Contacts of the helix formed by residues 317 - 335 (chain Q) in PDB entry 3K9Q
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 317 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187P GLN* 4.0 13.7 + - - +
0Q NAD 4.1 13.3 + - - +
12Q ARG* 2.7 47.9 + - + +
13Q ILE* 4.1 7.1 - - + +
16Q LEU* 3.6 11.9 - - + -
50Q MET* 4.6 2.8 - - - +
51Q GLN* 3.0 20.1 + - - +
238Q ALA 4.5 0.5 - - - +
239Q THR* 3.2 22.0 + - - +
315Q ASP* 2.9 7.1 + - - +
316Q ASN* 1.3 85.1 - - - +
318Q MET* 1.3 61.0 + - - +
320Q TYR* 3.8 0.9 - - - +
321Q THR* 2.7 33.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 318 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16Q LEU* 4.1 32.5 - - + +
19Q ARG* 5.2 9.9 - - + +
20Q ARG* 4.6 18.2 - - + -
51Q GLN* 4.2 13.0 - - + +
285Q GLY* 3.6 19.3 - - - +
286Q MET 3.3 17.0 - - - +
287Q THR* 4.2 6.7 - - + -
315Q ASP* 3.3 20.7 - - - +
317Q GLU* 1.3 77.6 - - - +
319Q SER* 1.3 59.6 + - - +
321Q THR* 4.2 16.4 - - - -
322Q ALA* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 319 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286Q MET* 3.5 15.8 + - - +
288Q TYR 2.6 27.6 + - - -
289Q GLY* 3.9 16.0 - - - -
314Q TYR* 4.1 4.3 - - - -
315Q ASP* 2.8 39.6 + - - +
318Q MET* 1.3 71.4 - - - +
320Q TYR* 1.3 67.0 + - - +
322Q ALA* 3.4 4.2 + - - +
323Q GLN* 3.1 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 320 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0Q NAD 3.4 17.0 - + - -
13Q ILE* 4.1 11.9 - - + -
120Q SER* 2.9 44.2 - - - -
121Q ALA 3.2 0.3 + - - -
148Q GLY 3.1 23.3 + - - -
149Q ALA 2.6 29.4 + - - -
150Q SER* 3.3 12.1 - - - -
151Q GLY* 3.3 24.2 - - - -
154Q ASN* 3.5 11.2 - - - -
315Q ASP 3.6 1.4 + - - -
316Q ASN 3.2 21.1 - - - +
317Q GLU 3.4 1.0 + - - +
318Q MET 3.3 0.4 - - - -
319Q SER* 1.3 79.4 - - - +
321Q THR* 1.3 53.2 + - - +
323Q GLN* 3.1 7.5 + - - +
324Q LEU* 2.7 48.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 321 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13Q ILE* 3.8 19.8 - - - +
16Q LEU* 3.4 35.3 - - + +
17Q ALA* 3.4 22.2 - - + +
20Q ARG* 4.2 9.0 - - + -
317Q GLU 2.7 23.3 + - - -
318Q MET* 3.8 11.4 - - - -
320Q TYR* 1.3 76.5 - - - +
322Q ALA* 1.3 59.7 + - - +
324Q LEU* 3.2 7.0 + - - +
325Q VAL* 2.9 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 322 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20Q ARG* 4.0 21.2 + - - +
287Q THR* 3.4 37.9 - - + +
318Q MET 2.9 18.2 + - - +
319Q SER 3.7 2.0 - - - +
321Q THR* 1.3 76.5 - - - +
323Q GLN* 1.3 61.2 + - - +
325Q VAL* 3.5 2.1 + - - +
326Q ARG* 3.1 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 323 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131Q VAL* 3.7 6.3 - - - +
132Q PHE* 2.8 35.3 + - + +
148Q GLY 6.0 0.4 - - - +
154Q ASN* 3.1 36.0 + - + +
270Q SER* 2.7 30.7 + - - -
289Q GLY* 3.6 17.1 - - - -
319Q SER 3.1 17.7 + - - +
320Q TYR* 3.4 7.4 - - + +
322Q ALA* 1.3 73.9 - - - +
324Q LEU* 1.3 65.9 + - - +
326Q ARG* 3.0 24.7 + - - +
327Q THR* 2.9 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 324 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13Q ILE* 3.9 16.8 - - + -
17Q ALA* 5.1 2.7 - - + -
94Q LEU* 3.7 31.9 - - + -
96Q CYS* 4.7 0.4 - - - -
118Q LEU* 3.5 17.4 - - + +
119Q ILE 3.9 14.4 - - - +
120Q SER* 3.6 23.6 - - - -
148Q GLY* 3.9 13.9 - - - -
320Q TYR* 2.7 45.3 + - + +
321Q THR* 3.5 7.4 - - - +
323Q GLN* 1.3 73.9 - - - +
325Q VAL* 1.3 57.5 + - + +
327Q THR* 3.4 3.8 + - - -
328Q LEU* 2.8 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 325 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17Q ALA* 4.1 31.0 - - + +
20Q ARG* 4.2 19.7 - - + +
21Q ILE* 4.0 23.3 - - + -
24Q VAL* 4.1 24.2 - - + -
27Q LEU* 4.1 8.3 - - + -
94Q LEU* 5.2 1.6 - - + -
321Q THR 2.9 20.5 + - - +
322Q ALA 4.1 3.6 - - - +
324Q LEU* 1.3 77.0 - - + +
326Q ARG* 1.3 61.6 + - + +
328Q LEU* 3.5 7.4 - - + +
329Q ALA* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 326 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20Q ARG* 4.1 14.6 - - - +
132Q PHE* 3.6 40.8 - - + -
269Q GLU* 3.3 37.8 + - - +
270Q SER* 4.1 2.4 + - - -
287Q THR* 2.9 41.8 + - - -
289Q GLY 4.3 1.2 - - - +
322Q ALA* 3.1 24.7 + - - +
323Q GLN* 3.0 35.0 + - - +
325Q VAL* 1.3 78.3 - - - +
327Q THR* 1.3 62.1 + - - +
329Q ALA* 3.4 5.8 + - - +
330Q TYR 3.0 18.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 327 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118Q LEU* 4.1 23.1 - - + -
130Q ILE* 3.8 35.9 + - + +
132Q PHE* 3.5 26.0 + - - +
139Q LEU* 4.4 11.4 - - + -
146Q VAL* 4.9 1.1 - - + -
148Q GLY* 5.5 2.0 - - - -
323Q GLN 2.9 12.4 + - - -
324Q LEU* 3.6 10.5 - - - -
326Q ARG* 1.3 77.4 - - - +
328Q LEU* 1.3 57.4 + - - +
330Q TYR* 3.2 2.2 + - - +
331Q LEU* 2.8 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 328 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5Q VAL* 4.1 21.1 - - + -
21Q ILE* 3.9 28.3 - - + -
27Q LEU* 4.0 18.4 - - + -
92Q VAL* 3.6 42.0 - - + -
94Q LEU* 4.2 14.1 - - + -
118Q LEU* 3.7 14.9 - - + +
324Q LEU 2.8 17.8 + - - +
325Q VAL* 3.5 8.5 - - - +
326Q ARG 3.3 0.2 - - - -
327Q THR* 1.3 76.9 - - - +
329Q ALA* 1.3 64.3 + - - +
331Q LEU* 3.4 4.5 - - + +
332Q ALA* 2.9 26.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 329 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24Q VAL* 4.7 11.2 - - + -
27Q LEU* 4.2 22.4 - - + +
325Q VAL 2.9 16.6 + - - +
326Q ARG* 3.7 6.1 - - - +
328Q LEU* 1.3 77.7 - - - +
330Q TYR* 1.3 62.1 + - - +
332Q ALA* 3.4 2.5 + - - +
333Q GLU* 3.0 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 330 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132Q PHE* 3.7 13.7 - + + -
136Q HIS* 3.4 52.0 - + + -
137Q GLN* 4.1 17.3 + - + +
139Q LEU* 4.3 14.2 + - + -
326Q ARG 3.0 17.4 + - - +
327Q THR* 3.8 2.9 - - - +
329Q ALA* 1.3 75.4 - - - +
331Q LEU* 1.3 65.0 + - - +
333Q GLU* 3.2 21.0 + - + +
334Q LEU* 3.3 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 331 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92Q VAL* 4.6 11.4 - - + -
116Q LYS* 3.9 31.1 - - + +
117Q VAL 4.8 3.4 - - - +
118Q LEU* 4.3 28.0 - - + -
139Q LEU* 4.4 20.2 - - + -
143Q GLU* 4.4 11.4 - - + +
146Q VAL* 4.2 32.3 - - + -
327Q THR* 2.8 21.7 + - + +
328Q LEU 3.4 4.0 - - - +
330Q TYR* 1.3 76.7 - - - +
332Q ALA* 1.3 61.6 + - - +
334Q LEU* 3.3 22.0 + - + +
335Q SER* 3.9 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 332 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3Q VAL* 3.7 42.8 - - + +
27Q LEU* 4.8 2.5 - - + -
91Q ASP* 5.9 0.2 - - + -
92Q VAL* 4.2 15.0 - - + +
116Q LYS* 5.1 1.1 - - - +
328Q LEU* 2.9 20.6 + - + +
329Q ALA* 3.8 4.7 - - - +
331Q LEU* 1.3 73.5 - - - +
333Q GLU* 1.3 61.3 + - - +
335Q SER* 3.2 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 333 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3Q VAL* 5.8 1.6 - - - -
329Q ALA* 3.0 24.6 + - - +
330Q TYR* 3.2 12.8 + - + +
332Q ALA* 1.3 74.6 - - - +
334Q LEU* 1.3 64.0 + - + +
335Q SER 3.4 5.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 334 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139Q LEU* 3.7 32.5 - - + +
140Q ASP* 4.6 7.9 - - - +
141Q GLY* 3.4 36.4 - - - +
143Q GLU* 4.8 0.7 - - - +
330Q TYR* 3.3 40.9 + - + +
331Q LEU* 3.6 13.0 - - + +
332Q ALA 3.2 1.0 - - - -
333Q GLU* 1.3 77.1 - - + +
335Q SER* 1.3 63.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 335 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116Q LYS* 3.1 33.6 - - - +
141Q GLY* 5.1 4.5 - - - -
331Q LEU 3.9 0.3 + - - -
332Q ALA* 3.2 16.8 + - - +
333Q GLU 3.4 5.6 - - - +
334Q LEU* 1.3 81.2 - - - +
----------------------------------------------------------
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