Contacts of the helix formed by residues 250 - 264 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ALA* 3.5 27.8 + - + +
35A ALA* 5.2 0.3 - - - -
38A HIS* 3.6 45.7 - + + +
62A ASP* 3.7 11.6 + - - -
65A ASP* 3.1 16.6 + - + +
66A PHE* 3.6 43.7 - + + -
69A ALA* 4.2 4.7 - - + -
35C ALA* 4.6 7.6 - - + -
245C LYS* 3.3 31.3 - - - -
247C TYR* 5.6 1.7 + - - -
249C SER* 1.3 83.1 - - - +
251C GLY* 1.3 66.0 + - - +
253C ALA* 4.5 3.1 - - - -
254C THR* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 251 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASP* 2.9 31.6 + - - -
68A ASP* 4.3 2.0 - - - +
69A ALA* 4.1 13.8 - - - -
72A ASN* 5.0 2.6 + - - -
170C LEU* 3.7 21.7 - - - +
250C TYR* 1.3 74.8 - - - +
252C VAL* 1.4 60.5 + - - +
254C THR* 3.9 3.1 - - - -
255C SER* 3.4 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 252 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASP* 4.9 0.4 + - - -
32C VAL* 3.8 26.9 - - + -
141C ILE* 3.7 24.1 - - + +
166C THR* 4.2 11.0 - - - +
170C LEU* 3.8 23.1 - - + +
248C THR* 4.4 2.3 + - - +
249C SER* 3.6 12.1 - - - +
250C TYR 3.4 0.2 - - - -
251C GLY* 1.4 71.8 - - - +
253C ALA* 1.3 70.8 + - - +
255C SER* 3.1 22.4 + - - +
256C ALA* 3.3 7.3 + - - +
330C NAD 3.7 36.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 253 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A HIS* 5.3 2.7 - - + -
32C VAL* 4.3 3.1 - - + +
35C ALA* 4.0 12.8 - - + +
36C VAL* 3.6 39.7 - - + +
249C SER 2.8 23.9 + - - +
250C TYR* 3.9 3.4 - - - +
252C VAL* 1.3 74.2 - - - +
254C THR* 1.3 63.2 + - - +
256C ALA* 3.3 4.7 + - - +
257C ILE* 3.1 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 254 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A HIS* 5.0 8.8 + - - -
69A ALA* 3.5 24.1 - - - +
72A ASN* 3.5 32.5 - - + +
73A LEU* 3.9 19.9 - - + +
250C TYR* 2.9 20.1 + - - +
251C GLY 3.9 4.3 - - - -
253C ALA* 1.3 75.7 - - - +
255C SER* 1.3 64.3 + - - +
257C ILE* 3.4 13.4 + - + +
258C ARG* 3.0 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 255 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASN* 3.9 14.2 + - - +
166C THR* 4.3 13.5 - - - -
169C LEU* 3.9 21.2 - - - +
170C LEU* 3.7 21.8 + - - +
251C GLY 3.4 13.1 + - - -
252C VAL* 3.1 13.6 + - - -
254C THR* 1.3 76.0 - - - +
256C ALA* 1.3 65.4 + - - -
258C ARG* 3.2 4.2 + - - +
259C ILE* 3.2 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 256 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C VAL* 4.5 3.8 - - + -
94C ILE* 4.3 21.5 - - + +
139C VAL* 4.6 6.2 - - + +
141C ILE* 3.8 28.7 - - + -
166C THR* 4.1 12.1 - - + -
252C VAL 3.3 2.6 + - - -
253C ALA 3.6 7.6 - - - +
255C SER* 1.3 78.5 - - - +
257C ILE* 1.3 52.4 - - - +
259C ILE* 3.3 7.8 + - - +
260C ALA* 2.8 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 257 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A HIS* 5.5 2.5 - - - +
74A GLU* 5.6 1.6 - - - +
35C ALA 4.7 1.6 - - - +
36C VAL* 3.9 28.0 - - + +
39C GLY* 3.9 20.6 - - - -
40C LEU* 4.2 22.2 - - + -
43C GLN* 4.2 13.0 - - - +
94C ILE* 5.6 0.9 - - + -
253C ALA* 3.1 23.3 + - + +
254C THR* 3.6 15.0 - - + +
255C SER 3.2 0.2 - - - -
256C ALA* 1.3 75.7 - - - +
258C ARG* 1.3 62.3 + - - +
260C ALA* 3.3 7.9 + - - +
261C LYS* 3.0 46.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 258 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ALA* 3.7 13.8 + - - +
72A ASN* 2.6 57.6 + - + +
169C LEU* 4.8 6.3 - - + +
176C GLN* 5.8 0.8 + - - -
254C THR 3.0 16.7 + - - +
255C SER* 3.2 5.4 + - - +
257C ILE* 1.3 77.4 - - - +
259C ILE* 1.3 62.4 + - - +
261C LYS* 3.4 8.8 + - - +
262C ALA* 3.2 20.8 + - - +
270C GLU 5.0 3.8 + - - -
271C LEU* 3.4 32.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 259 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C VAL* 4.0 20.4 - - + -
164C ILE* 4.0 26.7 - - + -
165C GLY 4.8 0.9 - - - +
166C THR* 4.0 29.4 - - + +
169C LEU* 3.9 16.2 - - + -
255C SER 3.2 15.3 + - - +
256C ALA* 3.5 5.4 - - - +
258C ARG* 1.3 73.3 - - - +
260C ALA* 1.3 64.8 + - - +
262C ALA* 3.1 4.0 + - - +
263C VAL* 3.1 26.0 + - + +
271C LEU* 4.1 13.0 - - + -
273C VAL* 3.8 25.1 - - + -
290C ILE* 4.6 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 260 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ILE* 5.0 6.5 - - + -
40C LEU* 5.2 4.0 - - + -
92C VAL* 3.9 28.8 - - + +
94C ILE* 4.5 11.4 - - + -
139C VAL* 5.2 0.9 - - + +
256C ALA 2.8 19.5 + - - +
257C ILE* 3.3 10.1 + - - +
259C ILE* 1.3 72.5 - - - +
261C LYS* 1.3 61.8 + - - +
263C VAL* 3.4 3.4 + - - +
264C MET* 3.1 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 261 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLU* 2.9 33.6 + - - +
22C ARG* 6.5 0.9 - - - -
43C GLN* 2.7 32.1 + - - +
45C VAL* 3.6 37.7 - - + +
257C ILE* 3.0 32.4 + - + +
258C ARG* 3.8 7.6 - - - +
260C ALA* 1.3 75.9 - - + +
262C ALA* 1.3 65.6 + - - +
264C MET* 4.2 6.8 - - + +
265C ALA* 3.0 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 262 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C ARG* 3.2 11.0 + - + +
259C ILE 3.1 9.7 + - - +
261C LYS* 1.3 76.8 - - - +
263C VAL* 1.4 62.3 + - - +
266C ASP* 3.2 3.3 + - - -
267C ALA* 3.1 44.5 + - + -
269C ALA* 4.4 8.1 - - + -
271C LEU* 4.0 20.9 - - + -
290C ILE* 4.2 10.3 - - + +
291C GLY* 4.0 5.0 - - - -
188D ARG* 5.9 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 263 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C ASP* 4.3 5.8 - - + +
92C VAL* 3.7 20.2 - - + -
137C VAL* 3.7 41.1 - - + -
139C VAL* 5.5 0.9 - - + -
259C ILE* 3.1 19.9 + - + +
260C ALA* 3.6 7.2 - - - +
262C ALA* 1.4 75.0 - - - +
264C MET* 1.3 64.9 + - + +
266C ASP 3.1 10.7 + - - -
290C ILE* 3.8 14.1 - - + -
291C GLY 3.4 20.4 - - - +
292C ARG* 3.1 27.3 - - + +
294C GLY* 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 264 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ALA* 3.6 4.1 - - + +
47B ASP* 3.2 21.8 - - - +
22C ARG* 3.6 33.9 - - + +
24C ILE* 3.7 33.0 - - + -
45C VAL* 3.7 23.8 - - + -
91C ASP* 4.0 29.6 - - + +
92C VAL* 4.1 5.2 - - + -
260C ALA* 3.1 25.5 + - + +
261C LYS* 4.2 6.7 - - - +
263C VAL* 1.3 76.0 - - - +
265C ALA* 1.3 51.4 + - - +
292C ARG* 2.6 34.8 + - - +
----------------------------------------------------------
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