Contacts of the helix formed by residues 11 - 31 (chain C) in PDB entry 1SIW
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 ILE 11 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C MET* 3.5 14.8 - - + +
7C PHE* 2.9 27.9 + - + +
10C ASP* 1.3 81.4 - - + +
12C TYR* 1.3 67.0 + - - +
13C PRO* 3.1 2.2 - - - -
14C TYR* 2.9 20.5 + - - +
15C ILE* 3.4 28.2 + - + +
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Residues in contact with TYR 12 (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 PHE* 2.7 40.5 + + + +
8C PHE* 3.6 21.8 - + - +
11C ILE* 1.3 75.3 - - - +
13C PRO* 1.3 65.8 - - + +
15C ILE* 2.9 18.4 + - + +
16C ALA* 2.9 29.9 + - + +
189C VAL* 4.0 16.4 - - + -
192C MET* 3.9 28.5 - - + -
193C THR* 2.7 41.6 + - - +
196C LEU* 4.0 21.2 - - + +
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Residues in contact with PRO 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C PHE 3.3 19.5 - - - +
9C PHE* 3.9 11.7 - - - +
10C ASP* 3.8 17.0 - - - +
11C ILE 3.1 6.7 - - - +
12C TYR* 1.3 90.4 - - - +
14C TYR* 1.3 67.8 + - + +
16C ALA* 4.2 3.7 - - + +
17C GLY* 3.1 21.8 + - - -
162C TRP* 4.6 0.9 - - + -
166C VAL* 4.2 25.3 - - + +
192C MET* 3.5 26.0 - - + -
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Residues in contact with TYR 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ASP* 3.2 28.5 - - - -
11C ILE* 2.9 7.5 + - - +
13C PRO* 1.3 85.5 - - + +
15C ILE* 1.3 66.5 + - + +
17C GLY* 3.7 2.1 - - - +
18C ALA* 3.0 24.1 + - - +
165C SER 3.7 1.4 + - - -
166C VAL* 2.6 49.3 + - + -
169C PHE* 3.4 49.9 - + - -
170C HIS 4.3 2.6 + - - -
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Residues in contact with ILE 15 (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 PHE* 4.7 9.4 - - + -
11C ILE* 3.4 30.5 + - + +
12C TYR* 2.9 20.1 + - + +
14C TYR* 1.3 79.1 - - + +
16C ALA* 1.3 63.2 + - - +
18C ALA* 3.1 5.4 + - - +
19C VAL* 3.0 35.1 + - + +
196C LEU* 4.4 13.5 - - + -
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Residues in contact with ALA 16 (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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12C TYR* 2.9 20.9 + - + +
13C PRO 4.2 3.6 - - - +
15C ILE* 1.3 78.6 - - - +
17C GLY* 1.3 58.0 + - - +
19C VAL* 4.0 0.7 - - - +
20C PHE* 3.0 30.1 + - - +
192C MET* 3.6 33.0 - - + +
195C PHE* 4.0 8.3 - - + +
196C LEU* 3.6 24.4 - - + +
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Residues in contact with GLY 17 (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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13C PRO 3.1 18.8 + - - -
14C TYR* 3.5 2.7 + - - -
15C ILE 3.1 1.0 - - - -
16C ALA* 1.3 77.0 - - - +
18C ALA* 1.3 63.1 + - - +
20C PHE* 3.7 6.8 + - - +
21C LEU* 3.3 30.7 + - - +
195C PHE* 5.8 1.8 - - - -
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Residues in contact with ALA 18 (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 TYR 3.0 17.7 + - - +
15C ILE* 3.1 5.1 + - - +
17C GLY* 1.3 74.1 - - - +
19C VAL* 1.3 64.1 + - + +
21C LEU* 3.3 3.7 + - - +
22C ILE* 2.9 38.8 + - + +
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Residues in contact with VAL 19 (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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15C ILE* 3.0 24.2 + - + +
16C ALA 4.0 0.4 - - - +
18C ALA* 1.3 76.6 - - + +
20C PHE* 1.3 58.5 + - - +
22C ILE* 4.1 7.0 - - + -
23C GLY* 2.9 27.5 + - - -
196C LEU* 3.7 31.9 - - + +
199C PRO* 3.5 2.4 - - - +
200C PHE* 3.6 33.4 - - + -
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Residues in contact with PHE 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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16C ALA 3.0 19.9 + - - +
17C GLY* 3.8 7.6 - - - +
19C VAL* 1.3 77.8 - - - +
21C LEU* 1.3 80.7 + - + +
24C SER* 2.8 32.2 + - - -
195C PHE* 3.3 47.1 + + + +
198C PHE* 3.3 50.3 - + + -
199C PRO* 4.1 4.3 - - - +
207C TRP* 3.6 23.8 - + - -
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Residues in contact with LEU 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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1309A 3PH 3.7 42.7 - - + +
17C GLY 3.3 18.3 + - - +
18C ALA* 4.0 3.1 - - - +
19C VAL 3.3 0.2 - - - -
20C PHE* 1.3 98.8 - - + +
22C ILE* 1.3 66.5 + - - +
23C GLY 3.2 1.6 - - - -
24C SER* 3.2 3.4 + - - -
25C TRP* 3.0 24.6 + - - +
207C TRP* 4.6 13.0 - - + -
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Residues in contact with ILE 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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493B LEU* 4.7 10.3 - - + -
1310B 3PH 6.1 3.8 - - + -
18C ALA* 2.9 32.8 + - + +
19C VAL* 4.1 6.3 - - + -
21C LEU* 1.3 76.0 - - - +
23C GLY* 1.3 60.2 + - - +
25C TRP* 4.4 22.9 - - + -
26C LEU* 2.9 52.3 + - + +
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Residues in contact with GLY 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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19C VAL* 2.9 21.2 + - - -
22C ILE* 1.3 83.3 - - - +
24C SER* 1.3 55.7 + - - +
26C LEU* 4.1 5.2 - - - +
27C ARG* 3.0 31.4 + - - +
199C PRO* 3.6 15.5 - - - +
200C PHE* 5.0 11.4 - - - -
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Residues in contact with SER 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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1309A 3PH 4.0 10.5 - - - -
20C PHE 2.8 23.3 + - - -
21C LEU 3.2 5.0 + - - -
23C GLY* 1.3 74.7 - - - +
25C TRP* 1.3 66.2 + - - +
27C ARG* 3.4 1.4 + - - -
28C TYR* 2.9 25.3 + - - +
35C TRP* 3.6 9.9 - - - -
198C PHE* 3.9 11.3 - - - -
199C PRO* 3.7 6.0 - - - +
204C ILE* 4.8 0.9 - - - +
207C TRP* 2.9 38.8 + - - -
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Residues in contact with TRP 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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1A SER* 3.8 2.4 + - - -
3A PHE* 3.6 37.9 - + + +
4A LEU* 4.5 12.6 - - + -
1309A 3PH 3.5 43.9 - - + +
491B PHE* 4.6 12.8 - + - -
493B LEU* 3.7 33.0 - - + +
1310B 3PH 5.4 9.4 - - + -
21C LEU 3.0 16.2 + - - +
22C ILE* 3.8 20.2 - - + +
24C SER* 1.3 76.7 - - - +
26C LEU* 1.3 62.4 + - - +
28C TYR* 3.1 2.8 + - - +
29C ASP* 3.0 41.7 + - - +
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Residues in contact with LEU 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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493B LEU* 3.3 31.4 - - + -
494B PHE* 3.7 31.6 - - + -
22C ILE* 2.9 39.4 + - + +
23C GLY* 4.1 4.3 - - - +
25C TRP* 1.3 76.2 - - - +
27C ARG* 1.3 58.0 + - - +
30C TYR* 3.0 43.3 + - + +
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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 GLY 3.0 19.1 + - - +
24C SER* 4.0 3.6 - - - +
26C LEU* 1.3 77.6 - - - +
28C TYR* 1.3 59.5 + - - +
30C TYR 5.0 0.4 - - - -
31C GLY* 2.9 31.8 + - - +
34C THR* 2.9 45.7 + - - +
35C TRP* 4.0 11.6 - - + -
36C ARG* 3.7 10.1 - - - +
199C PRO 3.0 26.8 + - - +
200C PHE* 3.7 4.4 - - - +
201C SER 2.8 36.5 + - - +
202C ARG* 5.2 1.6 - - - +
204C ILE* 3.7 20.1 - - - +
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Residues in contact with TYR 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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2A LYS* 3.6 25.8 - - + +
3A PHE* 3.7 14.6 - + + -
6A ARG* 3.1 19.7 - - - +
1309A 3PH 2.7 62.0 + - + -
216B LYS* 3.1 14.8 + - - -
218B ARG* 4.0 5.2 - - - -
24C SER 2.9 18.2 + - - +
25C TRP* 3.1 4.9 + - - +
27C ARG* 1.3 80.8 - - - +
29C ASP* 1.3 72.1 + - - +
30C TYR 3.7 0.2 + - - -
32C GLN* 2.7 50.9 + - - +
35C TRP* 3.7 23.1 - + + -
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Residues in contact with ASP 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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1A SER* 2.7 28.2 + - - -
2A LYS* 3.3 33.1 + - - +
3A PHE* 2.7 32.0 + - - +
483B GLY 5.3 1.9 - - - +
492B ASN* 5.8 0.2 - - - -
493B LEU* 4.5 7.3 + - + +
25C TRP* 3.0 32.0 + - + +
28C TYR* 1.3 79.4 - - - +
30C TYR* 1.3 84.1 + - + +
31C GLY 3.7 0.2 - - - -
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Residues in contact with TYR 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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2A LYS* 5.9 1.6 - - - +
483B GLY* 3.6 32.9 + - - -
492B ASN* 3.9 10.7 + - - +
493B LEU* 3.6 12.4 + - + -
494B PHE* 3.2 74.4 + + + +
26C LEU* 3.0 31.0 + - + +
27C ARG* 5.0 0.7 - - - -
29C ASP* 1.3 94.2 - - + +
31C GLY* 1.3 57.2 + - - +
32C GLN 3.9 1.1 - - - -
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Residues in contact with GLY 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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27C ARG* 2.9 23.4 + - - +
30C TYR* 1.3 81.6 - - - +
32C GLN* 1.3 56.5 + - - +
33C TYR 3.1 3.4 - - - -
34C THR* 2.6 47.1 + - - -
35C TRP* 3.3 5.1 + - - +
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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
------------------------------------------------------------
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