Contacts of the helix formed by residues 259 - 269 (chain I) in PDB entry 3SWD
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 LEU 259 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232I ARG* 3.4 33.2 - - + +
233I ILE* 6.1 0.2 - - + -
235I THR* 3.6 35.0 - - + -
236I GLY* 4.6 3.8 - - - +
239I LEU* 4.6 6.1 - - + -
255I GLN 5.1 4.3 - - - +
256I PRO 2.9 9.4 + - - +
258I THR* 1.3 89.0 - - + +
260I ASP* 1.3 65.7 + - - +
261I ALA 3.4 2.2 - - - -
262I VAL* 3.2 29.2 + - + -
263I LEU* 2.9 32.7 + - + +
280I ILE* 3.8 15.7 - - + -
303I PRO* 6.1 1.6 - - + -
306I MET* 5.7 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 260 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256I PRO 4.1 8.8 - - - +
257I ASP* 3.7 21.4 + - - +
258I THR 3.7 2.0 + - - -
259I LEU* 1.3 75.3 - - - +
261I ALA* 1.3 64.0 + - - +
263I LEU* 3.3 6.3 + - - +
264I ALA* 3.0 22.1 + - - +
267I ARG* 5.4 0.2 + - - -
299I HIS* 6.1 0.8 - - - -
300I PRO* 5.5 9.2 - - + +
155L HIS* 4.4 14.2 - - + -
157L VAL* 4.5 21.9 - - + +
183L GLU* 3.6 22.9 - - + +
212L ARG* 5.3 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 261 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259I LEU 3.4 0.6 - - - -
260I ASP* 1.3 76.9 - - - +
262I VAL* 1.3 62.6 + - - +
264I ALA* 3.2 8.4 + - - +
265I LYS* 3.0 27.3 + - + +
300I PRO 3.6 23.2 + - - +
301I ALA* 3.8 3.8 - - - +
302I PHE* 3.7 29.8 - - + +
303I PRO* 5.0 2.2 - - + -
157L VAL* 4.7 11.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 262 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236I GLY* 4.6 14.6 - - - +
239I LEU* 5.2 0.4 - - + -
259I LEU* 3.2 30.0 + - + +
261I ALA* 1.3 76.1 - - - +
263I LEU* 1.3 67.6 + - + +
265I LYS* 3.2 4.0 + - - +
266I LEU* 3.0 33.9 + - + +
302I PHE* 4.3 15.0 - - + -
303I PRO* 4.1 24.5 - - + -
306I MET* 4.1 18.4 - - + -
310I PHE* 4.0 16.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 263 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239I LEU* 3.7 30.1 - - + -
256I PRO* 4.3 12.3 - - + +
259I LEU* 2.9 33.3 + - + +
260I ASP* 3.9 5.4 - - - +
262I VAL* 1.3 75.9 - - + +
264I ALA* 1.3 63.1 + - - +
266I LEU* 3.2 5.9 + - + +
267I ARG* 3.1 41.7 + - - +
273I ILE* 3.8 20.1 - - + +
275I VAL* 4.2 24.0 - - + -
280I ILE* 4.1 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 264 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260I ASP 3.0 12.4 + - - +
261I ALA* 3.4 11.2 - - - +
263I LEU* 1.3 77.1 - - - +
265I LYS* 1.3 66.5 + - + +
267I ARG* 3.2 17.6 + - - +
268I ASP* 3.0 30.3 + - - +
157L VAL* 4.9 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 265 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261I ALA* 3.0 17.5 + - + +
262I VAL 3.2 4.5 + - - +
264I ALA* 1.3 81.4 - - + +
266I LEU* 1.3 62.1 - - - +
268I ASP* 3.2 22.6 + - - +
269I ALA* 3.0 21.0 + - - +
292I VAL* 3.9 11.8 - - + +
293I ASN 2.9 29.7 + - - +
294I VAL* 3.9 24.0 - - + +
295I ARG 5.7 0.7 - - - +
302I PHE* 4.5 14.4 - - + -
310I PHE* 3.6 21.6 - - + -
159L ASP* 3.5 26.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 266 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239I LEU* 3.7 24.0 - - + -
240I VAL* 4.3 8.5 - - + -
243I ALA* 4.2 16.4 - - + -
262I VAL* 3.0 28.8 + - + +
263I LEU* 3.7 2.9 - - + +
264I ALA 3.2 0.2 - - - -
265I LYS* 1.3 73.0 - - - +
267I ARG* 1.3 64.9 + - - +
269I ALA* 2.9 16.1 + - + +
270I GLY 3.2 0.5 + - - -
271I ALA* 3.1 22.4 + - + +
273I ILE* 3.6 21.3 - - + -
282I LEU* 3.7 17.7 - - + -
310I PHE* 3.6 22.7 - - + -
313I LEU* 4.1 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 267 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260I ASP 5.4 0.2 + - - -
263I LEU* 3.1 35.5 + - - +
264I ALA* 3.2 14.1 + - - +
266I LEU* 1.3 73.9 - - - +
268I ASP* 1.3 57.0 + - - +
270I GLY* 2.5 28.2 + - - -
271I ALA 3.5 19.1 + - - +
273I ILE* 4.1 40.2 + - + +
275I VAL* 5.1 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 268 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264I ALA* 3.0 19.3 + - - +
265I LYS* 3.2 27.3 + - - +
267I ARG* 1.3 76.9 - - - +
269I ALA* 1.3 59.8 + - - +
270I GLY* 3.0 1.1 + - - -
290I LYS* 4.2 8.5 - - - +
291I ALA 4.7 1.2 - - - +
292I VAL* 3.7 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 269 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243I ALA* 6.1 0.9 - - + -
265I LYS 3.0 9.9 + - - +
266I LEU* 2.9 13.8 + - + +
268I ASP* 1.3 76.6 - - - +
270I GLY* 1.3 59.0 + - - +
271I ALA* 5.0 1.1 - - + +
284I MET* 4.3 2.2 - - + +
288I ARG 4.6 0.5 - - - +
289I PRO* 3.5 10.9 - - + +
290I LYS* 2.7 50.1 + - - +
292I VAL* 3.7 5.6 - - + +
310I PHE* 5.8 0.4 - - + -
313I LEU* 4.1 26.2 - - + -
----------------------------------------------------------
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