Contacts of the helix formed by residues 11 - 22 (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 GLY 11 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190P PRO* 5.3 0.2 - - - -
0Q NAD 3.2 32.3 + - - -
9Q GLY 3.1 8.9 + - - -
10Q PHE* 1.3 73.6 - - - +
12Q ARG* 1.3 61.4 + - - +
13Q ILE 3.5 2.0 - - - -
14Q GLY 3.8 1.2 - - - +
15Q ARG* 2.9 43.5 + - - +
96Q CYS 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 12 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187P GLN* 4.0 26.7 + - + -
188P ASP* 3.5 27.1 - - - +
0Q NAD 2.9 39.5 + - - +
11Q GLY* 1.3 71.3 - - - +
13Q ILE* 1.3 63.4 + - - +
15Q ARG* 3.0 24.1 - - - +
16Q LEU* 3.2 38.7 + - - +
48Q ASP* 2.7 43.9 + - - -
50Q MET* 5.1 2.4 - - - +
51Q GLN* 3.3 8.5 - - - +
182Q GLY* 6.1 0.9 - - - +
317Q GLU* 2.7 45.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 13 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0Q NAD 2.8 81.3 + - + +
12Q ARG* 1.3 73.7 - - - +
14Q GLY* 1.3 58.1 + - - +
16Q LEU* 3.4 0.9 + - - +
17Q ALA* 2.8 32.5 + - + +
96Q CYS* 4.5 6.1 - - + -
120Q SER* 4.0 9.9 - - - -
316Q ASN 4.2 0.2 - - - +
317Q GLU* 4.1 15.3 - - + +
320Q TYR* 4.1 7.4 - - + -
321Q THR* 3.8 21.9 + - - +
324Q LEU* 3.9 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 14 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0Q NAD 4.6 0.2 + - - -
7Q ILE* 3.4 23.8 - - - +
9Q GLY 3.4 23.9 + - - -
10Q PHE* 4.0 5.8 - - - -
11Q GLY 3.5 4.9 + - - +
12Q ARG 3.3 0.6 - - - -
13Q ILE* 1.3 79.8 - - - +
15Q ARG* 1.3 56.9 + - - +
17Q ALA* 3.4 1.6 + - - +
18Q PHE* 3.0 21.8 + - - +
96Q CYS* 4.0 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 15 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188P ASP* 3.1 32.5 + - - +
189P ALA* 4.5 2.4 - - - +
190P PRO* 4.6 1.2 - - - +
10Q PHE* 2.7 76.8 + - + +
11Q GLY* 2.9 31.4 + - - +
12Q ARG* 3.0 32.8 - - - +
14Q GLY* 1.3 70.1 - - - +
16Q LEU* 1.3 66.5 + - + +
18Q PHE* 3.1 4.4 + - - +
19Q ARG* 2.9 31.1 + - - +
44Q LEU* 3.1 54.1 + - - +
45Q LEU* 3.8 8.0 - - + +
47Q TYR 5.6 0.2 + - - -
48Q ASP* 5.2 0.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 16 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Q ARG* 3.2 27.6 + - - +
15Q ARG* 1.3 75.1 - - + +
17Q ALA* 1.3 67.6 + - - +
19Q ARG* 3.2 22.5 + - - +
20Q ARG* 2.9 25.3 + - - +
48Q ASP* 3.7 20.6 - - - +
51Q GLN* 3.7 28.7 - - + +
317Q GLU* 3.6 38.1 - - + -
318Q MET* 4.1 14.3 - - + +
321Q THR* 3.4 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 17 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7Q ILE* 4.5 0.9 - - + -
13Q ILE 2.8 20.1 + - - +
14Q GLY 3.7 4.3 - - - +
16Q LEU* 1.3 76.3 - - - +
18Q PHE* 1.3 62.3 + - - +
20Q ARG* 3.2 0.9 + - - +
21Q ILE* 2.9 31.9 + - + +
94Q LEU* 3.4 32.5 - - + -
321Q THR* 3.4 15.2 - - + +
324Q LEU* 5.1 4.7 - - + -
325Q VAL* 4.1 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 18 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7Q ILE* 3.9 6.2 - - + +
10Q PHE* 3.8 22.0 - + + -
14Q GLY 3.0 15.1 + - - +
15Q ARG* 3.2 9.0 - - - +
17Q ALA* 1.3 79.3 - - - +
19Q ARG* 1.3 66.2 + - - +
21Q ILE* 3.3 2.1 + - - +
22Q GLN* 3.3 47.0 + - + +
29Q VAL* 3.7 40.8 - - + -
32Q VAL* 4.7 0.2 - - + -
45Q LEU* 3.9 29.6 - - + -
54Q PHE* 4.9 1.1 - + - -
65Q PHE* 4.8 2.9 - + - -
67Q VAL* 3.9 27.8 - - + -
72Q VAL* 3.8 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 19 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15Q ARG* 2.9 15.6 + - - +
16Q LEU* 3.2 23.9 + - + +
18Q PHE* 1.3 78.7 - - - +
20Q ARG* 1.3 61.9 + - + +
22Q GLN* 3.2 23.5 + - - +
23Q GLU* 4.0 9.4 + - - -
44Q LEU 4.9 0.6 + - - -
45Q LEU* 3.1 30.2 + - + +
46Q LYS 4.2 1.2 + - - -
48Q ASP* 3.4 21.2 + - - +
51Q GLN* 3.6 19.8 + - - +
52Q GLY 2.9 30.1 + - - -
53Q ARG 4.1 5.1 + - - -
54Q PHE* 3.5 39.0 - - + +
318Q MET* 5.2 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 20 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16Q LEU 2.9 16.9 + - - +
17Q ALA 3.8 3.1 - - - +
19Q ARG* 1.3 77.5 - - + +
21Q ILE* 1.3 63.5 + - - +
23Q GLU* 3.1 47.3 + - - +
24Q VAL* 3.3 23.0 - - + +
287Q THR* 3.6 24.7 + - - +
318Q MET* 4.6 15.9 - - + -
321Q THR* 4.2 7.0 - - + -
322Q ALA* 4.0 22.2 + - - +
325Q VAL* 4.2 22.4 - - + +
326Q ARG* 4.1 25.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 21 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5Q VAL* 4.4 7.4 - - + -
7Q ILE* 4.8 0.9 - - + -
17Q ALA* 2.9 27.6 + - + +
18Q PHE 3.3 4.0 + - - +
20Q ARG* 1.3 72.5 - - - +
22Q GLN* 1.3 65.1 + - - +
23Q GLU 3.0 6.8 + - - -
24Q VAL* 3.2 21.1 + - - +
27Q LEU* 3.5 39.1 - - + +
28Q GLU* 4.4 0.4 - - - -
29Q VAL* 3.7 34.5 - - + +
94Q LEU* 4.7 3.1 - - + -
325Q VAL* 4.0 21.3 - - + -
328Q LEU* 3.9 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 22 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18Q PHE* 3.3 48.1 + - + +
19Q ARG* 3.2 12.5 + - - +
20Q ARG 3.2 1.0 - - - -
21Q ILE* 1.3 84.4 - - - +
23Q GLU* 1.3 59.4 + - + +
24Q VAL 3.6 0.8 + - - -
29Q VAL* 4.9 3.1 + - - +
54Q PHE* 4.3 19.3 - - + -
67Q VAL* 4.5 14.5 + - - +
68Q ASN* 4.9 8.2 + - - +
70Q LYS* 4.6 21.4 - - - +
----------------------------------------------------------
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