Contacts of the helix formed by residues 1048 - 1054 (chain A) in PDB entry 1SIW
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 HIS1048 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A TRP* 3.8 27.8 - + - -
862A GLN 5.5 1.0 + - - -
865A ASP 6.1 0.2 - - - -
866A VAL* 3.9 14.3 - - + +
1046A GLN* 3.3 3.2 - - + +
1047A ASP* 1.3 79.7 + - - +
1049A GLN* 1.3 67.8 + - - +
1050A TRP* 3.2 26.9 + - + +
1051A MET* 2.8 27.5 + - + -
1052A ARG* 2.9 11.2 + - - +
1198A ILE* 3.5 38.0 - - + +
1199A GLY 4.4 0.6 + - - -
1201A TYR* 3.4 52.3 - + + +
1204A LEU* 4.3 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1049 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A ARG* 3.4 33.6 + - - +
638A TYR* 2.9 25.5 + - - +
864A LEU 5.5 1.9 + - - +
865A ASP* 3.7 15.9 - - - +
866A VAL* 3.2 49.8 + - + +
1047A ASP 3.4 3.6 + - - -
1048A HIS* 1.3 73.0 + - - +
1050A TRP* 1.3 62.7 + - - +
1052A ARG* 3.1 24.9 + - - +
1053A ASP* 2.8 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1050 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A TYR* 3.9 28.5 - + - -
645A PHE* 3.9 48.5 - + + -
648A ARG* 5.3 9.9 - - + -
649A ALA* 5.1 1.8 - - + -
652A MET* 5.8 2.5 - - - -
654A TRP* 3.7 28.0 - + - -
866A VAL* 3.8 32.8 - - + +
1048A HIS* 3.2 12.7 + + - +
1049A GLN* 1.3 82.4 - - - +
1051A MET* 1.3 62.3 + - - +
1053A ASP 4.5 0.4 - - - +
1054A PHE* 2.9 47.8 + + + +
1194A PRO* 3.7 27.8 - - + -
1195A THR* 4.7 1.6 - - - -
1197A MET* 4.4 9.4 - - + -
1198A ILE* 3.7 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1051 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A GLN* 4.0 25.8 - - + +
555A ARG* 4.1 1.6 - - - +
1046A GLN* 3.6 45.8 - - + +
1048A HIS* 2.8 27.1 + - + +
1050A TRP* 1.3 74.3 - - - +
1052A ARG* 1.3 59.2 + - - +
1054A PHE 3.9 0.2 - - - -
1055A GLY 3.4 2.9 + - - -
1056A GLU* 2.7 56.5 + - + +
1057A SER 3.4 2.6 + - - -
1195A THR* 3.7 35.9 - - - +
1198A ILE* 4.5 4.9 - - + -
1204A LEU* 4.2 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1052 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A GLU* 3.3 22.2 + - - -
351A ALA 3.6 12.9 + - - +
352A GLY* 3.5 28.5 - - - -
353A ARG* 3.8 20.2 - - - +
630A SER* 3.9 6.2 + - - -
864A LEU 5.2 5.9 + - - -
1045A TYR* 3.7 5.8 - - - -
1046A GLN 3.9 7.0 - - - +
1047A ASP* 2.7 39.7 + - - +
1048A HIS 2.9 11.0 + - - +
1049A GLN* 3.5 29.2 - - - +
1051A MET* 1.3 76.5 - - - +
1053A ASP* 1.3 64.6 + - - +
1055A GLY* 3.1 17.2 + - - -
1057A SER* 4.2 13.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1053 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ARG* 5.4 2.8 + - - -
629A LEU* 3.6 4.8 - - + +
630A SER* 2.6 30.5 + - - -
632A MET 4.8 2.1 - - - +
633A ALA* 3.4 26.7 - - + +
634A ASP 4.9 1.0 + - - -
637A ARG* 4.3 5.2 + - - -
638A TYR* 2.5 49.3 + - + +
1049A GLN* 2.8 28.3 + - - +
1050A TRP 4.3 2.2 - - - +
1052A ARG* 1.3 73.6 + - - +
1054A PHE* 1.3 52.6 + - - +
1055A GLY 3.1 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1054 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A PHE* 4.7 0.2 - - - -
625A ALA* 3.9 17.9 - - + -
628A LEU* 3.3 26.1 - - + +
629A LEU* 3.6 23.3 - - + -
630A SER 3.9 4.2 + - - +
638A TYR* 3.9 19.5 - + - -
645A PHE* 3.9 16.8 - + - -
1050A TRP* 2.9 42.0 + + + +
1051A MET 4.4 0.7 - - - +
1053A ASP* 1.3 77.8 - - - +
1055A GLY* 1.3 53.4 + - - +
1056A GLU 3.5 1.3 + - - -
1062A ARG* 2.4 38.2 + - - +
1193A LYS* 6.5 0.2 - - - -
1194A PRO* 3.5 40.4 - - + -
1195A THR* 3.8 21.1 - - + -
----------------------------------------------------------
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