Contacts of the helix formed by residues 690 - 708 (chain D) in PDB entry 1S77
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 VAL 690 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552D ASP* 5.0 5.4 + - - +
554D VAL* 6.0 7.6 - - + -
686D SER 3.5 17.3 - - - +
687D VAL* 4.7 3.6 - - - -
688D THR 3.6 11.6 + - - +
689D VAL* 1.3 79.6 - - - +
691D ALA* 1.3 86.7 + - + +
692D ALA 3.0 1.7 - - - +
693D VAL* 2.9 6.9 + - - +
694D GLU* 2.8 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 691 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550D LEU* 3.2 24.9 - - + +
552D ASP* 3.1 34.0 + - + +
690D VAL* 1.3 85.0 - - + +
692D ALA* 1.3 52.3 + - - +
694D GLU* 2.9 16.0 + - - +
695D ALA 2.7 31.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 692 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543D ILE* 4.3 5.4 - - + -
546D PHE* 3.6 42.2 - - + +
550D LEU* 3.9 2.4 - - - +
552D ASP* 4.8 1.0 + - - -
638D ALA* 3.7 6.3 - - + -
689D VAL* 3.3 26.9 - - + -
690D VAL 4.2 0.2 - - - +
691D ALA* 1.3 78.3 - - - +
693D VAL* 1.3 51.7 + - - +
695D ALA* 2.7 7.3 + - - +
696D MET* 2.7 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 693 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637D LEU* 3.8 30.5 - - + -
638D ALA* 4.5 2.4 - - - +
686D SER* 6.3 0.2 - - - -
689D VAL* 3.4 24.0 - - + +
690D VAL* 2.9 11.3 + - - +
692D ALA* 1.3 76.4 - - - +
694D GLU* 1.3 63.6 + - + +
696D MET* 3.4 22.5 - - + +
697D ASN* 2.9 44.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 694 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690D VAL* 2.8 26.1 + - + +
691D ALA* 3.1 12.5 - - - +
693D VAL* 1.3 77.9 - - + +
695D ALA* 1.3 58.2 + - - +
697D ASN* 3.3 6.4 + - - +
698D TRP* 3.0 28.3 + - - +
865D PRO* 4.5 19.8 - - + +
866D ALA* 5.1 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 695 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546D PHE* 3.9 17.7 - - + -
549D MET* 5.5 0.2 - - - -
550D LEU* 3.5 28.7 - - + +
691D ALA 2.7 14.6 + - - +
692D ALA 2.7 7.8 + - - +
694D GLU* 1.3 70.8 - - - +
696D MET* 1.3 67.0 + - - +
698D TRP* 3.4 8.3 + - - +
699D LEU* 3.1 26.4 + - + +
842D LEU* 4.4 8.6 - - + +
865D PRO* 4.8 6.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 696 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546D PHE* 4.5 4.0 - - + -
637D LEU* 3.8 12.6 - - + +
638D ALA* 3.4 19.7 - - - +
639D TYR 3.8 0.4 - - - -
640D GLY* 3.3 37.5 - - - -
642D LYS* 4.9 8.5 - - - +
692D ALA 2.7 15.0 + - - +
693D VAL* 3.4 39.5 - - + +
695D ALA* 1.3 73.6 - - - +
697D ASN* 1.3 62.4 + - - +
699D LEU* 2.8 33.5 + - - +
700D LYS* 2.8 31.6 + - + +
779D ALA* 4.1 9.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 697 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642D LYS* 5.6 3.8 - - - +
693D VAL* 2.9 38.4 + - - +
694D GLU* 3.7 6.5 - - - +
696D MET* 1.3 83.8 - - - +
698D TRP* 1.3 56.6 + - - +
700D LYS* 3.6 21.3 - - - +
701D SER* 2.8 34.0 + - - +
862D PRO* 5.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 698 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694D GLU 3.0 14.4 + - - +
695D ALA* 3.5 11.7 - - - +
696D MET 3.1 0.2 - - - -
697D ASN* 1.3 75.9 - - - +
699D LEU* 1.3 76.5 + - + +
701D SER* 3.3 7.9 + - - -
702D ALA* 3.2 16.9 + - + +
842D LEU* 3.4 34.8 - - + -
845D PHE* 3.3 28.5 - + - -
846D TYR* 3.7 22.4 - + + -
849D PHE* 3.8 20.4 - + - -
861D MET* 4.5 4.8 - - - +
862D PRO* 3.3 30.4 + - + -
863D ALA 3.2 22.9 - - - -
864D LEU* 3.3 33.0 - - + +
865D PRO* 4.1 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 699 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546D PHE* 4.5 11.9 - - + -
695D ALA 3.1 16.8 + - - +
696D MET* 2.8 9.9 + - - +
698D TRP* 1.3 87.1 - - + +
700D LYS* 1.3 64.7 + - - +
702D ALA* 3.0 6.7 + - - +
703D ALA* 2.9 22.7 + - - +
778D ILE* 3.8 19.5 - - + +
779D ALA* 4.1 19.5 - - - +
782D PHE* 3.8 35.2 - - + -
842D LEU* 4.6 6.5 - - + -
845D PHE* 3.3 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 700 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639D TYR 4.8 2.9 - - - -
640D GLY* 4.0 13.1 + - - -
642D LYS* 3.9 22.8 - - - +
696D MET* 2.8 37.5 + - + +
697D ASN* 3.6 21.5 - - - +
698D TRP 3.3 0.2 - - - -
699D LEU* 1.3 75.8 - - - +
701D SER* 1.3 57.0 + - - +
703D ALA 3.3 0.3 + - - -
704D LYS* 2.8 31.3 + - - +
775D GLU* 3.4 44.4 + - + +
776D SER* 4.6 10.9 - - - +
778D ILE* 3.9 10.8 - - + -
779D ALA* 5.3 2.2 - - + -
120T T 5.9 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 701 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697D ASN* 2.8 23.6 + - - +
698D TRP 3.5 5.8 - - - -
699D LEU 3.2 0.2 - - - -
700D LYS* 1.3 76.0 - - - +
702D ALA* 1.3 57.4 + - - +
704D LYS* 3.3 9.0 + - - +
705D LEU* 2.9 36.7 + - - +
861D MET* 3.9 2.9 - - - -
862D PRO* 3.3 41.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 702 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698D TRP* 3.2 9.8 + - + +
699D LEU 3.0 9.8 + - - +
701D SER* 1.3 78.5 - - - +
703D ALA* 1.3 65.9 + - - +
705D LEU* 3.9 1.4 - - - +
706D LEU* 3.1 30.6 + - - +
725D VAL* 5.2 0.2 - - - -
845D PHE* 4.0 15.0 - - + -
849D PHE* 3.7 33.7 - - + -
861D MET* 3.2 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 703 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699D LEU 2.9 12.5 + - - +
700D LYS 3.7 6.3 - - - +
702D ALA* 1.3 75.9 - - - +
704D LYS* 1.3 58.5 + - - +
706D LEU* 3.1 2.6 + - - +
707D ALA* 2.8 34.5 + - - +
725D VAL* 3.8 18.7 - - + +
774D GLN 3.2 28.0 - - - +
775D GLU* 3.8 11.0 - - - -
778D ILE* 3.8 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 704 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700D LYS 2.8 14.8 + - - +
701D SER* 3.5 9.9 - - - +
703D ALA* 1.3 76.6 - - - +
705D LEU* 1.3 66.0 + - + +
707D ALA* 3.9 4.1 - - - +
708D ALA* 3.0 29.9 + - + +
771D ALA 5.6 0.7 - - - -
775D GLU* 3.0 34.0 + - - +
24N G 3.8 26.0 + - - -
25N C 3.5 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 705 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701D SER* 2.9 21.9 + - - +
702D ALA 4.1 3.4 - - - +
704D LYS* 1.3 83.2 - - + +
706D LEU* 1.3 52.1 + - + +
708D ALA* 3.9 5.0 - - + +
720D ARG* 2.5 29.3 + - - -
854D HIS* 4.0 16.6 - - - +
858D LEU* 3.0 38.0 - - + +
859D ASP 4.8 0.2 - - - +
860D LYS* 4.2 14.1 - - + +
861D MET* 3.8 48.0 - - + +
862D PRO* 5.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 706 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702D ALA 3.1 20.5 + - - +
703D ALA* 3.7 4.0 - - - +
705D LEU* 1.3 78.5 - - + +
707D ALA* 1.3 58.6 + - - +
708D ALA 3.3 0.2 - - - -
720D ARG* 3.3 10.1 + - - +
723D CYS* 2.5 48.4 + - + +
724D ALA 4.5 2.9 - - - +
725D VAL* 4.1 31.2 - - + -
726D HIS 5.1 0.2 - - - +
849D PHE* 3.4 37.7 - - + +
853D LEU* 3.5 42.8 - - + +
854D HIS* 5.0 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 707 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703D ALA 2.8 16.4 + - - +
704D LYS* 3.9 3.6 - - - +
706D LEU* 1.3 73.5 - - - +
708D ALA* 1.3 65.4 + - - +
722D ARG* 2.5 37.6 + - - +
723D CYS 3.9 8.9 + - - +
769D ILE* 4.6 2.2 - - + -
771D ALA* 3.6 36.3 - - + +
774D GLN* 4.3 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 708 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704D LYS 3.0 18.2 + - - +
705D LEU* 3.9 14.4 - - + +
706D LEU 3.3 0.4 - - - -
707D ALA* 1.3 86.5 - - - +
709D GLU* 1.3 62.0 + - - +
710D VAL* 5.0 2.5 - - + -
720D ARG* 3.3 17.5 + - - +
722D ARG* 3.4 15.5 + - - +
771D ALA* 5.0 0.8 - - - +
858D LEU* 4.7 8.5 - - + -
----------------------------------------------------------
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