Contacts of the helix formed by residues 871 - 878 (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 ASN 871 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553D GLU* 5.0 1.0 + - - -
562D LEU* 4.9 1.8 - - - +
837D GLU* 5.0 2.8 + - - -
869D ASN 3.1 6.9 + - - +
870D LEU* 1.3 75.7 - - - +
872D LEU* 1.3 70.6 + - - +
873D ARG* 3.6 22.4 - - - +
874D ASP* 2.6 45.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 872 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548D ALA* 3.7 32.5 - - + +
551D ARG* 2.9 36.6 - - - +
832D MET 5.7 0.4 - - - +
833D VAL* 3.0 26.4 - - + +
836D TYR* 3.1 36.6 - - + +
837D GLU* 3.8 17.5 + - + +
870D LEU* 3.1 13.3 + - + -
871D ASN* 1.3 72.3 - - - +
873D ARG* 1.3 61.2 + - - +
874D ASP 3.0 1.6 + - - -
875D ILE* 3.1 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 873 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833D VAL* 4.1 12.1 - - + +
837D GLU* 2.7 46.1 + - - -
871D ASN* 3.0 17.5 + - - +
872D LEU* 1.3 78.7 - - - +
874D ASP* 1.3 62.6 + - - +
875D ILE 3.2 0.7 - - - -
876D LEU* 3.3 36.2 + - + +
877D GLU* 4.3 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 874 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562D LEU* 3.6 18.2 - - + +
563D PRO* 3.4 34.9 - - + +
871D ASN* 2.6 47.5 + - - +
873D ARG* 1.3 73.6 - - - +
875D ILE* 1.3 57.7 + - - +
876D LEU 3.0 2.5 - - - -
877D GLU* 2.7 33.0 + - - +
878D SER 3.3 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 875 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548D ALA* 5.1 2.0 - - + -
561D LEU* 3.4 40.4 + - + +
829D ARG* 3.3 32.7 - - + +
832D MET* 4.0 33.0 - - + -
833D VAL* 3.7 7.4 - - + +
870D LEU* 5.4 1.3 - - + -
871D ASN 5.0 0.4 - - - +
872D LEU* 3.1 41.3 + - + +
874D ASP* 1.3 77.2 - - - +
876D LEU* 1.3 61.6 + - - +
878D SER* 3.1 15.6 + - - -
881D ALA* 4.6 13.9 - - + -
883D ALA 5.0 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 876 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825D PHE* 5.6 2.3 - - - -
829D ARG* 3.7 34.6 - - + +
830D GLU* 4.0 16.2 - - + +
833D VAL* 3.3 31.6 - - + -
873D ARG* 3.3 36.5 + - + +
874D ASP 3.0 0.2 - - - -
875D ILE* 1.3 76.4 - - - +
877D GLU* 1.3 72.8 + - + +
878D SER 3.4 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 877 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563D PRO* 3.3 24.1 - - + +
873D ARG 4.5 4.9 - - - +
874D ASP* 2.7 15.1 + - - +
876D LEU* 1.3 92.9 - - + +
878D SER* 1.3 62.0 + - - +
879D ASP* 3.6 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 878 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560D ASN* 2.6 29.5 + - - +
562D LEU 3.5 20.6 + - - -
563D PRO* 3.9 6.3 - - - -
564D SER 5.3 0.2 + - - -
825D PHE* 4.4 1.5 - - - -
829D ARG* 2.7 32.1 + - - -
874D ASP 3.3 4.0 + - - -
875D ILE* 3.1 17.2 + - - -
876D LEU 3.4 0.6 - - - +
877D GLU* 1.3 78.2 - - - +
879D ASP* 1.3 59.6 + - - +
880D PHE* 3.7 2.8 + - - -
881D ALA* 3.5 11.6 + - - -
----------------------------------------------------------
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