Contacts of the helix formed by residues 298 - 310 (chain D) in PDB entry 1USK
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 GLU 298 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ALA* 4.0 26.8 - - - +
191B LYS* 5.9 5.1 - - + +
296D SER* 3.4 17.0 + - - +
297D ASP* 1.3 87.8 - - - +
299D PRO* 1.3 74.1 - - + +
300D LEU* 4.7 1.6 - - + +
301D ALA* 3.3 13.6 + - + +
302D LEU* 3.3 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 299 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B LYS* 5.8 7.0 - - + -
71D LYS* 4.2 26.7 - - + +
72D TYR* 4.6 2.5 - - + -
93D GLY 3.2 28.3 - - - +
95D LEU* 3.9 23.1 - - + +
113D HIS* 4.5 4.5 - - + -
297D ASP 3.6 7.9 - - - +
298D GLU* 1.3 84.7 - - + +
300D LEU* 1.3 62.9 + - - +
302D LEU* 3.3 20.7 + - + +
303D VAL* 3.4 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 300 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D GLN* 3.5 52.7 - - + +
113D HIS* 4.1 23.5 - - + +
298D GLU* 3.4 1.9 - - + +
299D PRO* 1.3 80.3 - - - +
301D ALA* 1.3 61.6 + - - +
303D VAL* 3.7 4.3 + - + +
304D LYS* 3.3 22.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 301 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294D THR* 5.1 3.1 - - - +
296D SER* 3.8 23.6 - - - +
298D GLU* 3.3 17.7 + - + +
299D PRO 3.3 0.4 - - - -
300D LEU* 1.3 77.4 - - - +
302D LEU* 1.3 60.1 + - - +
304D LYS* 3.7 7.2 + - - +
305D ASP* 3.2 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 302 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D TYR* 3.7 32.5 - - + +
95D LEU* 4.1 10.5 - - + -
287D LEU* 4.7 5.8 - - + +
290D ALA* 3.4 45.5 - - + +
291D LEU* 3.6 26.0 - - + +
294D THR* 3.9 7.6 - - - +
296D SER* 4.0 9.9 - - - +
298D GLU 3.3 18.6 - - - +
299D PRO* 3.3 7.5 + - + +
301D ALA* 1.3 76.7 - - - +
303D VAL* 1.3 63.7 + - - +
305D ASP* 3.3 4.2 + - - +
306D LEU* 3.2 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 303 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D LEU* 3.6 24.9 - - + -
112D GLN 3.1 28.7 - - - +
113D HIS* 4.0 17.7 - - - +
114D ILE 5.1 0.2 - - - +
115D MET* 3.9 24.4 - - + +
299D PRO 3.4 9.8 + - - +
300D LEU* 4.0 6.7 - - + +
301D ALA 3.5 0.2 - - - -
302D LEU* 1.3 73.8 - - - +
304D LYS* 1.3 65.2 + - - +
306D LEU* 3.4 3.3 + - - +
307D LYS* 3.2 46.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 304 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300D LEU* 3.3 18.7 + - + +
301D ALA* 4.0 7.6 - - - +
302D LEU 3.3 0.4 - - - -
303D VAL* 1.3 79.0 - - - +
305D ASP* 1.3 62.8 + - - +
307D LYS* 3.5 13.0 + - + +
308D ALA* 3.3 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 305 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D ALA* 3.4 20.1 - - - +
293D ARG* 2.9 45.1 + - - +
294D THR* 3.2 25.7 - - + +
301D ALA 3.2 19.0 + - - +
302D LEU* 3.7 4.3 - - - +
303D VAL 3.2 1.0 - - - -
304D LYS* 1.3 78.8 - - - +
306D LEU* 1.3 62.9 + - - +
308D ALA* 4.1 3.5 - - - +
309D ASN* 3.2 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 306 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D LEU* 5.4 2.9 - - + -
97D ILE* 4.2 16.6 - - + -
115D MET* 3.8 34.3 - - + -
286D SER* 3.2 38.1 - - - +
287D LEU* 4.8 1.1 - - - +
289D THR* 4.8 0.2 - - - -
290D ALA* 3.9 14.4 - - + +
293D ARG* 3.9 5.6 - - - +
302D LEU 3.2 20.2 + - - +
303D VAL 3.9 0.7 - - - +
304D LYS 3.4 0.2 - - - -
305D ASP* 1.3 73.9 - - - +
307D LYS* 1.3 63.3 + - - +
310D GLY* 2.9 39.6 + - - +
311D ALA* 4.2 2.2 - - + -
320D TRP* 3.4 28.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 307 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D TYR 4.6 2.4 + - - -
112D GLN* 4.2 16.6 + - - +
114D ILE 5.0 1.4 + - - -
115D MET* 4.1 11.0 - - + -
303D VAL* 3.2 39.7 + - + +
304D LYS* 3.8 10.5 - - + +
306D LEU* 1.3 79.0 - - - +
308D ALA* 1.3 58.2 + - - +
320D TRP* 3.3 25.9 + - + +
321D ASP 3.6 20.4 - - - +
322D GLU* 2.8 39.6 + - + +
323D LYS 4.4 1.8 - - - -
324D GLY* 4.0 14.4 - - - +
327D LYS* 5.7 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 308 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D LYS* 3.3 22.2 + - - +
305D ASP* 4.3 4.9 - - - +
306D LEU 3.2 0.6 - - - -
307D LYS* 1.3 82.0 - - - +
309D ASN* 1.3 71.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 309 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293D ARG* 3.3 30.8 + - - +
305D ASP* 3.2 20.4 + - - +
308D ALA* 1.3 94.4 - - - +
310D GLY* 1.3 62.4 + - - +
319D ASN* 4.7 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 310 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D THR* 4.0 0.5 - - - +
293D ARG* 2.9 27.7 + - - +
306D LEU* 2.9 20.1 + - - +
307D LYS 4.9 0.2 - - - -
309D ASN* 1.3 79.4 - - - +
311D ALA* 1.3 65.4 + - - +
318D LEU 3.2 17.3 - - - -
319D ASN* 4.3 7.6 - - - -
320D TRP* 3.9 4.7 - - - -
----------------------------------------------------------
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