Contacts of the helix formed by residues 941 - 949 (chain A) in PDB entry 6S1M
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 ASP 941 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
903A LEU* 3.7 16.5 - - + +
908A ARG* 6.0 4.5 - - - -
923A PRO* 4.0 10.9 - - - +
940A GLU* 1.3 86.0 + - - +
942A PRO* 1.3 78.2 - - - +
943A LEU* 3.4 25.2 + - - +
944A PHE* 3.2 10.7 + - + +
945A VAL* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 942 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878A ILE* 4.6 10.3 - - + +
882A VAL* 4.1 29.8 - - + -
923A PRO* 3.5 24.2 - - + +
924A TYR* 4.0 10.1 - - - +
925A VAL* 4.7 4.5 - - + -
940A GLU 3.7 4.5 - - - +
941A ASP* 1.3 95.0 - - - +
943A LEU* 1.3 57.3 + - - +
945A VAL* 3.3 13.1 - - + +
946A LEU* 3.0 28.8 + - - +
1074A ARG* 6.2 3.1 - - + -
1080A TYR* 6.1 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 943 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910A ARG* 5.2 12.1 - - - +
941A ASP* 3.3 14.4 + - - +
942A PRO* 1.3 77.7 - - - +
944A PHE* 1.3 58.2 + - - +
946A LEU* 3.3 8.7 + - + +
947A GLU* 2.9 55.2 + - + +
1072A THR* 5.4 0.9 - - - +
1074A ARG* 3.7 43.2 - - + +
1079A PHE* 4.3 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 944 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908A ARG* 3.2 40.8 - - - -
910A ARG* 5.8 8.1 - - + -
940A GLU* 3.7 34.5 - - + +
941A ASP* 3.2 15.8 + - + +
943A LEU* 1.3 79.2 - - - +
945A VAL* 1.3 57.4 + - - +
947A GLU* 3.5 2.9 + - + -
948A HIS* 2.9 78.1 + + + +
950A LEU* 5.0 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 945 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878A ILE* 5.1 9.4 - - + -
925A VAL* 3.8 17.9 - - + -
927A ILE* 4.3 9.4 - - + -
940A GLU* 4.4 4.6 - - + +
941A ASP 3.0 14.8 + - - +
942A PRO* 3.3 21.3 - - + +
944A PHE* 1.3 73.9 - - - +
946A LEU* 1.3 60.6 + - - +
949A SER* 3.0 23.3 + - - +
950A LEU* 3.4 52.0 - - + +
952A ILE* 4.6 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 946 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878A ILE* 4.7 8.5 - - + -
942A PRO 3.0 16.7 + - - +
943A LEU* 3.3 16.2 - - + +
944A PHE 3.2 0.2 - - - -
945A VAL* 1.3 80.1 - - - +
947A GLU* 1.3 89.2 - - - +
948A HIS 3.4 0.3 + - - -
949A SER* 3.8 10.0 + - - -
1079A PHE* 3.7 18.2 - - + -
1080A TYR* 3.6 44.0 - - + -
1083A LYS* 4.6 19.7 - - + +
106D PRO* 4.3 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 947 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
943A LEU* 2.9 36.3 + - + +
944A PHE* 4.4 2.9 - - + +
946A LEU* 1.3 87.7 - - - +
948A HIS* 1.3 72.7 + - + +
949A SER* 3.7 3.5 + - - -
1083A LYS* 5.5 1.6 - - - +
106D PRO* 3.3 39.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 948 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
944A PHE* 2.9 57.2 + + + +
947A GLU* 1.3 93.7 - - + +
949A SER* 1.3 72.5 + - - +
950A LEU* 3.6 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 949 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
945A VAL 3.0 17.0 + - - -
946A LEU 3.8 9.6 + - - -
947A GLU 4.4 2.4 + - - -
948A HIS* 1.3 81.2 - - - +
950A LEU* 1.3 62.5 + - - +
951A PRO* 4.1 4.0 - - - +
----------------------------------------------------------
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