Contacts of the helix formed by residues 658 - 670 (chain B) in PDB entry 3UEO
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 GLY 658 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B ASP* 5.7 1.8 - - - -
657B ALA* 1.3 72.0 - - - +
659B ALA* 1.3 52.8 + - - -
661B LYS* 3.1 8.0 + - - +
662B GLU* 2.8 45.5 + - - +
706D GLU* 3.4 25.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 659 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614B THR* 4.2 9.6 - - + +
617B VAL* 3.7 33.0 - - + -
618B THR* 3.8 15.9 - - - +
621B ASP* 4.6 7.1 + - - +
657B ALA 3.3 1.2 + - - -
658B GLY* 1.3 67.8 - - - -
660B GLU* 1.3 66.3 + - - +
661B LYS 3.1 1.1 - - - -
662B GLU* 3.3 12.8 + - - +
663B SER* 2.9 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 660 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614B THR* 4.3 4.9 - - + +
618B THR* 4.3 9.5 + - + +
631B ASN* 2.7 33.5 + - - +
633B LEU* 3.7 16.8 - - + +
634B PHE* 6.2 2.2 - - + -
656B CYS* 4.8 5.5 - - + -
657B ALA 3.6 10.8 + - - +
659B ALA* 1.3 76.9 - - - +
661B LYS* 1.3 58.0 + - - +
663B SER 3.4 0.2 + - - -
664B LEU* 3.1 44.9 + - + +
698B LYS* 2.8 39.6 + - - -
718B ILE* 4.1 8.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 661 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653B PHE* 4.8 25.3 + - + +
656B CYS* 3.4 31.6 + - + +
657B ALA* 3.5 17.8 + - - +
658B GLY 3.1 10.9 + - - +
659B ALA 3.1 0.6 - - - -
660B GLU* 1.3 76.6 - - - +
662B GLU* 1.3 61.0 + - + +
663B SER 3.1 1.3 - - - -
664B LEU* 4.0 3.7 - - - +
665B THR* 2.8 40.9 + - - +
677B GLU* 3.1 34.2 + - - -
6E TPO 4.9 8.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 662 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A SER* 4.5 0.9 + - - -
570A ASN* 2.2 45.1 + - - +
573A ASN* 4.3 20.2 + - + +
574A ILE* 5.2 6.4 - - - +
577A GLU* 4.2 19.7 - - - +
658B GLY* 2.8 27.1 + - - +
659B ALA* 3.3 10.9 + - - +
661B LYS* 1.3 72.9 - - - +
663B SER* 1.3 57.6 + - - +
665B THR* 3.7 6.8 - - - -
666B PHE* 3.2 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 663 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A GLU* 4.4 5.0 + - - -
598B LEU* 4.1 14.9 - - - +
614B THR* 2.6 30.8 + - - +
633B LEU* 3.6 23.1 - - - -
659B ALA 2.9 13.1 + - - -
661B LYS 3.1 0.2 - - - -
662B GLU* 1.3 75.8 - - - +
664B LEU* 1.3 64.0 + - - +
665B THR 3.2 1.3 - - - -
666B PHE* 3.4 7.8 + - - +
667B LEU* 3.1 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 664 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633B LEU* 3.8 23.1 - - + -
653B PHE* 3.6 24.9 - - + -
656B CYS* 3.6 22.2 - - + -
660B GLU* 3.1 27.6 + - + +
661B LYS* 4.0 3.6 - - - +
663B SER* 1.3 73.6 - - - +
665B THR* 1.3 61.3 + - - +
667B LEU* 3.3 4.0 + - + +
668B ALA* 2.9 31.4 + - - +
718B ILE* 3.6 50.9 - - + -
721B LEU* 3.9 17.6 - - + +
722B LEU* 5.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 665 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A SER* 5.0 0.9 - - - +
573A ASN* 3.7 26.9 - - - +
653B PHE* 3.7 20.2 - - - -
661B LYS* 2.8 27.1 + - - +
662B GLU* 3.7 6.9 - - - -
664B LEU* 1.3 78.1 - - - +
666B PHE* 1.3 57.4 + - - +
668B ALA* 3.2 3.3 + - - +
669B ASN* 2.9 49.3 + - - +
675B VAL* 4.1 17.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 666 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A ASN* 3.6 25.1 - - + -
566A GLU* 3.5 47.6 - - + -
569A SER* 3.5 33.2 + - - +
598B LEU* 3.7 29.2 - - + -
599B LEU* 4.3 13.0 - - + -
662B GLU 3.2 10.3 + - - +
663B SER* 3.5 7.4 - - - +
665B THR* 1.3 78.9 - - - +
667B LEU* 1.3 51.7 + - - +
669B ASN* 3.4 4.7 + - + +
670B LEU* 2.7 62.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 667 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B LEU* 4.0 18.2 - - + -
599B LEU* 4.4 6.7 - - + -
633B LEU* 4.1 17.3 - - + -
637B VAL* 4.3 6.5 - - + -
639B VAL* 4.2 25.8 - - + -
663B SER 3.1 15.4 + - - +
664B LEU* 3.5 8.7 - - - +
666B PHE* 1.3 78.7 - - + +
668B ALA* 1.3 65.2 + - - +
670B LEU* 3.1 10.3 + - + +
671B LEU* 3.0 31.8 + - + +
721B LEU* 3.9 16.2 - - + -
722B LEU* 3.5 31.6 - - + -
725B ALA* 5.1 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 668 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651B ILE* 4.3 9.9 - - + -
653B PHE* 4.2 9.9 - - + -
664B LEU 2.9 16.8 + - - +
665B THR 3.6 0.2 - - - +
667B LEU* 1.3 75.5 - - - +
669B ASN* 1.3 64.2 + - - +
671B LEU* 3.2 9.3 + - - +
673B ALA* 3.0 33.7 + - + +
675B VAL* 3.5 24.7 - - + -
721B LEU* 4.1 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 669 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A SER* 5.1 2.9 + - - +
573A ASN* 5.4 0.9 - - - +
665B THR* 2.9 38.5 + - - +
666B PHE* 3.8 5.8 - - + +
668B ALA* 1.3 75.5 - - - +
670B LEU* 1.3 58.9 + - - +
672B GLY* 2.8 22.3 + - - -
673B ALA 3.2 19.0 + - - +
674B SER* 4.0 2.4 - - - +
675B VAL* 3.9 19.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 670 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A ASN* 4.7 12.3 - - + +
599B LEU* 3.7 30.3 - - + -
639B VAL* 4.7 13.2 - - + -
643B MET 3.9 9.5 - - - +
644B THR* 4.3 6.4 - - - +
666B PHE* 2.7 46.1 + - + +
667B LEU* 3.1 15.9 + - + +
669B ASN* 1.3 74.2 - - - +
671B LEU* 1.3 61.0 + - + +
672B GLY 3.3 3.1 + - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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