Contacts of the helix formed by residues 255 - 260 (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 ASN 255 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A GLY 4.3 0.6 + - - -
254A SER* 1.3 68.9 + - - +
256A VAL* 1.3 60.5 + - - +
257A PRO* 3.4 1.9 - - - +
258A GLN* 3.0 40.8 + - - +
259A THR* 2.8 41.8 + - + +
281A THR* 6.3 0.4 - - + -
285A ALA* 3.7 16.3 - - + +
286A GLU* 3.5 11.6 + - - +
287A ILE* 2.9 32.2 + - + +
1091A PRO* 6.6 0.2 - - + -
1162A TYR* 5.8 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A TRP* 3.9 32.1 - - + -
251A ALA* 4.6 6.7 - - + -
254A SER* 3.2 25.0 + - - +
255A ASN* 1.3 70.8 - - - +
257A PRO* 1.3 66.9 - - + +
259A THR* 3.8 5.4 - - - -
260A ARG* 2.7 42.8 + - + +
264A ALA* 4.4 13.2 - - + -
267A PHE* 4.9 12.8 - - + -
287A ILE* 4.2 8.5 - - + -
539A ILE* 4.2 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ASN* 3.5 2.7 - - - +
256A VAL* 1.3 96.0 - - + +
258A GLN* 1.3 57.0 + - - +
261A THR* 2.8 26.6 + - - +
264A ALA* 4.1 12.3 - - + -
286A GLU* 3.7 21.7 - - + +
287A ILE* 3.7 33.4 - - + +
290A LEU* 4.2 13.2 - - + -
17B ILE* 3.8 34.9 - - + +
19B CYS* 5.2 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ARG* 3.6 15.8 + - - +
255A ASN* 3.0 26.4 + - + +
257A PRO* 1.3 79.4 - - - +
259A THR* 1.3 62.3 + - + +
260A ARG 3.6 0.4 - - - -
261A THR* 3.6 9.6 + - - -
286A GLU* 3.3 33.3 - - - +
1092A HIS 2.8 26.8 + - - +
1093A GLN* 3.4 16.7 - - - +
1094A LYS* 3.5 30.9 - - + +
1162A TYR* 4.0 17.9 + - - -
147B ASP* 4.3 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ARG* 5.7 1.3 - - - -
254A SER* 4.6 3.6 + - - -
255A ASN* 2.8 38.5 + - + +
256A VAL* 3.8 3.1 + - - -
258A GLN* 1.3 81.0 - - + +
260A ARG* 1.3 83.3 + - - +
261A THR 3.7 1.1 - - - -
577A TYR 5.3 4.8 + - - -
1092A HIS* 4.0 38.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLY* 4.0 9.4 - - - +
243A TRP* 4.4 4.9 - - + -
256A VAL* 2.7 28.3 + - + +
259A THR* 1.3 90.1 + - - +
261A THR* 1.3 66.0 + - - +
262A PRO* 3.4 6.5 - - - -
263A ASP* 2.9 25.7 + - + +
264A ALA* 3.2 8.8 + - - -
577A TYR* 3.6 22.2 + - + +
578A VAL* 3.5 37.8 + - - +
579A GLY* 4.2 1.8 - - - +
580A GLN* 2.9 38.4 + - - +
801A ASP* 4.5 1.7 + - - -
802A MET* 3.3 38.3 - - + -
----------------------------------------------------------
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