Contacts of the helix formed by residues 953 - 958 (chain B) in PDB entry 5M64
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 ALA 953 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934A LYS* 4.0 9.5 + - - +
784B ASP* 3.9 27.7 - - + +
923B GLN* 6.4 1.8 - - + -
949B ILE* 6.0 5.4 - - + -
950B ASN 3.9 9.3 + - - +
951B PRO 3.3 1.2 - - - -
952B HIS* 1.3 78.8 - - - +
954B PHE* 1.3 60.7 + - + +
955B PRO 3.4 1.3 - - - -
956B SER 3.5 1.7 + - - -
957B ARG* 2.7 49.0 + - + +
959B THR* 5.5 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 954 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828A CYS* 4.6 6.1 - - + -
925A MET* 4.7 9.3 - - + +
943A ILE* 5.7 0.5 - - - +
775B VAL* 3.6 15.7 - - + -
949B ILE* 5.0 1.1 - - + -
950B ASN 3.9 6.7 - - - -
951B PRO* 3.3 38.6 - - + +
953B ALA* 1.3 78.3 - - + +
955B PRO* 1.3 71.6 - - + +
958B MET* 3.1 29.6 + - - +
959B THR* 3.2 43.7 - - - +
960B ILE* 4.6 4.8 - - + +
962B MET* 3.5 25.6 - - + -
963B PHE* 3.4 43.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 955 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925A MET* 3.8 31.3 - - + +
928A MET* 3.8 28.5 - - + -
929A ALA* 4.6 5.6 - - + -
934A LYS* 3.3 26.2 - - + +
935A GLY* 4.4 1.3 - - - -
939A ASN* 3.3 29.7 + - - +
951B PRO 3.8 11.9 - - - +
952B HIS 3.9 5.2 - - - -
953B ALA 3.6 3.6 - - - -
954B PHE* 1.3 93.5 - - + +
956B SER* 1.3 57.0 + - - +
958B MET* 5.2 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 956 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934A LYS* 3.2 40.5 - - - +
935A GLY* 3.5 13.9 + - - -
939A ASN* 4.1 9.9 + - - +
711B GLN* 4.4 7.6 + - - +
714B ARG* 4.7 1.9 + - - -
953B ALA 3.5 2.0 + - - -
954B PHE 3.2 0.2 - - - -
955B PRO* 1.3 76.9 - - - +
957B ARG* 1.3 65.9 + - - +
958B MET* 3.2 7.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 957 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627A ASP* 5.8 1.8 + - - -
629A ASP* 5.5 1.2 + - - +
934A LYS* 4.9 6.5 - - - +
711B GLN* 3.9 2.1 - - - +
714B ARG* 3.4 58.0 + - - +
717B TYR* 3.5 32.4 + - - -
784B ASP* 4.2 20.1 + - - -
785B ASP* 4.0 22.8 + - - -
922B GLY 4.6 4.2 + - - -
923B GLN* 4.7 6.4 - - + +
924B LYS* 4.7 9.5 - - - +
953B ALA* 2.7 32.2 + - + +
956B SER* 1.3 76.5 - - - +
958B MET* 1.3 64.4 + - - +
959B THR* 3.7 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 958 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
939A ASN* 5.2 4.7 - - + +
942A GLN* 4.4 18.6 - - - +
943A ILE* 3.6 39.0 - - + -
986A PHE* 3.5 33.0 - - + -
710B ASN* 4.5 10.1 - - - +
711B GLN* 3.3 43.6 + - + +
714B ARG* 5.1 0.9 - - - +
953B ALA 3.7 1.2 + - - -
954B PHE* 3.1 23.8 + - - +
955B PRO 5.2 3.1 - - - +
956B SER 4.0 3.8 - - - +
957B ARG* 1.3 82.3 - - - +
959B THR* 1.3 57.3 + - - +
960B ILE* 3.3 16.2 + - + +
----------------------------------------------------------
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