Contacts of the helix formed by residues 26 - 39 (chain H) in PDB entry 5IXM
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 26 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100G ARG* 3.8 9.0 - - - -
23H ASP* 3.2 26.1 + - - -
24H PRO 4.7 0.2 - - - +
25H TYR* 1.3 82.1 - - - +
27H PRO* 1.3 77.4 - - - +
28H LEU* 3.3 3.4 - - - -
29H ALA* 3.3 5.8 + - - +
30H ARG* 3.3 19.7 + - - +
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Residues in contact with PRO 27 (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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100G ARG* 4.0 16.8 - - - +
25H TYR 4.6 0.7 - - - +
26H GLY* 1.3 82.1 - - - +
28H LEU* 1.3 60.3 + - + +
30H ARG* 3.1 13.8 + - + +
31H SER* 2.9 30.9 + - - -
125H GLN* 4.5 5.7 + - - +
128H ARG* 3.6 36.6 - - - +
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Residues in contact with LEU 28 (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* 3.3 0.6 - - - -
27H PRO* 1.3 80.3 - - + +
29H ALA* 1.3 59.1 + - - +
31H SER* 3.1 5.7 + - - -
32H ILE* 2.9 50.0 + - + +
57H ILE* 4.6 13.7 - - + -
60H SER* 3.6 34.1 - - - +
82H LEU* 4.9 2.2 - - + -
84H VAL* 3.9 26.5 - - + -
128H ARG* 3.6 42.3 - - + +
131H ALA* 4.7 3.8 - - + -
132H ALA 5.4 0.2 - - - +
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Residues in contact with ALA 29 (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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19H LEU* 4.6 3.6 - - + +
21H SER* 4.3 12.6 - - - +
23H ASP 3.5 23.7 + - - +
24H PRO* 3.8 14.4 - - + +
26H GLY 3.3 7.2 + - - +
27H PRO 3.3 0.4 - - - -
28H LEU* 1.3 79.0 - - - +
30H ARG* 1.3 57.8 + - - +
32H ILE* 3.4 10.8 + - - +
33H ARG* 2.9 42.7 + - - +
57H ILE* 6.2 1.6 - - + -
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Residues in contact with ARG 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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139G ASN 4.0 6.1 + - - -
140G GLU* 2.9 32.9 + - - +
141G ASN 4.5 0.6 - - - -
142G TRP 4.8 0.2 - - - +
143G ASN* 4.2 10.5 - - - +
174G TYR* 3.2 65.8 - - - +
25H TYR* 4.3 16.8 + - - +
26H GLY 3.3 8.4 + - - +
27H PRO* 3.1 14.3 + - - +
29H ALA* 1.3 76.5 - - - +
31H SER* 1.3 61.3 + - - +
33H ARG* 3.2 10.7 + - - +
34H GLN* 2.9 44.0 + - + +
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Residues in contact with SER 31 (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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27H PRO 2.9 13.4 + - - -
28H LEU* 3.1 9.8 + - - -
30H ARG* 1.3 77.4 - - - +
32H ILE* 1.3 57.3 + - - +
34H GLN* 3.3 11.5 + - - +
35H GLN* 3.0 32.7 + - - +
125H GLN* 3.6 21.5 + - - -
128H ARG* 3.9 15.4 - - - +
129H GLU* 3.9 28.3 - - - +
132H ALA* 4.0 4.0 - - - -
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Residues in contact with ILE 32 (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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19H LEU* 4.4 15.5 - - + -
28H LEU* 2.9 39.9 + - + +
29H ALA* 3.7 8.1 - - - +
30H ARG 3.2 0.2 - - - -
31H SER* 1.3 76.6 - - - +
33H ARG* 1.3 57.6 + - - +
35H GLN* 3.3 0.9 + - - +
36H LEU* 2.9 48.9 + - + +
55H LEU* 4.4 8.7 - - + -
57H ILE* 3.5 31.9 - - + -
84H VAL* 5.5 0.9 - - + -
132H ALA* 3.9 23.1 - - + -
135H LEU* 4.1 16.4 - - + -
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Residues in contact with ARG 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H LEU* 3.5 40.8 + - + +
21H SER* 5.8 2.0 - - - -
24H PRO* 3.1 33.1 + - - +
25H TYR* 6.3 1.2 - - - -
29H ALA* 2.9 36.3 + - - +
30H ARG* 3.2 9.6 + - + +
32H ILE* 1.3 75.7 - - - +
34H GLN* 1.3 58.4 + - + +
36H LEU* 3.9 1.6 - - - +
37H ARG* 2.9 31.8 + - - +
43H ILE* 4.2 26.0 - - + +
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Residues in contact with GLN 34 (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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174G TYR* 4.4 14.8 - - - -
176G ASN* 6.0 4.4 + - - +
30H ARG* 2.9 41.7 + - + +
31H SER* 3.7 9.1 - - - +
33H ARG* 1.3 75.9 - - + +
35H GLN* 1.3 61.3 + - + +
37H ARG* 3.4 10.6 + - - +
38H LEU* 2.9 27.2 + - - +
125H GLN* 5.9 0.9 + - - -
129H GLU* 5.3 8.1 - - - +
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Residues in contact with GLN 35 (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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31H SER 3.0 15.3 + - - +
32H ILE 3.8 2.2 - - - +
33H ARG 3.3 0.2 - - - -
34H GLN* 1.3 75.7 - - + +
36H LEU* 1.3 65.2 + - - +
38H LEU* 3.0 36.2 + - - +
39H ASN* 3.0 28.4 + - - +
129H GLU* 4.3 9.9 + - - +
132H ALA* 3.5 29.4 - - + -
133H GLN* 3.6 39.1 - - - +
136H VAL* 4.2 11.3 - - + +
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Residues in contact with LEU 36 (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 LEU* 3.9 25.8 - - + -
19H LEU* 4.5 6.3 - - + -
32H ILE* 2.9 29.1 + - + +
33H ARG 4.0 2.7 - - - +
35H GLN* 1.3 76.4 - - - +
37H ARG* 1.3 60.8 + - - +
39H ASN* 3.1 8.8 + - - +
41H VAL* 2.9 55.2 + - + +
43H ILE* 4.3 16.6 - - + -
55H LEU* 4.1 23.8 - - + -
136H VAL* 4.2 19.5 - - + -
139H LEU* 4.6 14.6 - - + -
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Residues in contact with ARG 37 (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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176G ASN* 4.1 21.8 - - - +
177G ASP* 2.7 33.9 + - - +
182G ASP* 2.3 45.5 + - - -
214G PRO* 4.2 12.7 - - - +
216G SER* 4.9 1.4 - - - -
602G C8E 3.7 41.2 - - + +
33H ARG 2.9 20.2 + - - +
34H GLN* 3.5 10.3 - - - +
36H LEU* 1.3 78.5 - - - +
38H LEU* 1.3 59.1 + - - +
40H ASN* 3.3 11.8 + - - +
41H VAL 4.3 3.3 + - - +
43H ILE* 5.2 2.7 - - + +
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Residues in contact with LEU 38 (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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214G PRO* 5.2 14.4 - - + -
215G LEU 5.5 1.1 - - - +
216G SER* 2.4 36.0 + - - -
221G SER* 4.2 26.6 - - - +
222G ILE 5.9 2.2 - - - +
223G ASN* 6.1 4.9 - - + -
34H GLN 2.9 14.2 + - - +
35H GLN* 3.0 37.0 + - - +
37H ARG* 1.3 76.4 - - - +
39H ASN* 1.3 57.8 + - - +
40H ASN 3.3 0.9 - - - -
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Residues in contact with ASN 39 (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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216G SER* 4.0 1.1 - - - -
217G ASN 5.3 6.3 + - - -
10H VAL 5.7 1.0 + - - -
11H PRO* 5.1 25.9 - - + +
15H GLN* 4.8 3.8 - - - +
35H GLN* 3.0 28.0 + - - +
36H LEU* 3.1 4.8 + - - +
38H LEU* 1.3 83.3 + - - +
40H ASN* 1.3 72.4 + - - +
41H VAL* 3.3 14.7 + - + +
136H VAL* 3.4 32.5 - - + +
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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
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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