Contacts of the helix formed by residues 22 - 37 (chain Q) in PDB entry 3H1I
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 ASP 22 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13Q SER* 3.7 28.9 + - - +
20Q ALA 3.8 2.0 + - - -
21Q LEU* 1.3 72.3 - - - +
23Q HIS* 1.3 50.7 + - - +
24Q SER* 2.6 26.5 + - - -
25Q SER* 2.6 58.4 + - - -
26Q VAL* 3.4 7.3 + - - +
28Q ARG* 4.7 1.7 + - - -
184Q LYS* 4.1 8.1 + - - -
188Q THR* 4.4 2.4 - - + +
78U LYS 4.5 6.4 - - - +
49W GLY 4.2 1.7 - - - +
50W LYS* 3.9 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 23 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21Q LEU* 2.8 41.5 + - + +
22Q ASP* 1.3 68.8 - - - +
24Q SER* 1.3 63.7 + - - +
26Q VAL* 3.5 10.5 + - + -
27Q ARG* 3.3 17.2 + - - +
53Q GLY 4.6 1.1 - - - -
54Q VAL* 2.8 44.0 + - + +
55Q THR* 3.7 8.9 - - - +
192Q TRP* 5.9 2.5 - + - -
199Q ASP* 3.2 25.3 + - - -
50W LYS 2.9 18.0 + - - +
51W LEU* 4.3 6.2 - - + +
52W TRP* 3.4 31.2 + - + +
55W ILE* 4.7 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 24 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22Q ASP* 2.6 24.0 + - - -
23Q HIS* 1.3 78.2 - - - +
25Q SER* 1.3 61.5 + - - -
27Q ARG* 3.2 19.3 + - - +
28Q ARG* 3.5 23.9 + - - +
49W GLY 3.9 4.3 + - - -
55W ILE* 2.8 37.6 - - - +
58W LYS* 6.2 0.7 - - - -
59W TYR* 6.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 25 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22Q ASP* 2.6 29.3 + - - -
24Q SER* 1.3 73.2 - - - +
26Q VAL* 1.3 53.2 + - - -
28Q ARG* 3.4 7.2 + - - +
29Q GLY 2.7 28.6 + - - -
184Q LYS* 3.6 15.0 + - - -
185Q ASP* 2.6 41.8 + - - +
188Q THR* 3.5 18.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 26 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21Q LEU* 4.6 10.1 - - + -
22Q ASP 3.4 8.9 + - - +
23Q HIS* 4.0 8.7 - - + +
24Q SER 3.3 0.8 - - - -
25Q SER* 1.3 72.3 - - - +
27Q ARG* 1.3 57.9 + - - +
28Q ARG 3.0 1.8 - - - -
29Q GLY 4.0 0.7 - - - +
30Q PHE* 2.6 34.8 + - - +
54Q VAL* 5.6 0.9 - - + -
55Q THR* 3.7 19.3 - - + -
188Q THR* 3.5 29.2 - - + +
189Q PHE* 3.2 35.7 - - + +
192Q TRP* 4.0 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 27 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23Q HIS 3.3 10.6 + - - +
24Q SER* 3.2 13.6 + - - +
26Q VAL* 1.3 78.6 - - - +
28Q ARG* 1.3 63.1 + - + +
30Q PHE* 3.9 9.3 - - - +
31Q GLN* 3.7 18.7 + - - +
55Q THR* 2.6 49.2 + - - +
56Q HIS* 3.1 27.9 + - + +
60Q GLU* 2.8 30.5 + - - -
172Q ASP* 4.8 16.2 + - - -
173Q ASP* 6.3 1.7 - - - +
55W ILE* 5.6 2.5 - - + -
59W TYR* 3.0 44.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 28 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22Q ASP* 4.7 1.4 + - - -
24Q SER* 3.5 21.5 + - - +
25Q SER* 3.4 16.2 + - - +
26Q VAL 3.0 0.4 - - - -
27Q ARG* 1.3 80.1 - - + +
29Q GLY* 1.3 69.5 + - - +
30Q PHE 2.9 1.6 - - - -
31Q GLN* 2.6 20.7 + - - +
32Q VAL* 2.8 11.4 + - - +
171Q TYR* 3.3 46.2 - - + -
173Q ASP* 2.8 27.9 + - - +
175Q THR* 3.5 11.8 + - - -
181Q GLN* 3.7 3.8 - - - +
185Q ASP* 3.0 40.7 + - - -
78U LYS* 3.4 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 29 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Q SER 2.7 16.2 + - - -
26Q VAL 3.1 2.0 + - - -
28Q ARG* 1.3 72.4 - - - +
30Q PHE* 1.3 56.0 + - - +
32Q VAL* 3.1 7.3 - - - +
33Q TYR* 2.9 26.5 + - - +
185Q ASP* 2.8 36.2 + - - +
186Q VAL* 3.5 3.3 - - - -
189Q PHE* 3.5 11.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 30 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26Q VAL 2.6 20.2 + - - +
27Q ARG* 3.9 7.9 - - - +
28Q ARG 2.8 2.2 + - - -
29Q GLY* 1.3 66.5 - - - -
31Q GLN* 1.3 59.1 + - + +
33Q TYR* 2.8 11.1 + + - +
34Q LYS* 2.7 53.6 + - + +
48Q PHE* 5.4 3.6 - + - -
51Q LEU* 3.9 27.6 - - + -
55Q THR* 5.2 0.4 - - - +
56Q HIS* 3.6 22.0 - + + -
64Q LEU* 3.6 37.2 - - + -
91Q PHE* 4.1 17.7 - + - -
189Q PHE* 3.5 35.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 31 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27Q ARG* 3.7 12.0 + - - +
28Q ARG* 2.6 16.5 + - - +
30Q PHE* 1.3 84.6 - - + +
32Q VAL* 1.3 55.9 + - - +
34Q LYS* 4.4 6.1 - - + -
35Q GLN* 2.9 63.9 + - - +
169Q LEU* 4.0 5.4 - - + +
170Q GLU 3.3 25.7 + - - -
171Q TYR* 3.7 17.0 - - + +
172Q ASP* 3.7 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 32 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28Q ARG 2.8 9.4 + - - +
29Q GLY* 3.1 11.4 - - - +
31Q GLN* 1.3 76.7 - - - +
33Q TYR* 1.3 60.0 + - - +
36Q VAL* 3.0 33.6 + - + +
37Q CYS* 3.7 0.2 - - - -
169Q LEU* 4.3 7.9 - - + -
171Q TYR* 3.4 36.8 - - + +
182Q ILE* 3.5 21.1 - - + +
186Q VAL* 3.3 32.8 - - + +
501Q HEC 3.6 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 33 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29Q GLY 2.9 6.3 + - - +
30Q PHE* 2.8 14.8 + + - +
32Q VAL* 1.3 77.0 - - - +
34Q LYS* 1.3 62.7 + - + +
37Q CYS* 3.2 22.4 + - + -
38Q SER* 2.8 47.6 + - - -
41Q HIS* 2.6 37.7 + - + -
42Q SER* 4.0 0.2 - - - -
43Q MET* 3.0 40.7 + - + +
91Q PHE* 4.2 20.4 - + + +
92Q PRO 4.9 3.8 + - - -
113Q LEU* 4.9 9.9 - - + -
186Q VAL* 5.0 2.5 - - + -
189Q PHE* 3.5 34.3 - + + -
190Q LEU* 5.1 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 34 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30Q PHE* 2.7 36.2 + - + +
31Q GLN* 3.8 7.6 - - + +
33Q TYR* 1.3 79.7 - - + +
35Q GLN* 1.3 71.5 + - + +
38Q SER* 2.3 35.3 + - - -
48Q PHE* 5.3 5.3 - - - -
64Q LEU* 4.1 35.1 + - + +
67Q GLU* 3.5 27.8 + - - +
68Q VAL* 4.8 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 35 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31Q GLN* 2.9 38.8 + - - +
34Q LYS* 1.3 87.6 - - + +
36Q VAL* 1.3 65.9 + - + +
38Q SER* 4.8 0.9 - - - -
39Q ALA* 5.8 2.6 - - - +
169Q LEU* 3.5 34.0 - - + +
170Q GLU 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 36 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32Q VAL* 3.0 29.7 + - + +
34Q LYS 3.4 0.6 - - - -
35Q GLN* 1.3 87.0 - - + +
37Q CYS* 1.3 64.3 + - - +
38Q SER 3.5 0.7 - - - -
39Q ALA* 4.1 8.4 + - - +
163Q PRO* 3.5 28.0 - - + +
164Q ILE* 4.4 4.7 - - + -
168Q ILE* 3.9 28.7 - - + +
169Q LEU* 5.0 7.4 - - + -
501Q HEC 2.8 32.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 37 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32Q VAL* 3.7 1.6 - - - -
33Q TYR* 3.2 34.0 + - + +
36Q VAL* 1.3 72.3 - - - +
38Q SER* 1.3 50.9 + - - +
39Q ALA 2.7 6.0 + - - -
40Q CYS* 2.6 10.9 + - - +
41Q HIS* 2.5 42.5 + - + +
113Q LEU* 4.6 0.7 - - + -
186Q VAL* 4.4 1.8 - - - -
501Q HEC 1.8 86.1 - - + -
----------------------------------------------------------
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