Contacts of the helix formed by residues 653 - 666 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379B THR 5.8 3.6 - - - +
381B HIS* 4.8 3.6 - - - +
603B ASN* 4.0 11.0 - - + +
604B GLY 3.9 3.6 - - - -
606B VAL* 5.1 1.3 - - - -
651B ALA* 3.8 7.4 - - - +
652B PRO* 1.3 90.3 - - + +
654B PRO* 1.3 76.3 - - - +
655B SER* 3.3 11.9 + - - -
656B ALA* 3.0 28.6 + - - +
657B MET 3.1 9.4 + - - -
110C GLY 5.8 2.2 - - - +
111C ARG* 4.4 12.7 + - + +
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Residues in contact with PRO 654 (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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602B GLU 3.3 24.5 - - - +
603B ASN* 3.9 7.6 - - - -
604B GLY 3.5 14.8 - - - +
606B VAL* 5.0 11.2 - - + -
653B THR* 1.3 87.8 - - - +
655B SER* 1.3 58.0 + - - +
657B MET* 3.1 10.9 + - + +
658B HIS* 2.9 27.9 + - - +
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Residues in contact with SER 655 (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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653B THR* 3.1 11.1 + - - -
654B PRO* 1.3 80.4 - - - +
656B ALA* 1.3 57.8 + - - +
658B HIS* 3.1 10.3 + - - +
659B GLU* 3.0 32.3 + - - +
111C ARG* 3.9 13.2 - - - -
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Residues in contact with ALA 656 (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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635B THR* 3.4 18.0 - - - +
637B VAL* 3.5 7.1 - - + +
652B PRO* 3.4 32.1 - - + -
653B THR* 3.0 12.2 + - - +
655B SER* 1.3 76.7 - - - +
657B MET* 1.3 58.7 + - - +
659B GLU* 3.3 3.4 + - - +
660B ALA* 2.9 28.4 + - - +
111C ARG* 3.7 22.8 - - - +
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Residues in contact with MET 657 (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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606B VAL* 3.7 18.6 - - + -
608B GLU* 3.2 48.7 - - + +
610B VAL* 6.0 4.3 - - + -
649B VAL* 3.9 31.0 - - + +
651B ALA* 3.5 24.6 - - + +
653B THR 3.1 6.4 + - - +
654B PRO* 3.4 9.4 - - + +
656B ALA* 1.3 76.2 - - - +
658B HIS* 1.3 58.2 + - - +
660B ALA* 3.5 4.9 - - - +
661B ARG* 2.8 40.4 + - + +
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Residues in contact with HIS 658 (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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654B PRO 2.9 12.1 + - - +
655B SER* 3.3 12.8 - - - +
657B MET* 1.3 75.1 - - - +
659B GLU* 1.3 65.8 + - + +
661B ARG* 2.8 51.8 + - - +
662B ASP* 2.8 35.9 + - - -
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Residues in contact with GLU 659 (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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634B GLU 4.0 10.2 - - - +
635B THR* 3.9 12.4 - - + +
655B SER* 3.0 16.5 + - - +
656B ALA 3.3 4.7 + - - +
658B HIS* 1.3 77.6 - - + +
660B ALA* 1.3 57.5 + - - +
662B ASP* 3.5 6.7 + - - +
663B PHE* 2.9 30.0 + - - +
111C ARG* 2.5 43.2 + - - -
161C GLY 5.7 0.3 - - - +
206C ARG* 5.1 7.6 + - - -
207C LYS* 2.6 32.5 + - - +
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Residues in contact with ALA 660 (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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631B LEU* 4.0 15.3 - - + -
635B THR* 3.9 1.1 - - - +
637B VAL* 3.6 30.3 - - + -
649B VAL* 4.8 4.5 - - + -
656B ALA 2.9 16.9 + - - +
657B MET* 3.5 13.0 - - - +
659B GLU* 1.3 74.4 - - - +
661B ARG* 1.3 60.3 - - - +
662B ASP 3.1 1.3 - - - -
663B PHE* 3.1 2.1 + - - +
664B ILE* 2.9 38.3 + - + +
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Residues in contact with ARG 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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657B MET* 2.8 39.2 + - + +
658B HIS* 2.8 52.4 + - - +
660B ALA* 1.3 72.0 - - - +
662B ASP* 1.3 62.9 + - - +
664B ILE* 4.0 10.5 - - - +
665B THR* 2.7 35.5 + - - -
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Residues in contact with ASP 662 (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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658B HIS* 2.8 48.0 + - - +
659B GLU* 3.7 6.8 - - - +
661B ARG* 1.3 87.0 + - - +
663B PHE* 1.3 65.0 + - - +
664B ILE 3.1 2.4 + - - -
665B THR* 3.2 16.3 + - - -
666B GLU* 3.2 14.3 + - - +
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Residues in contact with PHE 663 (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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627B ASN* 4.1 7.6 - - + -
630B LYS* 4.0 26.7 - - + -
631B LEU* 3.2 50.0 - - + -
634B GLU* 4.0 18.2 - - + -
635B THR* 4.6 5.2 - - + -
659B GLU 2.9 19.4 + - - +
660B ALA 3.1 3.8 + - - +
662B ASP* 1.3 75.3 - - - +
664B ILE* 1.3 62.2 + - + +
666B GLU* 3.7 28.4 + - - +
667B ILE* 4.3 18.8 - - + +
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Residues in contact with ILE 664 (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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610B VAL* 4.8 17.9 - - + -
620B PHE* 4.0 30.5 - - + -
631B LEU* 4.3 21.1 - - + -
649B VAL* 4.7 18.8 - - + -
660B ALA* 2.9 24.3 + - + +
661B ARG* 4.0 7.9 - - - +
663B PHE* 1.3 75.6 - - + +
665B THR* 1.3 61.5 + - - +
666B GLU 3.1 2.0 - - - -
667B ILE* 2.8 32.1 + - + +
668B CYS* 3.3 22.1 + - - -
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Residues in contact with THR 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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661B ARG 2.7 21.1 + - - -
662B ASP* 3.2 11.1 + - - -
664B ILE* 1.3 80.5 - - - +
666B GLU* 1.3 56.6 + - - +
667B ILE 2.9 3.5 + - - -
668B CYS* 2.7 29.3 + - - +
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Residues in contact with GLU 666 (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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619B LYS* 4.9 1.1 + - - -
662B ASP 3.2 8.6 + - - +
663B PHE* 3.8 22.3 - - - +
664B ILE 3.1 1.2 - - - -
665B THR* 1.3 75.8 - - - +
667B ILE* 1.3 65.0 + - - +
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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