Contacts of the helix formed by residues 653 - 668 (chain C) in PDB entry 3U1K
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 653 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379C THR* 5.7 7.9 - - + +
381C HIS* 4.6 4.7 - - - +
603C ASN* 4.0 9.4 - - + +
604C GLY 3.5 3.4 - - - -
606C VAL* 4.4 2.2 - - - +
651C ALA* 3.1 8.3 - - - +
652C PRO* 1.3 93.6 - - + +
654C PRO* 1.3 75.6 - - - +
655C SER* 3.5 8.0 + - - -
656C ALA* 3.0 25.1 + - - +
657C MET* 3.2 16.8 + - - +
110D GLY 6.1 1.1 - - - +
111D ARG* 4.4 10.8 + - + +
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Residues in contact with PRO 654 (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 GLU 3.6 20.9 - - - +
603C ASN* 3.5 15.7 - - + +
604C GLY 3.1 14.6 - - - +
606C VAL* 4.8 13.0 - - + -
653C THR* 1.3 85.5 - - - +
655C SER* 1.3 65.7 + - - +
657C MET* 3.2 9.1 + - + +
658C HIS* 3.1 39.7 + - + +
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Residues in contact with SER 655 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653C THR* 3.3 8.8 + - - -
654C PRO* 1.3 79.4 - - - +
656C ALA* 1.3 63.8 + - - +
658C HIS* 3.1 20.5 + - - +
659C GLU* 3.2 21.4 + - - +
111D ARG* 4.5 12.3 - - - -
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Residues in contact with ALA 656 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635C THR* 3.9 5.7 - - - +
637C VAL* 3.6 6.2 - - + +
651C ALA* 4.1 1.8 - - + -
652C PRO* 3.7 20.2 - - + -
653C THR* 3.0 23.9 + - - +
655C SER* 1.3 77.2 - - - +
657C MET* 1.3 62.6 + - - +
658C HIS 3.2 0.2 + - - -
659C GLU* 3.4 3.3 + - - +
660C ALA* 3.1 22.2 + - - +
111D ARG* 3.6 35.2 - - - +
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Residues in contact with MET 657 (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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606C VAL* 3.3 46.9 - - + +
608C GLU* 3.5 47.3 - - + +
649C VAL* 3.5 34.8 - - + +
651C ALA* 3.5 15.6 - - + +
653C THR 3.2 4.6 + - - +
654C PRO* 3.2 9.2 + - + +
656C ALA* 1.3 78.8 - - - +
658C HIS* 1.3 58.5 + - + +
660C ALA* 3.3 5.6 + - - +
661C ARG* 2.8 39.3 + - - +
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Residues in contact with HIS 658 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654C PRO* 3.1 28.7 + - + +
655C SER* 3.1 11.6 + - - +
657C MET* 1.3 75.0 - - + +
659C GLU* 1.3 66.8 + - + +
661C ARG* 2.9 47.0 + - - +
662C ASP* 2.9 31.7 + - - +
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Residues in contact with GLU 659 (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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634C GLU 4.3 1.9 - - - +
635C THR* 3.8 19.6 - - + +
655C SER* 3.2 12.0 + - - +
656C ALA 3.8 4.9 - - - +
658C HIS* 1.3 77.4 - - + +
660C ALA* 1.3 56.9 + - - +
662C ASP* 3.6 9.4 + - - +
663C PHE* 2.9 28.1 + - - +
111D ARG* 2.6 34.7 + - - -
206D ARG* 2.5 35.2 + - - -
207D LYS* 5.7 3.6 - - + +
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Residues in contact with ALA 660 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631C LEU* 3.9 17.7 - - + +
635C THR* 3.8 7.1 - - - +
637C VAL* 3.6 24.7 - - + -
649C VAL* 4.8 8.7 - - + -
656C ALA 3.1 12.5 + - - +
657C MET* 3.5 9.2 - - - +
658C HIS 3.1 0.8 - - - -
659C GLU* 1.3 76.5 - - - +
661C ARG* 1.3 60.2 + - - +
663C PHE* 3.7 1.0 - - - +
664C ILE* 2.9 39.8 + - + +
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Residues in contact with ARG 661 (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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608C GLU* 2.4 45.3 + - - +
657C MET* 2.8 23.1 + - + +
658C HIS* 2.9 48.5 + - - +
660C ALA* 1.3 74.8 - - - +
662C ASP* 1.3 65.6 + - - +
664C ILE* 3.4 9.3 + - + +
665C THR* 3.0 29.9 + - - +
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Residues in contact with ASP 662 (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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658C HIS* 2.9 14.9 + - - +
659C GLU* 3.6 11.7 - - - +
661C ARG* 1.3 76.3 - - - +
663C PHE* 1.3 66.8 + - - +
664C ILE 3.1 0.3 + - - -
665C THR* 3.2 4.7 + - - -
666C GLU* 3.0 25.4 + - - +
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Residues in contact with PHE 663 (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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627C ASN* 3.8 14.8 - - + -
630C LYS* 4.4 13.2 - - + -
631C LEU* 3.6 52.9 - - + -
634C GLU* 3.6 28.5 - - - -
635C THR* 4.5 6.1 - - + -
659C GLU 2.9 19.1 + - - +
660C ALA 3.7 4.5 - - - +
662C ASP* 1.3 74.3 - - - +
664C ILE* 1.3 66.0 + - - +
666C GLU* 3.4 6.8 - - - +
667C ILE* 3.2 50.5 + - + +
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Residues in contact with ILE 664 (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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610C VAL* 4.2 34.8 - - + -
620C PHE* 3.9 33.9 - - + -
631C LEU* 4.2 22.0 - - + -
639C ILE* 4.8 0.2 - - + -
649C VAL* 4.6 11.7 - - + -
660C ALA* 2.9 25.1 + - + +
661C ARG* 3.6 8.1 - - + +
663C PHE* 1.3 73.8 - - + +
665C THR* 1.3 71.0 + - - +
666C GLU 3.0 2.6 + - - -
667C ILE* 3.2 12.2 - - + +
668C CYS* 3.1 24.8 + - - +
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Residues in contact with THR 665 (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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661C ARG* 3.0 21.8 + - - +
662C ASP* 3.8 5.6 - - - -
664C ILE* 1.3 76.2 - - - +
666C GLU* 1.3 65.7 + - - +
668C CYS* 3.2 21.2 + - - +
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Residues in contact with GLU 666 (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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662C ASP 3.0 12.7 + - - +
663C PHE* 3.4 13.2 - - - +
664C ILE 3.0 0.2 - - - -
665C THR* 1.3 75.5 - - - +
667C ILE* 1.3 71.9 + - - +
668C CYS 3.0 11.8 + - - +
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Residues in contact with ILE 667 (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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619C LYS* 3.2 29.5 - - - +
620C PHE* 3.1 51.1 - - + +
627C ASN* 3.9 20.2 - - + +
628C LEU* 6.2 0.4 - - + -
631C LEU* 6.4 0.7 - - + -
663C PHE* 3.2 42.1 + - + +
664C ILE* 3.2 15.0 - - + +
666C GLU* 1.3 86.6 - - - +
668C CYS* 1.3 57.6 + - - +
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Residues in contact with CYS 668 (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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612C VAL* 5.3 5.4 - - - -
616C LYS* 4.6 29.5 + - + +
619C LYS* 4.1 22.2 + - - +
620C PHE* 3.9 35.2 - - - -
664C ILE* 3.1 22.9 + - - +
665C THR* 3.4 17.0 - - - +
666C GLU 3.0 6.6 - - - +
667C ILE* 1.3 82.4 - - - +
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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
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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