Contacts of the helix formed by residues 26 - 39 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100C ARG* 3.6 8.1 - - - -
23D ASP* 3.2 27.7 + - - -
24D PRO 4.7 0.2 - - - +
25D TYR* 1.3 83.4 - - - +
27D PRO* 1.3 76.1 - - - +
28D LEU* 3.3 3.4 - - - -
29D ALA* 3.3 4.6 + - - +
30D ARG* 3.2 19.6 + - - +
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Residues in contact with PRO 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C ARG* 3.8 17.5 - - - +
23D ASP* 5.1 0.2 - - - +
25D TYR 4.6 0.4 - - - +
26D GLY* 1.3 80.9 - - - +
28D LEU* 1.3 66.5 + - - +
30D ARG* 3.1 11.4 + - + +
31D SER* 2.9 26.8 + - - -
125D GLN* 4.6 7.1 + - - +
128D ARG* 3.5 37.7 - - - +
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Residues in contact with LEU 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D ASP* 6.5 1.6 - - + -
26D GLY* 3.3 1.1 - - - -
27D PRO* 1.3 81.5 - - + +
29D ALA* 1.3 58.3 + - - +
31D SER* 3.2 5.0 + - - +
32D ILE* 2.9 51.6 + - + +
57D ILE* 4.4 19.7 - - + -
59D GLY 5.3 0.2 - - - -
60D SER* 3.7 32.8 - - - +
82D LEU* 5.1 1.8 - - + -
84D VAL* 4.2 22.7 - - + -
128D ARG* 3.8 37.4 - - + +
131D ALA* 4.6 4.7 - - + -
132D ALA 5.2 0.4 - - - +
135D LEU* 6.2 0.2 - - + -
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Residues in contact with ALA 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 5.0 2.6 - - + +
21D SER* 4.6 9.9 - - - +
23D ASP 3.4 25.9 + - - +
24D PRO* 3.7 17.7 - - + +
26D GLY 3.3 4.5 + - - +
27D PRO 3.3 0.4 - - - -
28D LEU* 1.3 79.7 - - - +
30D ARG* 1.3 57.3 + - - +
32D ILE* 3.4 11.4 + - - +
33D ARG* 2.9 43.2 + - - +
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Residues in contact with ARG 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C ASN 4.1 9.3 + - - -
140C GLU* 2.5 35.8 + - - +
141C ASN 4.3 0.6 - - - -
142C TRP 4.7 0.4 - - - +
143C ASN* 4.2 11.1 - - - +
174C TYR* 3.3 63.5 - - - +
24D PRO 5.3 0.4 + - - -
25D TYR* 4.5 12.7 + - - +
26D GLY 3.2 8.2 + - - +
27D PRO* 3.1 13.0 + - + +
29D ALA* 1.3 76.3 - - - +
31D SER* 1.3 60.6 + - - +
33D ARG* 3.2 9.0 + - - +
34D GLN* 2.9 46.9 + - + +
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Residues in contact with SER 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D PRO 2.9 13.6 + - - -
28D LEU* 3.2 9.2 + - - -
30D ARG* 1.3 75.9 - - - +
32D ILE* 1.3 56.3 + - - +
34D GLN* 3.3 13.0 + - - +
35D GLN* 2.9 33.6 + - - +
125D GLN* 4.1 10.9 + - - -
128D ARG* 4.1 9.0 - - - +
129D GLU* 4.0 30.4 + - - +
132D ALA* 3.8 14.6 - - - -
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Residues in contact with ILE 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 4.4 15.0 - - + -
28D LEU* 2.9 41.5 + - + +
29D ALA* 3.7 10.1 - - - +
31D SER* 1.3 76.4 - - - +
33D ARG* 1.3 57.0 + - - +
35D GLN* 3.3 1.8 + - - +
36D LEU* 2.9 48.2 + - + +
55D LEU* 4.5 8.3 - - + -
57D ILE* 3.6 31.4 - - + -
132D ALA* 3.9 23.1 - - + +
135D LEU* 4.0 15.0 - - + -
136D VAL* 5.9 3.1 - - + -
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Residues in contact with ARG 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 3.7 38.9 + - + +
21D SER* 6.1 1.4 - - - -
24D PRO* 3.3 32.3 + - - +
25D TYR* 5.8 1.3 - - - -
29D ALA* 2.9 32.1 + - - +
30D ARG* 3.6 8.5 - - - +
32D ILE* 1.3 75.4 - - - +
34D GLN* 1.3 60.5 + - + +
36D LEU* 3.4 2.0 + - - +
37D ARG* 2.9 32.0 + - - +
43D ILE* 4.1 25.4 - - + +
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Residues in contact with GLN 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C TYR* 4.4 13.7 - - - -
176C ASN* 6.1 2.9 - - - +
30D ARG* 2.9 45.4 + - + +
31D SER* 3.6 10.5 + - - +
33D ARG* 1.3 75.5 - - + +
35D GLN* 1.3 61.3 + - + +
37D ARG* 3.4 9.0 + - - +
38D LEU* 2.9 28.2 + - - +
125D GLN* 5.9 0.9 + - - -
129D GLU* 5.4 7.3 - - - +
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Residues in contact with GLN 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D SER* 2.9 20.0 + - - +
32D ILE 3.7 4.0 - - - +
34D GLN* 1.3 76.6 - - + +
36D LEU* 1.3 64.4 + - - +
38D LEU* 3.1 21.7 + - - +
39D ASN* 2.9 40.7 + - - -
129D GLU* 4.6 8.3 + - - +
132D ALA* 3.6 21.1 - - + -
133D GLN* 3.5 40.1 - - - +
136D VAL* 4.1 15.2 - - + +
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Residues in contact with LEU 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D LEU* 4.3 23.1 - - + -
19D LEU* 4.1 14.4 - - + -
32D ILE* 2.9 37.8 + - + +
33D ARG 3.8 3.6 - - - +
35D GLN* 1.3 75.6 - - - +
37D ARG* 1.3 61.0 + - - +
39D ASN* 3.2 9.4 + - - -
41D VAL* 3.0 50.8 + - + +
43D ILE* 4.0 25.1 - - + -
55D LEU* 4.4 9.9 - - + -
136D VAL* 3.9 22.2 - - + -
139D LEU* 5.0 7.6 - - + -
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Residues in contact with ARG 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C ASN* 4.1 22.5 - - - +
177C ASP* 2.5 38.0 + - - +
182C ASP* 2.6 38.8 + - - -
214C PRO* 4.7 7.5 - - - +
216C SER* 5.1 0.9 - - - -
33D ARG 2.9 18.0 + - - +
34D GLN* 3.6 8.3 - - - +
36D LEU* 1.3 75.8 - - - +
38D LEU* 1.3 63.1 + - - +
40D ASN* 3.2 16.5 + - - +
41D VAL 4.5 8.5 + - - +
43D ILE* 5.2 3.5 - - + +
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Residues in contact with LEU 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C PRO* 5.2 13.5 - - + -
215C LEU 5.7 0.4 - - - -
216C SER* 2.2 47.8 + - - -
217C ASN 4.8 0.3 - - - +
221C SER* 4.6 18.2 - - - +
34D GLN 2.9 17.9 + - - +
35D GLN* 3.1 28.7 + - - +
37D ARG* 1.3 76.9 - - - +
39D ASN* 1.3 60.3 + - - +
40D ASN 3.2 0.9 - - - -
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Residues in contact with ASN 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C SER* 4.4 0.4 - - - -
217C ASN 5.4 3.3 - - - +
11D PRO* 4.1 21.3 - - + +
12D THR* 4.4 10.6 + - - +
15D GLN* 5.6 0.9 + - - -
35D GLN* 2.9 38.7 + - - +
36D LEU* 3.2 5.5 + - - +
38D LEU* 1.3 82.4 - - - +
40D ASN* 1.3 74.2 + - - +
41D VAL* 3.3 11.5 + - + +
136D VAL* 3.8 29.1 - - + +
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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