Contacts of the helix formed by residues 871 - 883 (chain D) in PDB entry 4AY5
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 871 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435D ILE* 5.6 0.7 - - + -
436D PRO* 4.7 24.7 - - + -
466D VAL* 3.3 34.5 - - + +
869D PRO* 4.3 11.7 - - + -
870D ALA* 1.3 79.4 - - + +
872D GLY* 1.3 63.9 + - - +
873D GLU 3.2 0.2 - - - -
874D PRO* 3.1 20.4 - - - +
875D ASN* 4.3 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 872 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466D VAL* 3.3 28.1 - - - +
840D LEU* 4.0 12.8 - - - -
869D PRO* 2.9 14.3 + - - +
871D VAL* 1.3 81.7 - - - +
873D GLU* 1.3 62.8 + - - +
874D PRO 3.6 0.2 - - - -
875D ASN* 3.3 5.6 + - - +
876D ILE* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 873 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840D LEU* 4.4 0.6 - - - +
867D ARG* 3.1 29.6 + - - -
869D PRO 4.0 1.6 + - - +
870D ALA* 2.9 18.3 + - - +
872D GLY* 1.3 73.6 - - - +
874D PRO* 1.4 71.3 - - + +
876D ILE* 2.9 4.7 + - - +
877D GLN* 2.8 31.4 + - + +
892D PHE* 3.3 59.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 874 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870D ALA 3.4 6.5 - - - +
871D VAL* 3.1 20.4 - - - +
873D GLU* 1.4 97.7 - - + +
875D ASN* 1.3 59.1 + - - +
877D GLN* 3.6 8.3 - - + +
878D GLN* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 875 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466D VAL* 2.7 28.8 + - - +
467D CYS* 3.1 24.7 + - + +
468D ASP* 3.5 15.7 - - - +
871D VAL 4.5 6.0 + - - +
872D GLY 3.3 10.5 + - - +
873D GLU 3.0 0.8 + - - -
874D PRO* 1.3 78.6 - - - +
876D ILE* 1.3 66.5 + - - +
878D GLN* 3.2 13.1 - - - +
879D TYR* 2.9 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 876 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467D CYS* 3.7 33.7 - - + -
469D TRP* 4.0 19.5 - - + -
840D LEU* 4.8 6.3 - - + -
843D ILE* 4.6 13.0 - - + -
848D LEU* 4.0 17.7 - - + -
865D LEU* 4.5 9.2 - - + -
872D GLY 3.1 13.2 + - - +
873D GLU 2.9 9.4 + - - +
875D ASN* 1.3 72.8 - - - +
877D GLN* 1.3 66.3 + - - +
878D GLN 3.1 0.3 + - - -
879D TYR* 3.1 6.0 + - - +
880D ALA* 2.8 23.9 + - - +
890D ILE* 4.3 17.9 - - + -
892D PHE* 3.9 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 877 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873D GLU* 2.8 25.4 + - + +
874D PRO* 3.6 8.5 - - + +
876D ILE* 1.3 76.7 - - - +
878D GLN* 1.3 64.6 + - - +
880D ALA* 3.1 15.1 - - - +
881D GLN* 3.1 42.5 + - - +
887D GLN* 3.5 33.6 + - + +
890D ILE* 3.3 35.6 + - - +
892D PHE* 3.8 19.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 878 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874D PRO 2.9 16.2 + - - +
875D ASN* 3.2 15.3 - - - +
877D GLN* 1.3 73.1 - - - +
879D TYR* 1.3 65.9 + - + +
880D ALA 3.0 0.2 - - - -
881D GLN* 2.7 32.3 + - - +
882D ASN* 3.1 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 879 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467D CYS 3.3 22.2 - - - -
468D ASP* 3.9 5.1 + - - -
469D TRP* 2.8 56.3 + + + -
470D THR* 3.3 13.5 + - - -
848D LEU* 4.1 13.5 - - + -
875D ASN* 2.9 27.0 - - + -
876D ILE* 3.1 6.1 + - + +
878D GLN* 1.3 87.1 - - + +
880D ALA* 1.3 60.7 + - - +
882D ASN* 3.3 19.9 + - - +
883D MET* 3.0 36.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 880 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848D LEU* 4.4 7.1 - - + +
876D ILE* 2.8 14.0 + - + +
877D GLN* 3.1 18.6 - - - +
879D TYR* 1.3 76.8 - - - +
881D GLN* 1.3 61.9 + - - +
883D MET* 3.2 16.3 + - - +
884D GLY 3.3 0.5 + - - -
885D LEU* 3.1 32.7 + - + +
890D ILE* 3.7 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 881 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877D GLN* 3.1 36.6 + - - +
878D GLN* 2.7 18.0 + - - +
880D ALA* 1.3 72.2 - - - +
882D ASN* 1.3 65.8 + - - +
883D MET 3.1 1.6 - - - -
884D GLY* 2.9 16.2 + - - -
885D LEU 3.0 21.6 + - - +
886D PRO* 4.7 1.1 - - + -
887D GLN* 3.1 38.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 882 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878D GLN* 3.1 31.1 + - - +
879D TYR* 3.3 25.5 + - - +
881D GLN* 1.3 75.6 - - - +
883D MET* 1.3 60.5 + - + +
884D GLY 3.0 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 883 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469D TRP* 5.3 1.3 - - + -
845D PRO* 3.9 24.0 - - + +
848D LEU* 3.9 24.2 - - + +
849D GLN* 3.7 46.4 - - - +
852D ALA* 4.0 17.9 - - + -
856D LYS* 2.7 32.7 + - - -
879D TYR* 3.0 24.9 + - + +
880D ALA* 3.6 9.4 - - - +
881D GLN 3.1 0.6 - - - -
882D ASN* 1.3 79.4 - - + +
884D GLY* 1.3 51.9 + - - +
885D LEU* 3.7 0.4 - - - -
----------------------------------------------------------
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