Contacts of the helix formed by residues 19 - 32 (chain C) in PDB entry 5ICS
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 ARG 19 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C GLY 4.2 3.2 + - - +
17C GLY 3.5 1.0 + - - -
18C GLY* 1.3 78.0 - - - +
20C GLY* 1.3 70.1 + - - +
21C ILE 3.4 0.3 + - - -
22C GLY* 3.1 7.6 + - - -
23C ALA* 3.1 17.7 + - - -
40C ASP* 4.6 1.5 + - - +
44C SER* 3.6 15.5 - - - +
45C GLY* 5.2 0.4 - - - -
190C PRO* 5.7 9.2 - - + -
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Residues in contact with GLY 20 (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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19C ARG* 1.3 77.3 - - - +
21C ILE* 1.3 64.8 + - - -
23C ALA* 3.2 5.0 + - - +
24C GLY 3.1 17.0 + - - -
189C THR* 4.0 21.3 - - - -
190C PRO* 4.6 9.2 - - - +
221C PRO* 3.4 15.1 - - - +
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Residues in contact with ILE 21 (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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19C ARG 3.4 0.2 + - - -
20C GLY* 1.3 70.6 - - - -
22C GLY* 1.3 64.3 + - - +
24C GLY* 3.1 3.3 + - - -
25C ILE* 3.0 24.9 + - + +
89C ASN* 3.6 20.9 - - - +
139C ILE* 4.6 4.7 - - + -
184C PRO* 4.4 13.9 - - + -
187C ILE* 3.9 41.7 - - + -
189C THR* 4.1 8.0 - - + +
221C PRO* 4.0 8.4 - - - +
224C VAL* 3.8 28.9 - - + -
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Residues in contact with GLY 22 (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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14C VAL* 4.2 1.4 - - - +
16C GLY 3.3 11.4 - - - -
17C GLY* 3.5 9.0 - - - -
19C ARG 3.1 4.4 + - - -
21C ILE* 1.3 79.2 - - - +
23C ALA* 1.3 56.7 + - - +
25C ILE* 3.2 9.0 + - - +
26C VAL* 3.0 30.0 + - - +
89C ASN* 3.2 27.2 - - - +
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Residues in contact with ALA 23 (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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17C GLY 3.3 12.6 + - - +
18C GLY 4.0 1.1 - - - +
19C ARG* 3.1 32.7 + - - +
20C GLY 3.7 3.1 - - - +
22C GLY* 1.3 76.1 - - - +
24C GLY* 1.3 58.2 + - - +
26C VAL* 3.3 1.7 + - - +
27C ARG* 2.9 40.3 + - - +
49C LEU* 3.8 20.4 - - + +
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Residues in contact with GLY 24 (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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20C GLY 3.1 11.1 + - - -
21C ILE 3.1 4.6 + - - -
23C ALA* 1.3 77.9 - - - +
25C ILE* 1.3 55.6 + - - +
27C ARG* 3.5 8.4 + - - +
28C ALA* 3.0 28.9 + - - +
221C PRO* 3.9 30.7 - - - +
222C ALA* 4.4 5.6 - - - -
225C GLY* 3.9 2.0 - - - -
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Residues in contact with ILE 25 (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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14C VAL* 4.1 10.8 - - + -
21C ILE* 3.0 27.9 + - + +
22C GLY* 3.2 9.2 + - - +
24C GLY* 1.3 74.3 - - - +
26C VAL* 1.3 65.5 + - - +
28C ALA* 3.2 1.9 + - - +
29C PHE* 3.0 49.1 + - + -
87C VAL* 4.0 19.1 - - + -
89C ASN* 4.3 5.6 - - + +
139C ILE* 3.8 33.4 - - + -
224C VAL* 4.1 4.9 - - + +
225C GLY* 3.8 23.8 - - - +
228C ALA* 4.3 5.6 - - + -
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Residues in contact with VAL 26 (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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14C VAL* 4.0 20.2 - - + -
17C GLY* 3.6 15.3 - - - +
22C GLY 3.0 19.1 + - - +
23C ALA* 3.6 8.7 - - - +
25C ILE* 1.3 75.3 - - - +
27C ARG* 1.3 63.7 + - + +
29C PHE* 3.2 3.3 + - - +
30C VAL* 2.9 24.6 + - + +
36C VAL* 4.0 20.0 - - + -
38C ILE* 3.8 31.2 - - + -
49C LEU* 4.3 6.7 - - + -
53C LEU* 4.3 9.4 - - + -
56C ALA* 4.3 13.5 - - + -
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Residues in contact with ARG 27 (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 ALA* 2.9 27.3 + - - +
24C GLY* 3.9 6.5 - - - +
26C VAL* 1.3 77.1 - - - +
28C ALA* 1.3 58.1 + - - +
30C VAL* 3.4 5.2 + - - +
31C ASN* 2.9 43.4 + - - +
49C LEU* 3.5 21.7 - - + +
52C GLU* 2.9 43.4 + - - -
53C LEU* 4.1 22.7 - - + +
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Residues in contact with ALA 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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24C GLY 3.0 19.6 + - - +
25C ILE 3.2 3.6 + - - +
27C ARG* 1.3 78.3 - - - +
29C PHE* 1.3 61.8 + - - +
31C ASN* 3.3 8.4 + - - +
32C SER* 3.1 22.0 + - - -
222C ALA* 5.1 2.5 - - - +
225C GLY* 3.5 32.3 - - - +
226C ALA* 4.1 2.5 - - - +
229C VAL* 3.7 10.6 - - + +
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Residues in contact with PHE 29 (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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7C TYR* 3.8 20.0 - + - -
12C VAL* 3.7 23.3 - - + -
14C VAL* 4.9 1.1 - - + -
25C ILE* 3.0 45.9 + - + +
26C VAL* 4.9 0.4 - - - -
28C ALA* 1.3 74.8 - - - +
30C VAL* 1.3 66.1 + - - +
32C SER* 2.7 22.5 + - - -
34C ALA* 3.1 14.1 + - + -
36C VAL* 3.6 21.5 - - + -
85C CYS* 4.3 10.3 - - - -
87C VAL* 4.0 9.6 - - + -
137C ILE* 4.4 0.2 - - + -
228C ALA* 3.6 35.4 - - + -
229C VAL* 3.9 14.8 - - + -
232C ALA* 3.6 24.7 - - + -
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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
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4C GLY* 5.3 0.2 - - - -
26C VAL* 2.9 30.1 + - + +
27C ARG* 3.8 6.1 - - - +
29C PHE* 1.3 75.5 - - - +
31C ASN* 1.3 64.2 + - - +
33C GLY* 3.0 20.1 + - - -
34C ALA 3.8 7.7 + - - +
36C VAL* 3.7 18.4 - - + -
53C LEU* 4.4 19.1 - - + -
54C PRO* 6.2 0.4 - - + -
55C GLY* 4.0 35.9 - - - +
56C ALA* 4.2 4.9 - - + +
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Residues in contact with ASN 31 (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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4C GLY* 3.2 18.4 - - - +
27C ARG* 2.9 30.5 + - - +
28C ALA* 3.6 7.8 - - - +
30C VAL* 1.3 82.8 - - - +
32C SER* 1.3 56.8 + - - +
33C GLY 3.2 1.0 + - - -
53C LEU* 6.0 1.2 - - - +
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Residues in contact with SER 32 (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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4C GLY* 3.4 11.3 - - - -
6C ARG* 3.3 15.1 + - - +
7C TYR* 2.9 52.8 + - - +
28C ALA 3.1 11.0 + - - -
29C PHE* 2.7 27.5 + - - -
31C ASN* 1.3 74.5 - - - +
33C GLY* 1.3 55.1 + - - +
34C ALA 4.1 0.2 + - - -
229C VAL* 4.1 17.0 - - - -
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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