Contacts of the helix formed by residues 920 - 929 (chain A) in PDB entry 3THW
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 920 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876A GLU* 3.0 37.7 + - - +
879A GLN* 3.5 14.6 - - - +
880A GLY* 3.5 12.5 - - - +
883A ILE* 4.9 10.2 - - + +
915A VAL 5.1 0.8 + - - -
918A LYS* 3.1 8.6 + - + +
919A ASN* 1.3 74.6 - - - +
921A SER* 1.3 67.2 + - - +
922A PHE* 3.0 36.0 + - - +
923A VAL* 3.3 16.2 + - + +
924A ASN* 2.7 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 921 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876A GLU* 4.0 24.7 - - - -
919A ASN 3.5 5.7 + - - -
920A ASN* 1.3 73.8 - - - +
922A PHE* 1.3 62.0 + - - +
924A ASN* 3.7 8.2 + - - +
925A GLU* 3.4 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 922 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853A GLU* 6.1 0.7 - - - -
876A GLU* 4.2 5.6 - - + +
877A ARG* 3.5 54.5 - - + -
880A GLY* 3.8 18.4 - - - -
881A GLU* 4.2 19.7 - - + -
884A ILE* 4.9 6.1 - - + -
920A ASN* 3.0 11.0 + - - +
921A SER* 1.3 75.1 - - - +
923A VAL* 1.3 69.6 + - + +
924A ASN 3.0 1.3 - - - -
925A GLU* 2.9 28.6 + - - +
926A ILE* 3.0 36.7 + - + +
929A ARG* 6.2 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 923 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880A GLY* 3.6 36.1 - - - +
883A ILE* 3.8 14.4 - - + -
884A ILE* 3.8 21.8 - - + -
915A VAL* 3.9 26.5 - - + -
920A ASN* 3.3 11.0 + - + +
922A PHE* 1.3 76.4 - - + +
924A ASN* 1.3 63.4 + - - +
926A ILE* 3.3 12.2 + - + +
927A ILE* 3.1 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 924 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915A VAL* 5.5 2.4 - - - +
916A ILE* 5.5 7.0 + - - +
919A ASN* 3.2 30.2 + - - +
920A ASN 2.7 30.3 + - - +
921A SER* 3.8 8.8 - - - +
922A PHE 3.0 0.8 - - - -
923A VAL* 1.3 84.7 - - - +
925A GLU* 1.3 60.2 + - - +
927A ILE* 3.6 13.5 + - - +
928A SER* 3.2 21.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 925 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852A GLU* 5.3 4.7 - - - +
921A SER 3.4 9.5 + - - +
922A PHE* 2.9 22.9 + - - +
924A ASN* 1.3 75.4 - - - +
926A ILE* 1.3 64.8 + - + +
928A SER* 2.6 23.1 + - - +
929A ARG* 3.2 42.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 926 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884A ILE* 4.9 12.1 - - + -
922A PHE* 3.0 65.5 - - + +
923A VAL* 3.3 9.8 + - + +
925A GLU* 1.3 78.9 - - + +
927A ILE* 1.3 65.3 + - + +
929A ARG* 3.1 28.7 + - - +
930A ILE* 3.0 32.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 927 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915A VAL* 5.0 4.5 - - + -
916A ILE* 3.9 29.6 - - + -
923A VAL* 3.1 34.3 + - + +
924A ASN* 3.8 11.7 - - - +
925A GLU 3.4 0.2 - - - -
926A ILE* 1.3 77.2 - - + +
928A SER* 1.3 62.1 + - - +
930A ILE* 3.2 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 928 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924A ASN 3.2 12.4 + - - -
925A GLU* 2.6 33.4 + - - +
927A ILE* 1.3 78.1 - - - +
929A ARG* 1.3 61.2 + - - +
930A ILE 3.1 5.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 929 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849A LEU* 3.1 57.6 + - + +
850A GLU* 4.5 1.8 - - - +
852A GLU* 4.0 12.5 + - - -
922A PHE* 6.2 1.6 - - - -
925A GLU* 3.2 44.1 + - + +
926A ILE* 3.1 22.3 + - - +
928A SER* 1.3 77.8 - - - +
930A ILE* 1.3 60.5 + - - +
----------------------------------------------------------
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