Contacts of the helix formed by residues 669 - 688 (chain F) in PDB entry 5JLH
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 669 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555F ASP* 2.7 34.9 + - - +
558F CYS* 4.0 17.7 - - - -
559F TRP* 4.0 11.2 - - + +
614F ASN* 3.3 28.5 - - - +
615F MET* 5.4 1.6 - - - -
616F ASP* 4.5 0.2 - - - -
663F ARG* 5.4 0.2 + - - -
667F PHE 3.5 13.2 - - - +
668F ARG* 1.3 73.9 - - - +
670F VAL* 1.3 65.5 + - - +
672F GLN* 2.9 29.1 + - - +
673F LEU* 2.9 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 670 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288F LYS* 4.6 8.5 - - + +
289F SER* 5.3 7.2 - - - -
445F LYS* 3.3 33.7 - - - +
490F PHE* 3.3 31.9 - - + -
613F LYS 3.4 15.9 - - - +
614F ASN* 3.0 17.8 + - - +
616F ASP* 3.7 13.2 - - + +
669F THR* 1.3 70.7 - - - +
671F GLY* 1.3 70.4 + - - +
673F LEU* 3.3 10.5 + - - +
674F TYR* 2.9 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 671 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490F PHE* 4.3 12.6 - - - -
494F CYS* 5.3 0.7 - - - -
551F LEU* 4.3 24.4 - - - +
555F ASP* 4.9 3.4 - - - -
614F ASN* 3.3 8.5 + - - -
669F THR* 3.2 0.8 - - - -
670F VAL* 1.3 87.3 - - - +
672F GLN* 1.3 55.8 + - - +
674F TYR* 3.6 6.4 - - - +
675F LYS* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 672 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A GLU* 4.3 16.8 + - - +
3A GLU* 4.8 11.4 + - - +
552F ALA* 6.1 0.7 - - - -
555F ASP* 3.7 12.0 + - - +
663F ARG* 3.9 27.3 + - - +
668F ARG* 5.5 1.6 - - - -
669F THR* 2.9 31.0 + - - +
671F GLY* 1.3 77.5 - - - +
673F LEU* 1.3 58.2 + - + +
675F LYS* 3.2 18.6 + - - +
676F GLU* 2.9 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 673 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288F LYS* 3.4 21.8 - - - +
449F GLU* 5.5 1.8 - - - +
616F ASP* 3.2 27.4 - - - +
664F ARG* 5.5 5.6 - - - -
668F ARG* 3.3 37.2 - - + +
669F THR 2.9 18.6 + - - +
670F VAL* 3.8 6.7 - - - +
672F GLN* 1.3 78.3 - - + +
674F TYR* 1.3 58.0 + - - +
676F GLU* 3.1 14.3 + - - +
677F SER* 2.9 30.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 674 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285F LEU* 2.9 44.2 - - + +
286F LEU 4.3 17.3 - - - -
287F GLU* 5.5 5.6 - - + -
494F CYS* 3.0 60.0 + - + -
495F ILE* 3.8 10.1 + - + +
497F TYR* 4.6 13.7 - + - -
498F THR* 3.2 10.0 - - - +
551F LEU* 5.7 3.6 - - + -
670F VAL 2.9 19.8 + - - +
671F GLY* 3.6 7.2 - - - +
673F LEU* 1.3 77.0 - - - +
675F LYS* 1.3 60.5 + - - +
677F SER* 3.3 6.5 + - - -
678F LEU* 2.9 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 675 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A GLU* 2.9 37.7 + - - +
497F TYR* 4.6 17.0 - - + +
501F LYS* 5.2 7.0 + - - +
542F GLU* 2.8 47.8 + - + +
544F PRO* 3.9 12.9 - - - +
551F LEU* 5.5 11.0 - - + -
671F GLY 3.0 14.9 + - - +
672F GLN* 3.4 24.1 + - - +
674F TYR* 1.3 80.9 - - - +
676F GLU* 1.3 57.7 + - - +
678F LEU* 3.4 7.1 + - - +
679F SER* 2.9 28.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 676 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662F PRO* 4.7 16.5 - - - +
672F GLN* 2.9 21.8 + - - +
673F LEU* 3.1 16.8 + - - +
675F LYS* 1.3 76.7 - - - +
677F SER* 1.3 58.8 + - - +
679F SER* 2.9 9.9 + - - -
680F ARG* 2.9 53.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 677 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284F TYR* 3.6 31.2 + - - +
285F LEU* 3.7 8.8 + - - +
286F LEU 5.0 0.4 + - - -
673F LEU 2.9 16.3 + - - -
674F TYR* 3.6 8.5 - - - -
676F GLU* 1.3 77.2 - - - +
678F LEU* 1.3 62.9 + - - +
680F ARG* 3.2 20.1 + - - +
681F LEU* 3.1 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 678 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285F LEU* 3.7 19.0 - - + +
497F TYR* 3.5 37.0 - - + -
498F THR* 3.4 36.3 - - - +
501F LYS* 3.9 18.8 - - + +
502F LEU* 5.5 0.7 - - + -
674F TYR* 2.9 20.5 + - + +
675F LYS* 3.7 4.5 - - - +
677F SER* 1.3 75.4 + - - +
679F SER* 1.3 58.2 + - - +
681F LEU* 3.2 9.7 + - + -
682F MET* 2.8 48.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 679 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501F LYS* 4.7 10.2 + - - +
675F LYS* 2.9 17.6 + - - -
676F GLU* 2.9 14.5 + - - -
678F LEU* 1.3 76.6 - - - +
680F ARG* 1.3 61.3 + - - +
682F MET* 3.4 5.4 + - - +
683F ALA* 2.9 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 680 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284F TYR* 4.6 15.3 - - + -
453F ARG* 5.2 14.5 - - - +
676F GLU* 2.9 40.5 + - + +
677F SER* 3.2 16.1 + - - +
679F SER* 1.3 76.3 - - - +
681F LEU* 1.3 57.3 + - - +
683F ALA* 3.1 8.4 + - - +
684F THR* 2.9 34.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 681 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263F GLY* 6.2 1.3 - - - -
265F PHE* 4.8 6.7 - - + -
284F TYR* 3.5 47.5 - - + -
285F LEU* 4.2 13.5 - - + +
477F LEU* 4.7 17.3 - - + -
479F ILE* 5.1 9.9 - - + -
498F THR* 5.2 0.4 - - - +
502F LEU* 5.1 4.7 - - + -
677F SER 3.1 9.6 + - - +
678F LEU* 3.5 18.2 - - + +
680F ARG* 1.3 80.3 - - - +
682F MET* 1.3 58.3 + - + +
684F THR* 2.6 28.1 + - - +
685F LEU* 2.9 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 682 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501F LYS* 3.4 58.1 - - + +
502F LEU* 4.1 22.2 - - - -
504F GLN* 5.1 4.0 - - - +
505F LEU* 4.2 22.7 - - + +
678F LEU* 2.8 34.2 + - + +
679F SER* 3.9 6.3 - - - +
681F LEU* 1.3 76.5 - - - +
683F ALA* 1.3 56.2 + - - +
685F LEU* 4.1 5.7 - - - +
686F SER* 2.9 33.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 683 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679F SER 2.9 14.6 + - - +
680F ARG* 3.3 11.4 - - - +
682F MET* 1.3 74.6 - - - +
684F THR* 1.3 65.8 + - + +
686F SER* 3.2 6.9 + - - -
687F ASN* 2.9 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 684 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265F PHE* 5.1 6.6 - - - -
267F ARG* 4.8 13.7 - - - +
284F TYR* 3.9 25.0 - - + +
473F PHE* 5.3 4.3 - - - -
680F ARG* 3.1 17.5 - - + +
681F LEU* 2.6 30.7 + - - +
683F ALA* 1.3 77.9 - - + +
685F LEU* 1.3 69.8 + - - +
687F ASN* 3.2 24.8 + - - +
688F THR* 3.7 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 685 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193F SER* 3.9 16.3 - - - +
195F LEU* 4.1 13.2 - - + -
265F PHE* 3.4 36.6 - - + -
477F LEU* 3.8 25.4 - - + -
502F LEU* 3.9 19.5 - - + -
505F LEU* 4.1 21.2 - - + +
681F LEU* 2.9 26.1 + - + +
682F MET* 4.1 5.4 - - - +
684F THR* 1.3 82.9 + - - +
686F SER* 1.3 58.2 + - - +
688F THR* 2.9 33.2 + - - +
690F PRO* 4.9 2.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 686 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505F LEU* 4.6 21.0 - - - +
682F MET* 2.9 22.7 + - - -
683F ALA* 3.2 7.4 + - - -
685F LEU* 1.3 76.5 - - - +
687F ASN* 1.3 63.3 + - - +
688F THR 3.3 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 687 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190F GLU* 5.0 6.2 - - - +
191F ASP 5.8 0.5 + - - -
473F PHE* 6.2 0.7 - - + -
683F ALA* 2.9 28.9 + - - +
684F THR* 3.4 13.5 - - - +
685F LEU 3.1 0.4 - - - -
686F SER* 1.3 79.0 - - - +
688F THR* 1.3 64.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 688 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190F GLU* 5.7 3.1 - - - -
191F ASP* 3.4 38.8 - - + +
192F GLN 4.1 0.4 - - - +
193F SER* 2.4 31.6 + - - +
265F PHE* 6.2 0.2 - - + -
473F PHE* 3.8 20.4 - - + -
505F LEU* 6.2 0.2 - - - +
684F THR 3.9 8.7 - - - +
685F LEU 2.9 18.0 + - - +
686F SER 3.6 5.7 - - - +
687F ASN* 1.3 86.8 - - + +
689F ASN* 1.3 60.8 + - - +
690F PRO* 3.4 7.6 - - - +
----------------------------------------------------------
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