Contacts of the helix formed by residues 27 - 41 (chain C) in PDB entry 5IYB
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 27 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C THR* 1.3 84.4 + - - +
28C LEU* 1.3 83.6 + - - +
29C ALA* 3.2 9.8 + - - +
30C VAL* 3.1 18.1 + - + +
31C ALA* 3.1 17.8 + - - +
225C LYS* 6.0 2.7 - - - +
226C PRO* 4.7 6.8 - - - +
229C PHE* 3.7 5.4 - - - -
45K ILE* 4.9 1.1 - - + +
48K SER* 2.8 36.9 + - - +
49K GLN* 5.5 1.4 - - - +
52K LYS* 5.1 17.3 - - - +
97K GLU* 5.2 1.0 + - - -
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Residues in contact with LEU 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033B THR 3.5 20.9 - - - +
1034B GLY* 4.0 14.8 - - - +
1035B ARG* 3.7 26.5 - - + +
27C ASP* 1.3 83.0 + - - +
29C ALA* 1.3 50.5 + - - +
31C ALA* 3.1 2.4 + - - +
32C ASN* 2.8 33.4 + - - +
184C PHE* 4.3 7.6 - - + -
186C TYR* 4.1 20.4 - - + +
194C HIS* 6.1 2.2 - - + -
226C PRO* 4.0 21.2 - - + +
229C PHE* 3.4 31.0 - - + -
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Residues in contact with ALA 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1033B THR 5.0 1.3 - - - -
27C ASP* 3.2 18.5 - - - +
28C LEU* 1.3 76.1 - - - +
30C VAL* 1.3 56.5 + - - +
32C ASN* 4.1 1.9 - - - +
33C SER* 2.6 37.0 + - - -
44K ASN* 3.9 31.6 + - - +
45K ILE* 3.7 11.5 - - + +
48K SER* 3.8 18.8 - - - +
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Residues in contact with VAL 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ILE* 6.4 0.2 - - + -
26C THR* 3.5 24.7 - - + +
27C ASP* 3.1 20.0 + - + +
29C ALA* 1.3 76.0 - - - +
31C ALA* 1.3 58.7 + - - +
33C SER* 3.2 5.8 + - - +
34C ILE* 2.9 52.3 + - + +
45K ILE* 3.4 20.9 - - + -
49K GLN* 5.2 2.2 - - - +
94K LEU* 4.4 13.0 - - + -
97K GLU* 4.8 8.7 - - - +
98K LEU* 4.3 13.7 - - + -
101K LEU* 5.1 3.6 - - + -
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Residues in contact with ALA 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ILE* 6.1 0.4 - - + -
26C THR* 5.1 2.4 - - + +
27C ASP 3.1 8.3 + - - +
28C LEU 3.3 8.3 - - - +
30C VAL* 1.3 78.1 - - - +
32C ASN* 1.3 61.8 + - - +
34C ILE* 5.2 0.4 - - - -
35C ARG* 3.2 17.8 + - - +
184C PHE* 3.6 23.5 - - + -
229C PHE* 3.7 25.4 - - + -
231C TYR* 3.0 29.1 + - - +
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Residues in contact with ASN 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956B PHE* 5.2 0.3 - - - -
1030B ASN 4.3 0.2 - - - +
1031B GLY 3.7 5.7 + - - +
1032B PHE 3.0 29.3 + - - -
1033B THR* 3.2 5.6 - - - +
1034B GLY* 3.2 35.7 + - - +
28C LEU* 2.8 18.8 + - + +
29C ALA* 4.1 3.6 - - - +
31C ALA* 1.3 74.3 - - - +
33C SER* 1.3 55.1 + - - +
35C ARG* 3.0 35.5 + - - +
36C ARG* 2.9 32.9 + - - +
184C PHE* 4.5 4.9 - - - -
44K ASN* 3.7 6.7 - - - +
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Residues in contact with SER 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ALA 2.6 24.6 + - - -
30C VAL* 3.2 12.1 + - - -
32C ASN* 1.3 73.8 - - - +
34C ILE* 1.3 59.1 + - - +
35C ARG 3.1 1.1 - - - -
36C ARG* 3.6 11.8 - - - +
37C VAL* 2.8 35.8 + - - +
252C LEU* 5.0 9.2 - - - +
41K THR* 3.8 26.9 - - - -
44K ASN* 5.8 2.0 - - - -
45K ILE* 3.9 14.3 - - - +
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Residues in contact with ILE 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ILE* 4.7 9.9 - - + -
30C VAL* 2.9 44.9 + - + +
31C ALA 4.1 3.6 - - - +
33C SER* 1.3 73.8 + - - +
35C ARG* 1.3 62.3 + - - +
37C VAL* 3.5 7.9 + - + +
38C PHE* 3.2 50.6 + - + -
231C TYR* 4.3 8.5 - - + +
245C VAL* 5.6 0.2 - - + -
248C ALA* 5.9 0.2 - - + -
249C LEU* 3.8 24.2 - - + -
252C LEU* 4.7 7.9 - - + -
98K LEU* 4.1 9.0 - - + -
101K LEU* 3.7 26.0 - - + -
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Residues in contact with ARG 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951B GLN 4.2 7.5 + - - -
952B GLU* 3.2 26.7 + - - +
954B MET 4.5 2.6 + - - -
956B PHE* 3.8 41.0 - - - +
962B THR* 5.1 1.2 - - - +
1031B GLY* 4.0 4.8 + - - -
31C ALA 3.2 14.0 + - - +
32C ASN* 3.0 36.4 + - - +
33C SER 3.1 0.2 - - - -
34C ILE* 1.3 75.1 - - - +
36C ARG* 1.3 81.6 + - - +
37C VAL 3.1 1.3 - - - -
38C PHE* 3.3 20.0 + - + +
39C ILE* 3.4 15.7 + - - +
182C VAL* 4.2 29.6 + - + +
184C PHE* 4.1 23.6 - - + -
231C TYR* 4.4 10.3 - - + -
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Residues in contact with ARG 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
950B ARG* 5.1 5.5 - - - +
952B GLU* 4.0 23.9 + - + +
953B ASP* 2.9 27.9 + - - -
1031B GLY 2.9 21.8 + - - -
1032B PHE* 4.1 6.7 - - - +
32C ASN* 2.9 37.8 + - - +
33C SER* 3.6 12.6 - - - +
35C ARG* 1.3 89.0 - - - +
37C VAL* 1.3 62.8 + - - +
39C ILE* 3.1 11.8 - - + +
40C ALA* 3.0 25.6 + - - +
41C GLU* 5.4 0.4 - - - -
39K ASP* 4.6 7.1 + - - +
40K HIS* 4.1 16.4 - - - +
41K THR* 2.9 41.5 + - + +
44K ASN* 6.6 0.2 - - - -
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Residues in contact with VAL 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C SER 2.8 21.5 + - - +
34C ILE* 3.7 7.2 - - - +
35C ARG 3.1 0.2 - - - -
36C ARG* 1.3 78.3 - - - +
38C PHE* 1.3 63.6 + - - +
41C GLU* 2.9 50.7 + - + -
42C VAL* 3.4 6.7 + - + +
248C ALA* 3.4 40.8 - - + +
252C LEU* 4.0 34.1 - - + +
41K THR* 4.2 8.5 - - + -
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Residues in contact with PHE 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C PHE* 4.6 5.4 - + - -
34C ILE* 3.2 42.0 + - + -
35C ARG* 3.3 13.7 + - - +
37C VAL* 1.3 75.8 - - - +
39C ILE* 1.3 56.4 + - - +
42C VAL* 3.8 4.7 - - - +
178C PRO* 3.2 28.6 - - - +
179C THR* 3.8 18.8 + - + +
182C VAL* 4.4 11.0 - - + -
231C TYR* 3.8 22.4 - + - -
233C VAL* 4.1 17.7 - - + -
244C ILE* 4.7 6.0 - - + +
245C VAL* 3.5 50.9 - - + -
248C ALA* 3.7 17.3 - - + -
249C LEU* 5.3 0.2 - - + -
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Residues in contact with ILE 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803B ARG* 4.6 0.4 - - - +
951B GLN* 3.6 27.8 - - + +
952B GLU* 3.1 39.5 - - + +
35C ARG* 3.4 13.1 + - - +
36C ARG* 3.1 15.9 - - - +
37C VAL 3.7 0.2 - - - -
38C PHE* 1.3 82.2 - - - +
40C ALA* 1.3 67.9 + - - +
41C GLU 3.7 0.2 - - - -
170C GLY* 3.7 3.1 - - - -
177C ASN* 3.2 50.7 - - - +
178C PRO* 3.8 7.8 - - - +
179C THR* 3.7 16.8 + - - +
182C VAL* 5.4 8.7 - - + -
10J CYS 5.5 0.9 - - - +
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Residues in contact with ALA 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
950B ARG* 4.6 0.4 - - - +
952B GLU* 3.2 30.3 - - + +
36C ARG 3.0 14.1 + - - +
39C ILE* 1.3 74.6 - - - +
41C GLU* 1.3 67.7 + - + +
42C VAL 3.6 0.7 - - - -
169C PHE* 3.3 8.0 - - - +
170C GLY 2.9 22.3 + - - -
171C LYS* 3.0 32.0 + - + +
41K THR* 6.0 1.8 - - - +
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Residues in contact with GLU 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ARG 4.9 0.2 - - - +
37C VAL* 2.9 44.1 + - + -
40C ALA* 1.3 78.7 - - + +
42C VAL* 1.3 65.0 + - - +
43C PRO* 3.3 8.0 - - - +
169C PHE* 4.2 16.1 - - - +
171C LYS* 2.8 43.3 + - - +
248C ALA* 5.9 0.4 - - - -
251C GLY* 6.0 3.3 - - - -
252C LEU* 6.0 2.7 - - + +
255C LYS* 4.0 22.4 + - + +
39K ASP* 4.4 3.5 - - - +
41K THR* 5.0 10.1 - - + +
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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
------------------------------------------------------------
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