Contacts of the helix formed by residues 26 - 41 (chain O) in PDB entry 2JA7
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 26 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25O VAL* 1.3 81.3 - - - +
27O LEU* 1.3 70.5 + - - +
28O ALA* 4.1 12.3 - - + +
29O MET* 2.9 23.4 + - + +
30O ALA 3.1 7.4 + - - -
225O ALA 4.8 0.4 - - - -
228O PHE* 4.2 0.9 - - - -
45W LEU* 6.4 0.2 - - + -
48W ALA* 5.1 12.7 - - + +
49W GLU* 3.8 19.2 - - - +
52W ASN* 4.3 16.3 + - - +
97W LYS* 4.8 8.7 - - - +
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Residues in contact with LEU 27 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1077N THR* 4.3 6.3 - - - +
1078N GLY* 3.7 7.9 - - - +
1079N LYS* 3.3 40.8 - - + +
26O ASP* 1.3 70.2 - - - +
28O ALA* 1.3 69.6 + - - +
30O ALA* 2.6 16.1 + - - +
31O ASN 3.0 8.1 + - - -
178O PHE* 3.6 28.0 - - + -
180O TYR* 3.6 15.9 - - + +
188O HIS* 5.3 3.4 - - + -
225O ALA* 4.4 10.8 + - + +
228O PHE* 3.3 37.6 - - + -
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Residues in contact with ALA 28 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1077N THR* 4.4 4.3 - - - -
26O ASP* 4.1 5.8 - - + +
27O LEU* 1.3 80.4 - - - +
29O MET* 1.3 52.5 - - - +
31O ASN* 3.0 2.8 + - - +
32O SER* 2.6 41.6 + - - +
44W ASN* 4.2 24.4 + - - +
45W LEU* 4.6 8.7 - - + -
48W ALA* 3.8 28.9 - - + -
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Residues in contact with MET 29 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6O PRO* 5.1 2.2 - - - -
22O LEU* 5.5 1.3 - - + -
25O VAL* 4.4 22.7 - - + -
26O ASP* 2.9 24.6 + - + +
28O ALA* 1.3 73.1 - - - +
30O ALA* 1.3 69.6 + - - +
32O SER* 3.7 7.7 - - - -
33O LEU* 3.0 22.4 + - + +
251O LEU* 5.1 2.2 - - + +
45W LEU* 3.8 17.9 - - + +
49W GLU* 6.5 0.7 - - + -
94W ILE* 4.1 18.4 - - + +
97W LYS* 4.6 20.6 - - + -
98W LEU* 3.1 49.6 - - + +
101W LEU* 5.1 7.4 - - + -
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Residues in contact with ALA 30 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22O LEU* 4.6 6.1 - - + -
25O VAL* 4.7 0.8 - - + +
26O ASP 3.1 4.9 + - - +
27O LEU 2.6 15.9 + - - +
29O MET* 1.3 75.8 - - - +
31O ASN* 1.3 57.2 + - - +
33O LEU* 3.2 5.6 - - - +
34O ARG* 2.9 23.6 + - - +
178O PHE* 3.5 26.9 - - + -
228O PHE* 3.9 28.3 - - + -
230O MET* 4.2 14.6 - - + +
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Residues in contact with ASN 31 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001N PHE* 4.1 0.3 - - - -
1075N GLY 3.2 10.2 + - - +
1076N HIS 3.1 21.4 + - - -
1077N THR 2.8 32.9 + - - +
1078N GLY* 3.6 13.4 - - - -
27O LEU 3.0 4.0 + - - +
28O ALA 3.5 2.7 - - - +
30O ALA* 1.3 75.6 - - - +
32O SER* 1.3 69.4 + - - +
33O LEU 2.9 2.0 - - - -
34O ARG* 2.5 52.8 + - - +
35O ARG* 2.8 26.2 + - - +
178O PHE* 3.8 6.6 - - + -
44W ASN* 5.2 0.8 - - - +
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Residues in contact with SER 32 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28O ALA* 2.6 34.1 + - - +
29O MET* 3.8 6.1 - - - -
31O ASN* 1.3 73.1 - - - +
33O LEU* 1.3 62.7 + - - +
35O ARG* 3.5 12.0 + - - +
36O VAL* 2.8 29.4 + - - +
251O LEU* 4.0 3.1 - - - -
41W THR* 3.8 20.0 + - - +
44W ASN* 5.2 2.8 + - - +
45W LEU* 3.6 34.3 + - - +
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Residues in contact with LEU 33 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20O PHE* 5.7 0.7 - - + -
22O LEU* 4.6 21.1 - - + -
29O MET* 3.0 13.3 + - + +
30O ALA* 3.2 10.1 - - - +
31O ASN 2.7 3.0 + - - -
32O SER* 1.3 73.7 - - - +
34O ARG* 1.3 69.9 + - - +
36O VAL* 2.7 18.2 + - + +
37O MET* 3.0 40.5 + - + +
230O MET* 5.0 2.2 - - + -
244O VAL* 5.0 4.0 - - + +
247O GLY 3.7 4.7 - - - +
248O ILE* 3.5 49.1 - - + +
251O LEU* 3.9 12.7 - - + +
98W LEU* 5.6 3.1 - - + -
101W LEU* 4.9 9.4 - - + -
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Residues in contact with ARG 34 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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996N ARG* 3.2 25.1 + - - +
997N GLU 3.8 5.3 + - - -
999N MET 4.0 0.8 + - - -
1001N PHE* 2.7 50.2 - - - +
1075N GLY* 3.8 7.5 + - - -
30O ALA 2.9 13.1 + - - +
31O ASN* 2.5 43.5 + - - +
33O LEU* 1.3 72.3 - - - +
35O ARG* 1.3 78.4 + - - +
37O MET* 3.2 21.1 + - + +
38O ILE* 3.0 39.3 + - + +
176O ILE* 4.3 15.6 + - + +
178O PHE* 4.0 22.6 - - + +
230O MET* 5.3 1.3 - - - -
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Residues in contact with ARG 35 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997N GLU* 3.3 34.9 + - + +
998N ASP* 2.7 31.7 + - - +
1075N GLY 3.3 14.5 + - - -
1076N HIS* 4.3 2.0 + - - -
31O ASN* 2.8 30.4 + - - +
32O SER* 3.6 4.7 - - - +
33O LEU 2.8 2.4 + - - -
34O ARG* 1.3 81.2 - - - +
36O VAL* 1.3 58.7 + - - +
38O ILE* 2.7 35.7 + - - +
39O ALA* 3.0 14.3 + - - +
40O GLU* 5.7 0.7 - - - -
39W ASP* 3.5 6.2 + - - -
40W HIS* 3.1 16.2 - - - +
41W THR* 2.5 68.4 + - - +
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Residues in contact with VAL 36 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32O SER 2.8 23.3 - - - +
33O LEU* 2.7 12.3 + - + +
35O ARG* 1.3 71.6 - - - +
37O MET* 1.3 62.2 + - - +
40O GLU* 3.1 34.1 + - + +
41O ILE* 3.6 7.2 + - + +
247O GLY* 3.9 10.3 - - - +
250O THR* 4.2 12.8 - - + -
251O LEU* 3.5 59.2 - - + +
254O LYS* 5.6 1.1 - - + -
41W THR* 3.8 14.8 + - + -
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Residues in contact with MET 37 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20O PHE* 5.4 0.2 - - + -
33O LEU* 3.0 46.3 + - + +
34O ARG* 3.3 25.8 - - - +
36O VAL* 1.3 79.5 - - - +
38O ILE* 1.3 65.4 + - - +
41O ILE* 3.6 25.5 + - - +
172O PRO* 4.2 5.0 - - - +
173O ALA* 4.1 7.4 - - - +
176O ILE* 4.0 16.6 - - + -
230O MET* 4.4 14.8 - - - -
232O VAL* 3.9 28.9 - - + -
243O VAL* 3.3 28.0 - - + +
244O VAL* 4.0 11.0 - - + -
247O GLY* 4.1 4.5 - - - -
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Residues in contact with ILE 38 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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996N ARG* 3.1 48.2 + - + +
997N GLU* 4.1 26.2 - - + +
34O ARG* 3.0 48.9 - - + +
35O ARG* 2.7 20.5 + - - +
37O MET* 1.3 75.2 - - - +
39O ALA* 1.3 57.9 + - - +
164O ALA* 3.7 10.8 - - + +
171O GLY* 3.8 10.4 - - - -
172O PRO* 4.2 0.2 - - - +
173O ALA* 3.5 15.5 - - - +
176O ILE* 4.6 9.6 - - + -
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Residues in contact with ALA 39 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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997N GLU* 3.5 37.7 - - + +
35O ARG 3.0 8.5 + - - +
38O ILE* 1.3 75.5 - - - +
40O GLU* 1.3 66.1 + - + +
41O ILE 3.6 2.0 - - - -
163O ILE* 3.5 2.1 - - - +
164O ALA* 3.0 41.5 + - + +
165O LYS* 3.3 15.5 + - + +
171O GLY* 5.7 0.4 - - - -
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Residues in contact with GLU 40 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35O ARG 5.8 0.2 - - - -
36O VAL* 3.1 25.5 + - + +
39O ALA* 1.3 82.8 - - + +
41O ILE* 1.3 61.0 + - - +
42O PRO* 3.1 13.9 - - - +
163O ILE* 3.4 21.1 - - + +
165O LYS* 3.6 33.1 + - + +
250O THR* 3.8 15.2 - - + +
254O LYS* 2.7 45.2 + - - +
41W THR* 3.5 21.4 + - - +
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Residues in contact with ILE 41 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36O VAL 3.6 11.0 - - - +
37O MET* 3.6 19.9 + - - +
39O ALA 3.6 2.5 - - - +
40O GLU* 1.3 77.0 - - - +
42O PRO* 1.3 79.1 - - + +
43O THR* 3.2 10.2 + - - -
163O ILE* 3.3 7.4 - - - +
170O TRP 4.5 1.6 - - - +
171O GLY* 5.0 1.2 - - - -
172O PRO* 4.0 21.6 - - + +
238O ILE* 4.4 15.5 - - + -
243O VAL* 3.5 26.7 - - + +
246O ARG* 4.1 10.3 - - + -
247O GLY* 3.5 36.6 - - - +
250O THR* 4.3 9.2 - - - +
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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
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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) + - + + + + + -
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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