - - - +
672C LEU* 1.3 67.4 + - + +
673C SER 3.3 3.2 + - - -
674C SER 4.6 1.9 + - - +
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Residues in contact with LEU 672 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584C PHE* 4.9 5.2 - - + -
587C LEU* 5.6 2.2 - - + -
595C LEU* 3.3 31.6 - - + -
668C THR* 3.6 15.3 - - + +
669C LEU* 2.5 15.6 + - + +
671C LEU* 1.3 81.9 - - + +
673C SER* 1.3 58.6 + - - +
674C SER 3.4 3.1 - - - -
686C PHE* 3.2 33.6 - - + +
689C ILE* 3.4 34.3 - - + -
690C ARG* 3.2 44.3 + - + +
693C TYR* 4.9 4.7 - - + -
772C LEU* 3.7 0.5 - - - +
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Residues in contact with SER 673 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602C TYR* 3.9 15.1 - - - -
669C LEU* 2.5 15.4 + - - -
670C LEU* 3.0 34.4 + - - -
671C LEU 3.3 1.0 - - - -
672C LEU* 1.3 73.0 - - - +
674C SER* 1.3 58.2 + - - +
690C ARG* 4.6 9.9 - - - +
722C LEU* 6.4 0.9 - - - -
726C HIS* 3.4 24.8 - - - -
772C LEU* 3.1 29.0 + - - +
774C PHE* 6.1 3.4 - - - -
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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
------------------------------------------------------------
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