Contacts of the helix formed by residues 653 - 664 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A THR 6.0 2.0 - - - +
381A HIS* 4.7 4.3 - - - +
603A ASN* 3.5 14.4 - - + +
604A GLY 3.8 3.4 - - - -
606A VAL* 4.4 3.8 - - - -
651A ALA* 3.2 7.9 - - - +
652A PRO* 1.3 89.6 - - + +
654A PRO* 1.3 74.6 - - - +
655A SER* 3.3 11.3 + - - -
656A ALA* 3.1 21.5 + - - +
657A MET* 3.2 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 654 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A GLU 3.7 17.5 - - - +
603A ASN* 3.6 12.1 - - - +
604A GLY 3.5 14.1 - - - +
606A VAL* 4.4 16.8 - - + -
653A THR* 1.3 87.5 - - - +
655A SER* 1.3 58.2 + - - +
657A MET* 3.3 3.9 + - + +
658A HIS* 2.9 29.0 + - - +
661A ARG* 4.5 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 655 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653A THR* 3.2 9.9 + - - -
654A PRO* 1.3 77.6 - - - +
656A ALA* 1.3 66.4 + - - +
658A HIS* 3.3 7.0 + - - +
659A GLU* 3.1 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 656 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A THR* 3.7 19.4 - - - +
637A VAL* 3.7 6.6 - - + +
652A PRO* 3.4 33.9 - - + -
653A THR* 3.1 16.2 + - - +
655A SER* 1.3 76.9 - - - +
657A MET* 1.3 57.1 + - - +
659A GLU* 3.2 12.3 + - - +
660A ALA* 2.8 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 657 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A VAL* 3.4 40.8 - - + +
608A GLU* 3.4 48.5 - - + +
649A VAL* 3.6 29.2 - - + +
651A ALA* 3.4 20.6 - - + +
653A THR 3.2 5.9 + - - +
654A PRO* 3.6 7.9 - - + +
655A SER 3.3 0.2 - - - -
656A ALA* 1.3 77.9 - - - +
658A HIS* 1.3 53.7 + - - +
660A ALA* 3.1 7.0 + - - +
661A ARG* 2.6 51.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 658 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A PRO 2.9 13.6 + - - +
655A SER* 3.5 12.3 - - - +
657A MET* 1.3 75.6 - - - +
659A GLU* 1.3 62.8 + - + +
661A ARG* 3.0 33.9 + - - +
662A ASP* 3.0 43.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 659 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A GLU 4.4 4.0 - - - +
635A THR* 4.2 28.1 - - + +
655A SER* 3.1 22.2 + - - +
656A ALA* 3.5 9.6 - - - +
658A HIS* 1.3 76.6 - - + +
660A ALA* 1.3 57.8 + - - +
662A ASP* 3.2 10.0 + - - +
663A PHE* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 660 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A LEU* 4.1 16.2 - - + -
635A THR* 4.2 1.9 - - - +
637A VAL* 3.5 40.4 - - + -
649A VAL* 4.7 9.0 - - + -
656A ALA 2.8 9.7 + - - -
657A MET* 3.5 9.6 - - - +
659A GLU* 1.3 73.6 - - - +
661A ARG* 1.3 58.6 + - - +
663A PHE* 3.2 0.5 + - - +
664A ILE* 2.9 39.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 661 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A GLU* 3.4 29.8 + - - +
610A VAL* 6.0 3.6 - - + -
654A PRO 4.5 3.2 + - - -
657A MET* 2.6 35.0 + - + +
658A HIS* 3.0 51.0 + - - +
660A ALA* 1.3 73.3 - - - +
662A ASP* 1.3 61.3 + - - +
664A ILE* 3.9 7.6 - - + +
665A THR* 2.9 28.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 662 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A HIS* 3.0 39.2 + - - +
659A GLU* 3.6 10.8 - - - +
661A ARG* 1.3 79.2 + - - +
663A PHE* 1.3 65.0 + - - +
664A ILE 3.2 0.9 - - - -
665A THR* 3.1 26.4 + - + +
666A GLU* 4.0 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 663 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627A ASN* 3.9 30.1 - - + -
630A LYS* 4.4 12.1 - - + -
631A LEU* 3.3 50.9 - - + -
634A GLU* 4.0 22.4 - - + -
635A THR* 4.9 5.2 - - + -
659A GLU 2.9 13.6 + - - +
660A ALA 3.8 0.2 - - - +
662A ASP* 1.3 77.0 - - - +
664A ILE* 1.3 62.5 + - + +
665A THR 3.6 0.2 + - - -
666A GLU* 3.9 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 664 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A VAL* 4.5 22.0 - - + -
620A PHE* 3.6 41.4 - - + -
631A LEU* 3.9 25.6 - - + -
639A ILE* 4.2 7.9 - - + -
649A VAL* 4.6 12.6 - - + -
660A ALA* 2.9 22.2 + - + +
661A ARG* 4.2 6.3 - - + +
663A PHE* 1.3 75.0 - - + +
665A THR* 1.3 58.1 + - - +
666A GLU* 3.1 24.1 + - - +
----------------------------------------------------------
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