Contacts of the helix formed by residues 651 - 669 (chain B) in PDB entry 4XUF
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 ASP 651 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649B LYS 3.7 3.9 + - - +
650B ALA* 1.3 74.7 - - - +
652B SER* 1.3 82.3 + - - +
653B SER* 3.1 8.5 + - - +
654B GLU* 2.9 31.3 + - - +
655B ARG* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 652 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651B ASP* 1.3 86.7 + - - +
653B SER* 1.3 58.0 + - - +
655B ARG* 2.9 38.6 + - - +
656B GLU* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 653 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651B ASP* 4.2 8.9 + - - +
652B SER* 1.3 77.3 - - - +
654B GLU* 1.3 87.3 + - - +
656B GLU* 3.9 7.3 + - - +
657B ALA* 3.6 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 654 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B PHE* 3.9 41.0 - - + -
646B LEU* 3.9 9.6 - - + -
649B LYS 5.6 0.2 - - - -
650B ALA* 3.9 14.1 - - + -
651B ASP* 2.9 24.4 + - - +
653B SER* 1.3 100.5 + - - +
655B ARG* 1.3 67.5 + - - +
657B ALA* 3.3 19.9 + - - +
658B LEU* 3.4 14.6 - - - +
832B LEU* 4.5 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 655 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B LEU* 3.8 19.7 - - + +
650B ALA 4.1 10.8 + - - -
651B ASP* 3.1 20.5 + - - +
652B SER* 2.9 43.2 + - - +
654B GLU* 1.3 77.3 - - - +
656B GLU* 1.3 63.8 - - + +
658B LEU* 3.1 7.0 + - - +
659B MET* 3.1 28.9 + - + +
687B ILE* 4.5 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 656 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652B SER* 3.0 28.9 + - - +
653B SER* 4.2 7.4 - - - +
654B GLU 3.3 0.2 - - - -
655B ARG* 1.3 78.0 - - + +
657B ALA* 1.3 56.6 + - - +
659B MET* 3.7 14.2 - - - +
660B SER* 3.0 32.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 657 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653B SER 3.6 11.9 + - - +
654B GLU* 3.3 14.1 + - - +
655B ARG 3.1 0.4 - - - -
656B GLU* 1.3 80.0 - - - +
658B LEU* 1.3 57.5 + - - +
660B SER* 3.0 18.5 + - - -
661B GLU* 3.2 18.3 + - - +
832B LEU* 3.8 22.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 658 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644B LYS* 4.2 28.9 - - + +
645B MET* 4.2 7.4 - - - +
646B LEU* 3.5 37.2 - - + -
654B GLU 3.4 14.6 - - - +
655B ARG* 3.1 8.8 + - - +
657B ALA* 1.3 77.1 - - - +
659B MET* 1.3 61.0 + - - +
661B GLU* 3.2 12.8 + - - +
662B LEU* 2.8 29.9 + - - +
687B ILE* 4.4 16.8 - - + +
689B LEU* 4.3 17.2 - - + +
832B LEU* 3.5 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 659 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655B ARG* 3.1 21.4 + - + +
656B GLU* 3.2 18.8 + - - +
658B LEU* 1.3 78.3 - - - +
660B SER* 1.3 56.7 + - - +
662B LEU* 3.2 9.6 + - + +
663B LYS* 3.0 32.6 + - - +
682B THR* 5.2 12.3 - - + -
687B ILE* 3.8 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 660 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656B GLU 3.0 14.1 + - - -
657B ALA* 3.0 17.8 + - - -
659B MET* 1.3 76.3 - - - +
661B GLU* 1.3 57.3 + - - +
663B LYS* 3.5 9.3 + - - +
664B MET* 3.1 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 661 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644B LYS* 2.6 37.1 + - - +
657B ALA 3.2 16.3 + - - +
658B LEU* 3.2 9.8 + - - +
659B MET 3.2 0.6 - - - -
660B SER* 1.3 82.7 + - - +
662B LEU* 1.3 59.0 + - - +
664B MET* 3.6 13.2 + - + +
665B MET* 3.2 32.1 + - + +
689B LEU* 4.3 11.6 - - + +
691B PHE* 4.9 0.5 - - - -
832B LEU* 4.2 10.4 - - - +
1001B P30 2.4 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 662 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B ASP* 3.8 26.7 - - + +
658B LEU 2.8 16.2 + - - +
659B MET* 3.2 10.5 + - + +
661B GLU* 1.3 74.3 - - - +
663B LYS* 1.3 63.3 + - - +
664B MET 3.1 2.5 + - - -
665B MET* 3.4 2.6 + - + +
666B THR* 3.4 23.9 + - + +
677B LEU* 3.7 26.2 - - + -
680B ALA* 3.8 27.4 - - + -
682B THR* 3.9 15.0 - - + -
687B ILE* 4.7 2.9 - - + -
689B LEU* 3.7 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 663 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B ASP* 5.3 11.4 - - + +
659B MET 3.0 18.5 + - - +
660B SER* 3.9 8.7 - - - +
661B GLU 3.5 0.2 - - - -
662B LEU* 1.3 76.7 - - + +
664B MET* 1.3 59.9 + - - +
666B THR* 3.3 19.5 - - + +
667B GLN* 3.3 18.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 664 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660B SER 3.1 15.0 + - - +
661B GLU* 3.7 19.1 - - + +
662B LEU 3.1 0.2 - - - -
663B LYS* 1.3 76.3 - - - +
665B MET* 1.3 61.2 + - + +
667B GLN* 3.5 2.2 + - - +
668B LEU* 2.9 46.5 + - + +
807B CYS* 5.7 9.4 - - - -
1001B P30 3.3 44.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 665 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B TRP* 5.9 0.7 - - - -
661B GLU* 3.2 17.6 + - + +
662B LEU* 3.4 4.0 + - - +
664B MET* 1.3 80.0 - - + +
666B THR* 1.3 61.4 + - - +
667B GLN 3.4 0.7 + - - -
668B LEU* 3.5 12.8 + - - +
669B GLY* 3.6 13.5 + - - +
674B ILE* 5.7 2.0 - - - -
675B VAL* 4.5 12.1 - - + +
677B LEU* 3.8 28.3 - - + +
689B LEU* 5.3 0.2 - - + -
691B PHE* 3.7 36.1 - - + -
1001B P30 2.8 67.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 666 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B ASP* 4.2 19.6 + - + +
601B LEU* 5.3 2.6 - - - +
603B TRP* 2.6 53.5 + - - +
662B LEU* 3.4 13.2 + - - +
663B LYS* 3.3 20.2 - - - +
665B MET* 1.3 79.5 - - - +
667B GLN* 1.3 77.9 + - + +
669B GLY* 4.1 6.4 + - - -
677B LEU* 4.3 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 667 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B ASP 5.7 0.2 + - - -
601B LEU* 4.9 11.8 - - - +
663B LYS* 3.3 19.7 - - + +
664B MET* 3.5 3.0 + - - +
665B MET 3.2 0.4 - - - -
666B THR* 1.3 93.9 + - + +
668B LEU* 1.3 63.7 + - - +
669B GLY* 3.1 3.9 + - - -
805B LYS* 4.1 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 668 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664B MET* 2.9 30.4 + - + +
665B MET* 3.5 8.5 + - - +
667B GLN* 1.3 76.7 - - - +
669B GLY* 1.3 70.0 + - - +
674B ILE* 3.8 24.0 - - + -
801B PHE* 3.2 43.2 - - + -
802B LEU* 4.3 16.6 - - + -
805B LYS* 3.3 24.4 - - + +
807B CYS* 4.1 25.1 - - + -
1001B P30 4.5 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 669 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B TRP* 6.4 2.7 - - - -
665B MET 3.6 11.9 + - - +
666B THR 4.1 5.8 + - - -
667B GLN 3.1 5.4 - - - -
668B LEU* 1.3 97.1 - - - +
670B SER* 1.3 63.6 + - - -
671B HIS 3.8 1.2 + - - -
674B ILE* 4.8 2.3 - - - +
801B PHE* 4.2 3.1 - - - -
805B LYS* 5.4 1.8 - - - -
----------------------------------------------------------
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