Contacts of the strand formed by residues 713 - 721 (chain D) in PDB entry 3AOI
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 ILE 713 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032C PHE* 4.4 4.3 - - + -
1036C GLU* 3.9 10.8 - - + +
1039C ALA* 3.5 27.8 - - + -
1040C LEU* 3.5 22.7 - - + -
1043C TYR* 2.5 44.1 + - + -
701D LEU* 3.7 34.1 - - + -
702D LEU 2.8 19.7 - - - +
703D ASN* 3.3 25.6 - - + +
707D THR* 3.9 5.8 - - + -
710D ARG 3.6 1.6 + - - -
712D GLY* 1.3 78.1 - - - +
714D GLN* 1.3 57.7 + - - +
736D PHE* 3.7 0.2 - - - -
748D HIS* 5.8 3.6 - - + -
763D MET* 5.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 714 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1043C TYR* 3.8 6.5 - - - +
701D LEU* 3.3 3.3 - - - -
702D LEU 2.9 27.3 + - - -
711D LEU* 3.4 42.1 - - + +
713D ILE* 1.3 76.5 - - - +
715D ALA* 1.3 61.1 + - - +
716D PHE* 3.3 25.4 - - + -
732D VAL* 2.8 36.1 - - - +
735D ALA* 3.7 10.1 - - - +
736D PHE* 3.3 18.6 - - + -
763D MET* 3.9 7.6 - - - +
765D SER* 3.7 15.5 - - - +
768D ASN* 4.5 8.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 715 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699D VAL* 4.1 13.7 - - + -
700D VAL 3.2 11.7 - - - +
701D LEU* 4.3 4.0 - - + +
714D GLN* 1.3 71.6 - - - +
716D PHE* 1.3 68.0 + - - +
759D ALA* 3.4 30.7 - - + +
763D MET* 3.2 12.7 + - + +
764D LEU* 3.3 15.4 - - + +
765D SER 3.0 21.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 716 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639D LEU 3.4 15.3 - - - -
640D HIS 3.6 4.0 - - - -
641D GLN 3.0 22.7 - - - -
642D CYS* 3.2 24.9 - - + -
699D VAL* 3.0 7.9 - - - +
700D VAL* 2.9 32.4 + - - +
702D LEU* 4.2 22.7 - - + -
714D GLN* 3.3 50.7 - - + -
715D ALA* 1.3 76.5 - - - +
717D GLN* 1.3 60.6 + - - +
718D PRO* 3.2 4.3 - - - +
728D LEU* 4.4 7.6 - - + -
729D HIS* 4.7 1.6 - - + -
732D VAL* 4.1 21.1 - - + -
736D PHE* 4.4 5.8 - + - -
764D LEU* 4.9 0.4 - - - -
765D SER* 3.4 16.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 717 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640D HIS* 3.2 46.0 + - + +
641D GLN* 3.5 10.3 - - + +
642D CYS 3.1 19.1 + - - -
695D ILE 5.2 0.2 - - - +
696D HIS 4.0 15.3 + - - +
697D GLY* 3.7 12.3 - - - +
698D LYS 3.9 9.6 - - - +
699D VAL* 3.9 9.5 - - + +
716D PHE* 1.3 70.9 - - - +
718D PRO* 1.3 76.2 - - - +
719D VAL* 3.4 4.9 + - + +
760D ARG* 3.0 27.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 718 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642D CYS* 3.5 7.0 - - - +
644D LEU* 3.6 22.0 - - + -
692D GLU* 5.1 0.2 - - - +
695D ILE* 3.5 39.8 - - + +
696D HIS 5.7 0.3 - - - +
698D LYS 3.4 17.9 - - - +
699D VAL* 3.6 4.3 - - - -
700D VAL* 3.3 39.0 - - + -
716D PHE 3.2 7.4 - - - +
717D GLN* 1.3 91.2 - - - +
719D VAL* 1.3 61.7 + - - +
720D LEU* 3.9 2.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 719 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637D LEU* 4.6 7.6 - - + -
641D GLN* 3.8 42.4 - - + +
642D CYS 3.3 8.2 + - - +
643D GLY* 4.0 1.8 - - - -
644D LEU 3.7 12.0 + - - -
692D GLU* 4.9 2.9 - - - +
717D GLN* 3.9 5.4 - - + +
718D PRO* 1.3 74.8 - - - +
720D LEU* 1.3 72.5 + - - +
721D VAL* 3.4 14.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 720 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B THR* 3.6 19.0 - - + +
644D LEU* 3.4 7.2 - - + +
646D LYS* 4.0 24.0 - - + -
649D ALA* 4.6 4.9 - - + -
688D TRP* 5.1 4.5 - - + +
691D LEU* 3.9 33.2 - - + -
692D GLU* 2.9 46.7 + - + +
695D ILE* 3.7 39.5 - - + -
718D PRO* 4.1 2.2 - - + +
719D VAL* 1.3 77.1 - - - +
721D VAL* 1.3 66.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 721 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ASP* 5.7 6.3 - - + +
190B THR* 4.5 7.9 - - + -
636D GLN* 6.2 1.3 - - - +
643D GLY* 4.1 9.9 - - - -
644D LEU 3.0 32.4 + - - +
645D PRO* 3.5 7.6 - - + +
646D LYS* 3.2 28.7 + - - +
719D VAL* 3.4 12.3 - - + +
720D LEU* 1.3 81.8 - - - +
722D GLU* 1.3 71.3 + - - +
723D GLY 4.6 0.2 - - - +
725D SER 5.1 2.5 - - - +
727D GLN* 4.8 21.1 - - + +
----------------------------------------------------------
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