Contacts of the helix formed by residues 11 - 35 (chain H) in PDB entry 1JH0
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 11 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H LEU* 1.3 66.9 + - - +
13H ALA* 3.7 11.1 + - - +
14H SER* 2.7 42.9 + - - -
15H LEU* 3.1 10.9 + - - +
290M VAL* 4.1 14.2 - - + +
291M VAL* 4.4 1.4 - - - +
297M TRP* 3.5 24.8 + - - -
301M HIS 4.1 8.4 + - - +
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Residues in contact with LEU 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H ASP* 1.3 73.0 - - - +
13H ALA* 1.3 56.9 + - - +
15H LEU* 3.3 24.7 + - + +
16H ALA* 3.0 28.7 + - + +
286M LEU* 4.9 10.5 - - + -
290M VAL* 4.2 31.2 - - + +
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Residues in contact with ALA 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H ASP* 2.9 10.7 + - - +
12H LEU* 1.3 76.4 - - - +
14H SER* 1.3 61.8 + - - +
16H ALA* 3.2 7.7 + - - +
17H ILE* 3.1 25.3 + - - +
201M PHE* 4.6 3.1 - - + -
286M LEU* 4.3 16.8 - - + +
290M VAL* 4.6 3.1 - - + +
291M VAL* 3.8 17.9 - - + -
294M TRP* 4.5 4.9 - - + -
297M TRP* 3.6 28.8 - - + +
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Residues in contact with SER 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H ASP* 2.7 29.5 + - - -
13H ALA* 1.3 72.4 - - - +
15H LEU* 1.3 62.1 + - - -
17H ILE* 4.1 7.0 - - - -
18H TYR* 2.9 40.6 + - - +
297M TRP* 3.8 7.3 - - - -
301M HIS* 3.0 31.9 + - - +
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Residues in contact with LEU 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H ASP 3.1 10.0 + - - +
12H LEU* 3.5 28.5 - - + +
14H SER* 1.3 77.5 - - - +
16H ALA* 1.3 58.8 + - - +
18H TYR* 4.0 2.8 - - + +
19H SER* 3.1 35.8 + - - -
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Residues in contact with ALA 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H LEU* 3.0 13.8 + - + +
13H ALA 3.2 9.8 + - - +
15H LEU* 1.3 75.5 - - - +
17H ILE* 1.3 65.1 + - - +
19H SER* 2.9 21.0 + - - -
20H PHE* 3.1 11.3 + - - +
201M PHE* 3.8 16.9 - - + -
282M ILE* 4.8 4.9 - - + -
286M LEU* 4.2 14.8 - - + -
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Residues in contact with ILE 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H ALA 3.1 10.8 + - - +
14H SER* 3.6 15.9 - - - +
16H ALA* 1.3 79.3 - - - +
18H TYR* 1.3 79.2 + - + +
20H PHE* 3.3 5.3 + - + +
21H TRP* 3.1 42.7 + - + +
200M PRO* 3.2 38.6 - - + -
201M PHE* 3.6 19.9 - - + -
204M LEU* 5.3 5.4 - - + -
297M TRP* 5.0 10.8 - - + -
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Residues in contact with TYR 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H SER* 2.9 33.9 + - - +
15H LEU* 4.0 3.6 - - + +
16H ALA 3.3 0.6 - - - -
17H ILE* 1.3 88.8 - - + +
19H SER* 1.3 67.4 + - - +
20H PHE 2.9 2.6 + - - -
21H TRP* 3.0 17.2 + + - +
22H ILE* 3.1 24.2 + - + +
301M HIS* 6.1 3.0 - + + -
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Residues in contact with SER 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H LEU* 3.1 18.4 + - - -
16H ALA* 2.9 22.5 + - - -
18H TYR* 1.3 78.5 - - - +
20H PHE* 1.3 56.0 + - - +
22H ILE* 3.5 15.8 + - - +
23H PHE* 3.0 26.2 + - - +
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Residues in contact with PHE 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H ALA 3.1 10.4 + - - +
17H ILE* 3.3 12.6 - - + +
18H TYR 2.9 0.8 - - - -
19H SER* 1.3 79.6 + - - +
21H TRP* 1.3 57.7 + + - +
22H ILE 2.9 5.2 - - - -
23H PHE* 2.9 27.3 + + + +
24H LEU* 2.7 54.7 + - + -
201M PHE* 4.5 13.5 - + + -
204M LEU* 3.9 29.4 - - + -
208M PHE* 4.4 5.2 - + - -
275M LEU* 4.3 16.4 - - + -
278M LEU* 4.6 7.6 - - + -
279M THR* 3.4 31.2 - - + -
282M ILE* 6.2 2.7 - - + -
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Residues in contact with TRP 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H ILE* 3.1 44.4 + - + +
18H TYR* 3.0 10.3 + + - +
20H PHE* 1.3 81.7 - + - +
22H ILE* 1.3 60.7 + - + +
24H LEU* 3.7 31.5 - - + +
25H ALA* 3.4 20.6 + - - +
204M LEU* 4.1 31.6 - - + +
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Residues in contact with ILE 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H TYR* 3.2 23.1 - - + +
19H SER* 3.5 15.3 - - - +
20H PHE 2.9 0.6 - - - -
21H TRP* 1.3 77.6 - - + +
23H PHE* 1.3 66.3 + - - +
25H ALA* 3.1 15.0 + - - +
26H GLY* 3.3 9.7 + - - -
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Residues in contact with PHE 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H SER 3.0 14.4 + - - +
20H PHE* 2.9 28.4 + + + +
22H ILE* 1.3 77.3 - - - +
24H LEU* 1.3 65.4 + - - +
26H GLY* 3.1 4.0 + - - -
27H LEU* 3.1 38.2 + - + +
271M TRP* 4.3 25.8 - + - -
275M LEU* 4.1 22.7 - - + -
278M LEU* 4.7 6.5 - - + -
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Residues in contact with LEU 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H PHE* 2.7 35.6 + - + +
21H TRP* 3.7 38.6 - - + +
23H PHE* 1.3 80.1 - - + +
25H ALA* 1.3 56.4 + - - +
27H LEU* 3.4 9.0 + - + +
28H ILE* 2.9 53.1 + - + +
204M LEU* 5.9 2.2 - - + -
208M PHE* 4.4 16.2 - - + -
275M LEU* 4.3 24.5 - - + -
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Residues in contact with ALA 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H TRP 3.4 12.1 + - - +
22H ILE* 3.1 10.8 + - - +
24H LEU* 1.3 78.2 - - - +
26H GLY* 1.3 58.8 + - - +
28H ILE* 3.9 8.2 - - - +
29H TYR* 3.1 24.9 + - - +
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Residues in contact with GLY 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H ILE 3.3 8.3 + - - -
23H PHE* 3.1 7.2 + - - -
25H ALA* 1.3 75.6 - - - +
27H LEU* 1.3 60.9 + - - +
29H TYR* 3.4 9.6 - - - +
30H TYR* 2.9 28.2 + - - +
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Residues in contact with LEU 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H PHE* 3.1 29.8 + - + +
24H LEU* 3.6 17.0 - - + +
26H GLY* 1.3 76.7 - - - +
28H ILE* 1.3 62.3 + - + +
30H TYR* 3.5 12.5 - - + +
31H LEU* 2.8 47.6 + - + +
271M TRP* 3.8 52.3 - - + +
275M LEU* 3.9 27.4 - - + -
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Residues in contact with ILE 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H LEU* 2.9 55.0 + - + +
25H ALA* 3.9 8.1 - - - +
26H GLY 3.4 0.2 - - - -
27H LEU* 1.3 80.9 - - + +
29H TYR* 1.3 63.5 + - - +
31H LEU* 4.1 9.3 - - + +
32H GLN* 3.0 25.5 + - + +
56H PHE* 4.9 13.5 - - + -
268M TRP* 5.1 17.5 - - + -
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Residues in contact with TYR 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H ALA 3.1 16.1 + - - +
26H GLY* 3.4 13.0 - - - +
27H LEU 3.1 0.2 - - - -
28H ILE* 1.3 75.4 - - - +
30H TYR* 1.3 68.5 - - - +
32H GLN* 3.4 1.4 + - - +
33H THR* 3.1 33.7 + - + +
55H PRO 5.5 1.1 - - - -
56H PHE* 3.5 38.1 - + + -
57H PRO* 3.2 34.3 - - + +
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Residues in contact with TYR 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H GLY 2.9 17.7 + - - +
27H LEU* 3.5 20.0 - - + +
29H TYR* 1.3 80.2 - - - +
31H LEU* 1.3 80.8 + - + +
33H THR* 2.8 22.4 + - - -
34H GLU* 3.1 40.2 + - + +
267M ARG* 3.3 33.0 + - + -
271M TRP* 4.6 14.4 - + - -
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Residues in contact with LEU 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H LEU* 2.8 45.9 + - + +
28H ILE* 4.1 6.1 - - + +
30H TYR* 1.3 79.0 - - + +
32H GLN* 1.3 59.4 + - - +
34H GLU* 3.3 5.8 + - - +
35H ASN* 2.7 32.9 + - - +
267M ARG* 3.4 45.5 - - + +
268M TRP* 3.4 48.7 - - + +
271M TRP* 4.2 11.7 - - + -
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Residues in contact with GLN 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H ILE* 3.0 22.3 + - + +
29H TYR 3.9 2.7 - - - +
31H LEU* 1.3 76.5 - - - +
33H THR* 1.3 64.2 + - - +
35H ASN* 3.2 13.6 + - - +
36H MET* 3.3 31.3 + - - +
40H TYR* 4.8 7.7 + - - -
56H PHE* 3.5 41.1 - - + -
258M PHE* 3.7 35.3 - - - +
259M ASN 4.6 10.9 + - - +
268M TRP* 4.1 11.4 - - + -
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Residues in contact with THR 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H TYR* 3.1 23.6 + - + +
30H TYR* 2.8 20.1 + - - -
32H GLN* 1.3 73.2 - - - +
34H GLU* 1.3 62.7 + - - +
36H MET* 2.8 29.7 + - - +
56H PHE* 4.2 16.6 - - + -
57H PRO* 3.3 34.1 - - + +
58H LEU 5.4 0.2 - - - -
59H PRO* 3.6 24.3 - - + +
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Residues in contact with GLU 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H TYR* 3.1 51.4 + - + +
31H LEU* 3.5 10.1 - - - +
32H GLN 3.3 0.2 - - - -
33H THR* 1.3 77.9 + - - +
35H ASN* 1.3 60.3 + - - +
36H MET 3.1 3.3 + - - -
37H ARG* 2.9 63.3 + - - +
59H PRO* 4.5 3.6 - - - +
62H LYS* 4.6 5.7 + - - -
261M THR* 3.9 7.9 + - - -
263M GLU* 4.9 0.9 - - - +
264M GLY* 5.0 2.0 - - - -
267M ARG* 3.7 30.7 + - + -
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Residues in contact with ASN 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H LEU* 2.7 25.2 + - - +
32H GLN* 3.2 13.2 + - - +
33H THR 3.0 1.4 - - - -
34H GLU* 1.3 77.9 - - - +
36H MET* 1.3 59.5 + - - +
37H ARG 3.4 2.9 - - - -
38H GLU 4.5 3.5 - - - +
40H TYR* 4.6 4.2 - - - -
259M ASN* 4.0 14.1 - - - +
260M ALA* 2.9 38.3 - - - +
261M THR* 3.0 29.4 + - - +
264M GLY* 3.1 19.8 + - - -
267M ARG* 5.8 0.2 - - - +
268M TRP* 2.9 28.2 - - - +
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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