Contacts of the helix formed by residues 9 - 32 (chain B) in PDB entry 3HAO
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 9 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ARG* 3.0 40.3 + - - +
8B PRO* 1.2 94.8 - - - +
10B TRP* 1.3 62.6 + - - +
11B ILE 3.2 1.1 - - - -
12B TRP* 3.3 18.3 + - - +
13B LEU* 3.5 13.8 + - + +
79B TYR* 3.5 15.5 + - + +
201B LEU* 3.9 15.2 - - + +
202B ASN* 3.4 26.9 + - - +
205B THR* 3.4 21.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 10 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLY* 4.3 13.3 - - - +
7B ARG* 2.9 29.7 + - + +
8B PRO* 3.2 6.2 - - + -
9B GLU* 1.3 78.7 - - - +
11B ILE* 1.3 81.5 + - + +
13B LEU* 3.1 18.5 + - + +
14B ALA* 3.0 43.9 + - + +
61B LEU* 3.7 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 11 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PRO 3.7 17.5 - - - +
10B TRP* 1.3 107.7 - - + +
12B TRP* 1.3 86.6 + - + +
14B ALA* 3.9 2.6 - - + +
15B LEU* 3.6 19.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 12 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PRO 5.0 0.6 + - - -
9B GLU* 3.3 13.7 + - - +
10B TRP 3.1 0.6 - - - -
11B ILE* 1.3 99.0 - - + +
13B LEU* 1.3 53.8 + - - +
14B ALA 3.2 2.0 - - - -
15B LEU* 3.5 23.8 + - + +
16B GLY* 3.2 23.2 + - - -
57B TYR* 4.6 3.7 - - - -
202B ASN* 3.0 36.9 + - - +
203B ILE* 5.1 2.4 - - + +
205B THR* 3.6 22.4 - - + +
206B LEU* 3.4 41.2 - - + +
209B MET* 4.6 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ARG* 6.4 0.9 - - + -
9B GLU* 3.5 6.7 + - + +
10B TRP* 3.1 29.3 + - + +
12B TRP* 1.3 72.8 - - - +
14B ALA* 1.3 55.6 + - - +
16B GLY 4.1 0.9 - - - -
17B THR* 2.5 33.6 + - - -
57B TYR* 4.0 22.1 - - + +
60B MET* 4.0 36.3 - - + +
61B LEU* 3.9 20.6 - - + +
79B TYR* 4.0 25.1 - - + +
82B ARG* 5.1 1.8 - - - +
205B THR* 3.9 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B TRP* 3.0 35.2 + - + +
11B ILE* 3.9 6.7 - - + +
13B LEU* 1.3 78.5 - - - +
15B LEU* 1.3 59.0 + - - +
16B GLY 3.5 0.2 - - - -
17B THR* 3.6 6.5 - - - -
18B ALA* 3.2 25.8 + - - +
61B LEU* 4.1 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 3.6 13.3 + - + +
12B TRP* 3.5 21.6 + - + +
14B ALA* 1.3 78.7 - - - +
16B GLY* 1.3 59.2 + - - +
17B THR 3.2 0.7 - - - -
18B ALA* 3.6 6.2 + - + -
19B LEU* 2.9 60.6 + - + +
209B MET* 3.8 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TRP 3.2 15.4 + - - -
15B LEU* 1.3 75.3 - - - +
17B THR* 1.3 64.0 + - - +
20B MET* 2.8 33.7 + - - +
57B TYR* 4.2 19.7 - - - -
209B MET* 4.5 5.8 - - - +
213B VAL* 4.5 16.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU 2.5 26.3 + - - -
14B ALA* 3.6 8.6 - - - -
15B LEU 3.2 0.2 - - - -
16B GLY* 1.3 76.9 - - - +
18B ALA* 1.3 57.8 + - - +
20B MET* 3.9 0.8 - - - +
21B GLY* 2.9 24.9 + - - -
54B PHE* 3.2 34.5 - - + -
57B TYR* 3.7 24.6 + - - +
58B LEU* 3.7 23.3 + - + -
61B LEU* 4.1 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ALA 3.2 15.6 + - - +
15B LEU* 3.7 10.8 - - + +
17B THR* 1.3 79.5 - - - +
19B LEU* 1.3 61.1 + - + +
21B GLY* 3.3 0.8 + - - -
22B LEU* 2.9 43.2 + - + +
54B PHE* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU* 2.9 54.1 + - + +
16B GLY 4.1 0.4 - - - +
18B ALA* 1.3 78.2 - - + +
20B MET* 1.3 57.5 + - - +
22B LEU* 3.7 13.4 - - + +
23B GLY* 3.0 25.5 + - - -
209B MET* 4.8 7.4 - - + -
213B VAL* 4.0 40.2 - - + -
217B VAL* 4.1 8.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLY 2.8 26.8 + - - +
17B THR 3.9 2.7 - - - +
19B LEU* 1.3 71.9 - - - +
21B GLY* 1.3 56.4 + - - +
23B GLY* 3.5 0.7 + - - -
24B THR* 2.6 38.6 + - - -
50B PRO* 3.8 17.2 - - - +
53B ALA* 4.1 19.7 - - + -
54B PHE* 3.9 9.9 - - - -
57B TYR* 4.2 12.1 - - + -
212B ASP* 3.4 19.7 - - + -
213B VAL* 3.3 39.3 - - + +
216B LYS* 3.7 18.4 - - + -
217B VAL* 4.0 20.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B THR 2.9 12.6 + - - -
18B ALA* 3.8 0.9 - - - -
20B MET* 1.3 74.9 - - - +
22B LEU* 1.3 67.4 + - - +
24B THR* 3.2 5.4 + - - -
25B LEU* 3.1 26.4 + - - +
54B PHE* 3.4 28.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ALA* 2.9 29.5 + - + +
19B LEU* 3.7 14.8 - - + +
21B GLY* 1.3 76.0 - - - +
23B GLY* 1.3 59.1 + - - +
25B LEU* 3.1 11.2 + - + +
26B TYR* 2.9 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU 3.0 14.5 + - - -
20B MET 3.8 1.6 - - - -
22B LEU* 1.3 80.3 - - - +
24B THR* 1.3 60.5 + - - +
26B TYR* 3.6 5.7 + - - +
27B PHE* 3.2 35.8 + - - -
50B PRO* 4.6 3.4 - - - -
217B VAL* 4.3 22.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B MET 2.6 23.5 + - - -
21B GLY* 3.5 8.0 - - - -
22B LEU 3.2 0.4 - - - -
23B GLY* 1.3 73.0 - - - +
25B LEU* 1.3 68.4 + - + +
27B PHE 3.2 1.9 + - - -
28B LEU* 2.8 32.4 + - + +
47B THR* 3.6 28.6 - - + +
50B PRO* 3.3 27.0 + - - +
51B ALA* 3.7 15.9 - - + -
54B PHE* 4.4 3.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLY 3.1 14.4 + - - +
22B LEU* 3.5 15.0 - - + +
24B THR* 1.3 85.1 - - + +
26B TYR* 1.3 57.3 + - - +
28B LEU* 3.2 17.5 + - + +
29B VAL* 2.9 39.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU 2.9 16.2 + - - +
23B GLY* 3.9 6.5 - - - +
25B LEU* 1.3 76.3 - - - +
27B PHE* 1.3 81.0 + + - +
29B VAL* 3.4 9.0 + - + +
30B LYS* 3.1 49.1 + - + +
221B LEU* 4.5 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLY* 3.2 19.8 + - - +
24B THR 3.2 2.9 + - - +
26B TYR* 1.3 95.8 - + - +
28B LEU* 1.3 60.7 + - - +
30B LYS* 4.4 4.5 - - + -
31B GLY* 2.8 24.8 + - - -
43B TYR* 3.3 10.8 - + - -
46B THR* 3.5 23.6 - - + -
47B THR* 2.9 17.6 + - + +
50B PRO* 4.2 13.9 - - + -
216B LYS 4.5 1.8 - - - -
217B VAL* 3.8 24.9 - - + -
220B GLY* 3.6 15.9 - - - -
221B LEU* 3.6 32.1 - - + -
224B LEU* 3.6 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B THR* 2.8 19.9 + - + +
25B LEU* 3.5 18.8 - - + +
27B PHE* 1.3 77.6 - - - +
29B VAL* 1.3 65.0 + - + +
31B GLY* 3.1 1.2 + - - -
32B MET* 2.9 53.1 + - + +
47B THR* 3.7 17.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 2.9 27.6 + - + +
26B TYR* 3.6 9.4 - - + +
28B LEU* 1.3 78.7 - - + +
30B LYS* 1.3 72.5 + - + +
32B MET* 3.7 3.6 + - - +
33B GLY* 3.6 14.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B TYR* 3.1 50.2 + - + +
27B PHE* 3.7 1.6 - - + +
28B LEU 3.1 0.2 - - - -
29B VAL* 1.3 86.7 - - + +
31B GLY* 1.2 69.5 + - - +
33B GLY* 3.1 12.5 + - - -
34B VAL* 3.5 10.4 + - - +
43B TYR* 3.2 30.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B PHE 2.8 12.7 + - - -
28B LEU* 3.6 1.3 - - - -
30B LYS* 1.2 81.6 - - - +
32B MET* 1.3 59.8 + - - +
34B VAL* 3.0 25.8 - - - +
40B LYS* 3.3 12.5 - - - -
43B TYR* 3.3 32.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 2.9 43.8 + - + +
29B VAL* 4.3 4.0 - - - +
31B GLY* 1.3 75.9 - - - +
33B GLY* 1.3 59.9 + - - +
34B VAL 4.3 3.5 - - - +
40B LYS* 4.6 9.6 - - - +
----------------------------------------------------------
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