Contacts of the strand formed by residues 692 - 702 (chain D) in PDB entry 1JZ3
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 692 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658D LEU* 3.6 12.0 - - - +
659D ASP* 3.8 13.2 - - - -
691D ALA* 1.3 74.2 - - - +
693D GLN* 1.3 61.0 + - - -
694D LEU* 4.0 1.0 + - - +
723D ALA 4.1 0.5 - - - +
724D GLU* 3.5 5.3 - - - -
725D ASN* 2.7 45.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 693 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874C SER* 2.7 29.3 + - - -
658D LEU* 3.8 2.4 - - - +
659D ASP* 3.2 36.1 + - - +
692D GLY* 1.3 72.7 - - - -
694D LEU* 1.3 74.2 + - - +
695D TRP* 3.3 34.3 - - + +
721D ARG* 3.6 18.3 + - + +
722D LEU 2.9 28.5 + - - -
723D ALA 3.2 11.0 + - - -
724D GLU* 3.5 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 694 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656D VAL* 4.0 24.7 - - + -
657D ALA 3.4 8.1 - - - +
658D LEU* 4.1 24.7 - - + -
663D LEU* 4.2 8.5 - - + -
685D LEU* 6.5 0.9 - - + -
686D PRO 5.0 4.5 - - - +
688D PRO* 4.1 27.8 - - + -
692D GLY 4.0 0.6 + - - +
693D GLN* 1.3 82.3 + - - +
695D TRP* 1.3 58.2 + - - +
721D ARG 3.7 0.5 - - - -
722D LEU* 2.9 37.1 + - + -
723D ALA* 2.9 37.7 + - + +
725D ASN* 5.5 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 695 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655D MET 3.6 1.0 - - - +
656D VAL* 3.2 4.8 - - - -
657D ALA* 2.8 38.3 + - + +
659D ASP* 5.0 2.7 - - - -
660D GLY 5.8 0.9 - - - -
693D GLN* 3.3 30.2 - - + +
694D LEU* 1.3 74.5 - - - +
696D LEU* 1.3 58.9 + - - +
697D THR* 4.1 2.0 + - - +
719D GLN* 3.9 38.6 - - + +
720D TRP* 3.5 21.8 - - - -
721D ARG* 3.3 60.1 - - + -
722D LEU* 4.5 3.1 - - - +
900D LEU* 5.7 3.1 - - + -
915D PHE* 3.1 57.2 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 696 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631D LEU* 4.3 20.0 - - + -
636D ILE* 4.3 11.7 - - + -
654D TRP* 4.2 1.6 - - + -
655D MET 3.2 20.0 - - - +
656D VAL* 3.8 14.4 - - + -
682D LEU* 3.9 25.4 - - + -
695D TRP* 1.3 73.2 - - - +
697D THR* 1.3 68.3 + - - +
698D VAL* 4.1 9.2 - - + -
719D GLN* 3.2 5.2 - - - +
720D TRP* 2.9 57.3 + - + +
722D LEU* 3.7 23.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 697 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653D HIS 3.9 0.3 - - - +
654D TRP* 3.4 1.9 - - - -
655D MET* 2.9 48.6 + - + +
695D TRP* 4.1 2.6 + - - +
696D LEU* 1.3 72.5 - - - +
698D VAL* 1.3 75.0 + - - +
699D ARG* 4.4 21.8 - - + +
717D TRP* 5.2 0.9 - - + -
718D GLN 3.6 6.1 - - - +
719D GLN* 2.9 37.1 + - + +
914D CYS* 4.7 10.8 - - + -
916D ASP* 5.0 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 698 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629D PHE* 4.2 27.6 - - + -
636D ILE* 3.7 29.2 - - + -
652D LEU* 4.1 8.7 - - + -
653D HIS 3.1 8.5 - - - +
654D TRP* 3.8 13.2 - - + -
696D LEU* 4.1 7.4 - - + -
697D THR* 1.3 80.5 - - - +
699D ARG* 1.3 63.5 + - - +
717D TRP* 3.2 6.2 - - - +
718D GLN* 2.9 39.6 + - + +
720D TRP* 4.0 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 699 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651D LEU 3.6 0.3 - - - +
652D LEU* 3.4 5.1 - - - -
653D HIS* 2.7 39.5 + - + +
655D MET* 3.7 26.6 - - + +
697D THR* 4.4 12.5 - - + +
698D VAL* 1.3 81.2 - - - +
700D VAL* 1.4 63.5 + - - +
701D VAL* 3.9 10.6 + - + +
714D ILE* 3.7 36.5 - - + +
716D ALA 3.3 9.0 - - - +
717D TRP* 4.1 12.9 - - + +
914D CYS* 5.7 6.3 - - - +
918D TRP* 4.7 17.8 - - - -
8415D DMS 4.5 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 700 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627D PHE* 4.2 13.5 - - + -
629D PHE* 3.8 27.8 - - + -
650D GLU* 3.5 38.4 - - + -
651D LEU 3.3 6.1 - - - +
652D LEU* 4.0 10.5 - - + -
670D LEU* 4.1 11.0 - - + -
699D ARG* 1.4 71.8 - - - +
701D VAL* 1.3 62.0 + - - +
714D ILE* 3.4 5.9 - - - +
715D SER* 3.0 42.9 + - - +
716D ALA* 2.8 19.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 701 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650D GLU* 3.3 3.3 - - - -
651D LEU* 2.9 40.1 + - + +
653D HIS* 2.8 38.1 - - + +
699D ARG* 4.2 9.6 - - + +
700D VAL* 1.3 76.8 - - - +
702D GLN* 1.3 66.2 + - - +
703D PRO* 3.3 5.6 - - + +
712D GLY* 3.5 33.4 - - - +
713D HIS 3.5 4.0 - - - -
714D ILE* 4.4 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 702 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642D TYR* 5.5 0.3 + - - -
649D ASN* 3.2 33.4 - - - +
650D GLU* 4.2 15.1 - - + +
701D VAL* 1.3 73.8 - - - +
703D PRO* 1.3 60.9 - - - +
704D ASN 3.3 3.9 + - - +
706D THR* 4.2 0.6 - - - +
708D TRP* 3.4 27.8 - - - -
709D SER* 3.1 26.7 + - - -
711D ALA 3.8 0.5 - - - -
712D GLY* 2.7 31.4 + - - -
713D HIS* 3.0 33.7 + - + +
715D SER* 4.0 14.2 - - - +
8403D DMS 4.4 3.8 - - - +
----------------------------------------------------------
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