Contacts of the helix formed by residues 300 - 314 (chain D) in PDB entry 4DVQ
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 SER 300 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D LYS* 4.9 6.2 - - - +
299D LEU* 1.3 77.8 - - - +
301D LEU* 1.3 55.1 + - - +
302D GLU* 3.7 7.1 + - - +
303D ALA* 3.0 25.0 + - - +
304D ILE* 2.8 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 301 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D ILE* 5.8 2.7 - - + -
275D TYR* 3.8 44.0 - - + +
294D LEU* 4.2 16.2 - - + -
300D SER* 1.3 73.1 - - - +
302D GLU* 1.3 67.5 + - + +
304D ILE* 3.3 5.4 + - + +
305D LYS* 3.0 54.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 302 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D GLY 4.6 8.0 - - - +
125D HIS* 4.6 18.0 + - - +
126D LYS* 4.2 25.0 + - + +
300D SER* 3.2 5.4 + - - +
301D LEU* 1.3 84.3 - - + +
303D ALA* 1.3 55.7 + - - +
305D LYS* 3.2 36.5 + - - +
306D ALA* 3.1 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 303 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D LYS* 4.7 9.6 - - + +
127D CYS 5.9 0.9 - - - -
140D ASN* 4.0 17.7 - - - +
299D LEU* 3.9 13.5 - - + -
300D SER* 3.0 29.9 + - - +
302D GLU* 1.3 73.8 - - - +
304D ILE* 1.3 66.8 + - - +
305D LYS 3.1 1.0 + - - -
306D ALA* 3.3 5.3 + - - +
307D ASN* 3.1 29.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 304 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D ILE* 4.8 3.6 - - + -
290D VAL* 4.3 3.8 - - + -
293D LEU* 3.3 47.5 - - + +
294D LEU* 3.5 41.1 - - + +
297D ALA* 5.0 2.0 - - - -
299D LEU* 4.0 27.5 - - + +
300D SER 2.8 21.5 + - - +
301D LEU* 3.7 8.3 - - + +
303D ALA* 1.3 71.2 - - - +
305D LYS* 1.3 51.2 + - + +
307D ASN* 3.4 5.4 + - - +
308D SER* 2.7 51.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 305 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D ASP* 4.8 7.2 + - - +
271D ILE* 4.1 35.9 - - + +
272D GLN* 4.3 14.9 + - - +
301D LEU* 3.0 41.4 + - + +
302D GLU* 3.2 35.6 + - - +
303D ALA 3.1 0.2 - - - -
304D ILE* 1.3 73.0 - - + +
306D ALA* 1.3 66.4 + - - +
308D SER* 3.3 6.9 + - - -
309D MET* 3.0 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 306 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D ARG* 5.8 0.3 + - - -
125D HIS* 6.0 0.9 - - + -
126D LYS* 3.4 30.5 - - + +
127D CYS 3.9 5.4 - - - +
128D GLY* 3.8 15.9 - - - +
264D PHE* 6.0 4.0 - - - -
302D GLU 3.1 13.9 + - - +
303D ALA* 3.7 4.9 - - - +
305D LYS* 1.3 78.9 - - - +
307D ASN* 1.3 62.7 + - - +
309D MET* 3.3 9.5 + - - +
310D GLU* 3.2 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 307 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D GLY* 4.1 2.8 - - - -
129D VAL* 2.9 32.4 + - - +
140D ASN* 2.8 27.3 + - - +
144D LEU* 3.3 40.6 - - + +
293D LEU* 5.5 2.0 - - + -
299D LEU* 4.3 4.9 - - - +
303D ALA 3.1 20.1 + - - +
304D ILE* 3.9 3.4 - - - +
306D ALA* 1.3 72.5 - - - +
308D SER* 1.3 66.7 + - - +
310D GLU* 3.0 7.8 + - - +
311D LEU* 3.0 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 308 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D LEU* 5.2 0.2 - - - +
205D PHE* 4.7 4.4 - - - -
271D ILE* 3.8 22.4 - - - +
290D VAL* 3.6 32.6 - - - +
293D LEU* 4.9 3.6 - - - +
304D ILE* 2.7 32.6 + - - +
305D LYS 3.3 5.1 + - - -
307D ASN* 1.3 73.7 - - - +
309D MET* 1.3 51.6 + - - +
311D LEU* 3.5 10.4 + - - +
312D THR* 2.7 37.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 309 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D ARG* 5.3 5.4 + - - +
260D TRP* 5.1 0.7 - - + -
263D ILE* 3.5 40.2 - - + +
264D PHE* 3.8 48.7 - - + +
267D GLY* 3.5 32.3 - - - -
268D ASP 4.3 0.2 - - - -
271D ILE* 6.4 1.3 - - + -
305D LYS* 3.0 15.1 + - + +
306D ALA 3.5 10.1 - - - +
307D ASN 3.2 0.2 - - - -
308D SER* 1.3 74.5 - - - +
310D GLU* 1.3 63.7 + - - +
312D THR* 4.4 4.9 - - + -
313D ALA* 3.0 32.9 + - + +
602D 1CA 4.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 310 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D TRP* 6.2 0.7 - - + -
120D ARG* 5.0 10.3 + - - +
128D GLY* 3.0 32.5 + - - +
129D VAL* 3.2 11.7 + - - +
130D PHE* 2.7 41.5 + - - +
131D LEU* 3.6 12.5 + - - +
306D ALA 3.2 12.8 + - - +
307D ASN* 3.0 9.5 + - - +
309D MET* 1.3 75.9 - - - +
311D LEU* 1.3 55.0 + - + +
314D GLY* 2.7 35.9 + - - -
601D HEM 3.8 8.1 - - + +
602D 1CA 3.3 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 311 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D LEU* 5.4 1.1 - - + -
148D VAL* 4.0 37.2 - - + -
204D LEU* 3.7 31.5 - - + +
289D ILE* 4.6 5.4 - - + -
290D VAL* 5.2 1.8 - - + -
293D LEU* 5.1 8.7 - - + -
307D ASN* 3.0 25.6 + - + +
308D SER* 3.7 8.3 - - - +
310D GLU* 1.3 77.6 - - - +
312D THR* 1.3 56.9 - - - +
315D SER* 2.9 32.1 + - - -
451D LEU* 4.1 17.7 - - + -
601D HEM 3.6 32.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 312 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D ASN* 5.5 0.9 - - - +
204D LEU* 4.0 7.0 - - + +
205D PHE* 3.5 30.5 - - + -
223D PHE* 3.8 12.7 - - + -
266D TYR* 4.0 33.0 - - + -
267D GLY* 4.5 12.5 - - - -
308D SER 2.7 22.4 + - - -
309D MET* 4.1 8.5 - - + -
310D GLU 3.3 0.2 - - - -
311D LEU* 1.3 76.5 - - - +
313D ALA* 1.3 62.9 + - - +
315D SER* 3.3 14.8 + - - -
316D VAL* 4.1 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 313 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223D PHE* 4.2 10.8 - - - -
227D LEU* 3.4 24.6 - - + +
230D MET* 5.9 0.9 - - + -
231D PHE* 5.0 2.4 - - - -
260D TRP* 4.6 10.5 - - + -
263D ILE* 3.9 24.9 - - + -
309D MET* 3.0 20.5 + - + +
310D GLU 4.1 1.8 - - - +
312D THR* 1.3 78.5 - - - +
314D GLY* 1.3 59.4 + - - +
315D SER 3.4 1.2 + - - -
316D VAL 4.5 3.1 + - - -
317D ASP* 4.9 2.6 + - - +
318D THR* 5.9 0.2 - - - +
602D 1CA 4.4 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 314 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D GLU 2.7 18.9 + - - -
311D LEU 3.8 1.3 - - - -
312D THR 3.2 0.2 - - - -
313D ALA* 1.3 77.1 - - - +
315D SER* 1.3 55.7 + - - +
316D VAL 3.6 0.9 - - - -
318D THR* 2.7 31.6 + - - +
601D HEM 3.2 16.2 - - - -
602D 1CA 3.8 25.7 - - - +
----------------------------------------------------------
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