Contacts of the helix formed by residues 250 - 265 (chain D) in PDB entry 1HYH
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 TYR 250 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ALA* 3.2 29.1 + - - +
35B ALA* 5.3 0.2 - - - -
38B HIS* 3.5 41.7 - + + +
62B ASP* 3.7 11.1 + - - -
65B ASP* 3.2 29.5 + - + +
66B PHE* 3.5 45.5 - + + -
69B ALA* 3.9 4.2 - - + +
35D ALA* 4.5 6.7 - - + -
245D LYS* 3.3 20.2 - - - -
249D SER* 1.3 82.5 + - - +
251D GLY* 1.3 62.4 + - - +
253D ALA* 4.4 3.8 - - - -
254D THR* 2.8 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ASP* 3.3 26.7 + - - -
68B ASP* 4.3 2.6 - - - +
69B ALA* 4.1 13.8 - - - -
72B ASN* 5.0 2.1 + - - -
170D LEU* 3.7 20.3 - - - +
250D TYR* 1.3 80.1 - - - +
252D VAL* 1.4 57.6 + - - +
254D THR* 4.1 2.4 - - - -
255D SER* 3.1 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ASP* 5.1 0.2 + - - -
32D VAL* 4.0 20.0 - - + -
141D ILE* 4.0 16.3 - - + +
166D THR* 4.1 13.2 - - - +
170D LEU* 4.0 17.3 - - + +
248D THR* 4.3 5.8 + - - +
249D SER 3.4 9.3 + - - +
251D GLY* 1.4 72.8 - - - +
253D ALA* 1.3 68.6 + - - +
255D SER* 3.2 14.1 + - - +
256D ALA* 3.2 13.2 + - - +
330D NAD 3.7 53.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B HIS* 5.3 1.8 - - + -
32D VAL* 4.3 4.0 - - + +
35D ALA* 3.9 13.2 - - + +
36D VAL* 3.6 39.3 - - + +
141D ILE* 5.0 0.2 - - - -
249D SER 2.8 20.6 + - - +
250D TYR* 4.0 3.6 - - - +
252D VAL* 1.3 78.8 - - - +
254D THR* 1.4 64.9 + - - +
256D ALA* 3.1 5.6 + - - +
257D ILE* 3.0 28.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B HIS* 4.8 9.9 + - - -
69B ALA* 3.6 24.4 - - - +
72B ASN* 3.5 32.0 - - + +
73B LEU* 3.8 19.4 - - + +
250D TYR* 2.8 24.5 + - - +
251D GLY 4.1 2.9 - - - -
253D ALA* 1.4 78.0 - - - +
255D SER* 1.3 59.4 + - - +
257D ILE* 3.4 13.4 + - + +
258D ARG* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ASN* 3.9 16.2 + - - +
166D THR* 4.4 12.1 - - - -
169D LEU* 3.6 26.3 - - - +
170D LEU* 4.0 14.4 + - - -
251D GLY 3.1 15.6 + - - -
252D VAL* 3.2 13.7 + - - -
254D THR* 1.3 76.0 - - - +
256D ALA* 1.3 62.4 + - - +
258D ARG* 3.5 3.0 + - - +
259D ILE* 3.3 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 256 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D VAL* 4.5 4.7 - - + -
94D ILE* 4.3 19.8 - - + +
139D VAL* 4.6 6.5 - - + +
141D ILE* 3.7 29.4 - - + -
166D THR* 4.1 13.0 - - + +
252D VAL 3.2 1.9 + - - +
253D ALA 3.1 10.1 + - - +
255D SER* 1.3 78.1 - - - +
257D ILE* 1.3 58.8 + - - +
259D ILE* 3.2 7.5 + - - +
260D ALA* 2.8 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 257 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B HIS* 5.6 1.8 - - - +
35D ALA 4.7 0.9 - - - +
36D VAL* 3.7 32.5 - - + +
39D GLY* 4.0 22.7 - - - -
40D LEU* 4.0 23.3 - - + +
43D GLN* 4.5 6.5 - - - +
94D ILE* 5.6 0.9 - - - -
253D ALA* 3.0 18.2 + - + +
254D THR* 3.6 15.3 - - + +
255D SER 3.3 0.2 - - - -
256D ALA* 1.3 76.1 - - - +
258D ARG* 1.3 62.4 + - - +
260D ALA* 3.2 7.7 + - - +
261D LYS* 3.0 49.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 258 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ALA 3.7 12.6 + - - -
72B ASN* 2.4 59.3 + - + +
169D LEU* 4.7 4.8 - - + +
254D THR 3.1 17.6 + - - +
255D SER* 3.7 6.5 - - - +
257D ILE* 1.3 77.9 - - - +
259D ILE* 1.3 61.9 + - - +
261D LYS* 3.4 9.1 + - - +
262D ALA* 3.1 21.7 + - - +
269D ALA* 6.3 0.4 - - - +
270D GLU 5.1 4.0 + - - -
271D LEU* 3.5 32.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D VAL* 4.0 19.5 - - + -
164D ILE* 3.7 27.4 - - + -
165D GLY 4.7 0.7 - - - +
166D THR* 4.1 26.7 - - + -
169D LEU* 3.7 19.1 - - + -
255D SER 3.3 15.2 + - - +
256D ALA* 3.2 7.5 + - - +
258D ARG* 1.3 75.0 - - - +
260D ALA* 1.3 64.3 + - - +
262D ALA* 3.1 3.6 + - - +
263D VAL* 3.0 26.1 + - + +
271D LEU* 4.2 13.0 - - + -
273D VAL* 3.7 26.5 - - + -
290D ILE* 4.7 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 260 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ILE* 4.6 13.2 - - + -
40D LEU* 5.3 3.4 - - + -
92D VAL* 4.3 28.9 - - + -
94D ILE* 4.5 10.3 - - + -
139D VAL* 5.2 0.6 - - - +
256D ALA 2.8 17.7 + - - +
257D ILE* 3.2 9.6 + - - +
259D ILE* 1.3 77.4 - - - +
261D LYS* 1.3 61.8 + - - +
263D VAL* 3.2 4.1 + - - +
264D MET* 3.0 30.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 261 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ASP* 4.9 0.2 - - - +
74B GLU* 2.7 32.8 + - - +
22D ARG* 6.5 0.2 - - - -
40D LEU* 5.8 0.2 - - + -
43D GLN* 3.0 28.3 + - - +
45D VAL* 3.7 38.4 - - + -
257D ILE* 3.0 31.9 + - + +
258D ARG* 3.7 7.9 - - - +
260D ALA* 1.3 72.6 - - + +
262D ALA* 1.3 65.5 + - - +
264D MET* 3.3 8.0 + - + +
265D ALA* 2.9 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 262 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C ARG* 6.0 1.3 - - - +
258D ARG 3.1 11.2 + - - +
259D ILE 3.1 8.0 + - - +
261D LYS* 1.3 77.8 - - - +
263D VAL* 1.4 62.1 + - - +
266D ASP* 3.1 2.6 + - - -
267D ALA* 3.1 34.0 + - + -
269D ALA* 4.2 17.7 - - + -
271D LEU* 3.9 22.0 - - + -
290D ILE* 4.2 10.8 - - + +
291D GLY* 4.0 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 263 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D ASP* 4.4 5.4 - - + +
92D VAL* 3.8 18.4 - - + -
137D VAL* 3.6 42.0 - - + -
139D VAL* 5.5 1.3 - - + -
164D ILE* 5.2 0.2 - - + -
259D ILE* 3.0 23.5 + - + +
260D ALA* 3.5 9.6 - - - +
262D ALA* 1.4 77.0 - - - +
264D MET* 1.3 64.6 + - + +
266D ASP 3.0 10.0 + - - -
290D ILE* 3.9 12.8 - - + -
291D GLY 3.5 15.3 - - - +
292D ARG* 3.1 31.0 - - + +
294D GLY* 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 264 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA* 3.5 7.6 - - + +
47A ASP* 3.3 20.6 - - - +
22D ARG* 3.7 31.4 - - - +
24D ILE* 3.7 36.1 - - + -
40D LEU* 5.5 0.2 - - + -
45D VAL* 3.9 24.0 - - + -
91D ASP* 3.9 24.5 - - + -
92D VAL* 3.9 6.5 - - + -
260D ALA* 3.0 25.6 + - + +
261D LYS* 4.2 6.1 - - - +
263D VAL* 1.3 74.9 - - - +
265D ALA* 1.3 57.3 + - - +
292D ARG* 2.8 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 265 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ASP* 3.2 19.2 + - + +
76A HIS* 3.3 38.4 - - + +
78A ASN* 2.7 28.9 + - - -
22D ARG* 5.7 0.2 - - - +
261D LYS* 2.9 18.2 + - + +
264D MET* 1.3 75.2 - - - +
266D ASP* 1.3 60.5 + - - +
267D ALA* 4.3 4.3 - - + +
292D ARG* 4.0 0.7 - - - -
----------------------------------------------------------
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