Contacts of the helix formed by residues 17 - 33 (chain B) in PDB entry 1IL5
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 THR 17 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLY 3.2 15.5 + - - +
16B ALA* 1.3 77.7 - - - +
18B VAL* 1.3 66.1 + - - +
19B GLN* 3.9 7.1 + - - +
20B SER* 2.6 40.4 + - - -
21B TYR* 3.2 9.5 + - - +
192B ILE* 4.0 9.5 - - - +
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Residues in contact with VAL 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B THR* 1.3 71.8 - - - +
19B GLN* 1.3 59.5 + - - +
21B TYR* 3.1 8.4 + - - +
22B THR* 2.8 39.8 + - - +
189B ARG* 3.5 43.1 - - + +
192B ILE* 4.1 5.5 - - + +
193B ARG* 3.2 57.4 - - + +
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Residues in contact with GLN 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B THR* 3.4 6.1 + - - +
18B VAL* 1.3 78.9 - - - +
20B SER* 1.3 57.7 + - - +
22B THR* 3.2 6.9 + - - -
23B ASN* 2.9 56.4 + - - +
26B ARG* 5.9 1.6 - - - +
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Residues in contact with SER 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B PHE* 4.2 14.3 - - - -
12B THR 5.8 1.3 - - - -
15B GLY 4.2 3.9 + - - -
16B ALA* 4.0 4.5 - - - -
17B THR* 2.6 44.6 + - - -
19B GLN* 1.3 78.4 - - - +
21B TYR* 1.3 56.6 + - - +
23B ASN* 3.6 4.8 + - - +
24B PHE* 3.0 28.9 + - - +
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Residues in contact with TYR 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 4.0 22.4 - + + -
17B THR 3.7 7.2 - - - +
18B VAL 3.1 7.5 + - - +
20B SER* 1.3 78.4 + - - +
22B THR* 1.3 66.7 + - - +
24B PHE* 3.2 14.7 + + - +
25B ILE* 2.9 42.9 + - + +
144B LEU* 5.9 2.5 - - + -
174B MET* 2.9 37.5 + - + -
178B ALA* 3.0 18.0 - - - +
185B GLU* 3.8 15.0 - - + -
188B MET* 3.2 32.7 - - + +
189B ARG* 3.9 17.9 - - + -
192B ILE* 3.8 22.9 - - + -
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Residues in contact with THR 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 2.8 26.4 + - - +
19B GLN* 3.2 12.4 + - - -
21B TYR* 1.3 80.2 - - - +
23B ASN* 1.3 58.5 + - - +
25B ILE* 3.1 1.6 + - - +
26B ARG* 2.8 66.7 + - - +
185B GLU* 3.8 20.2 - - - +
189B ARG* 3.5 26.0 - - - +
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Residues in contact with ASN 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLN* 2.9 42.6 + - - +
20B SER* 3.9 4.9 - - - +
22B THR* 1.3 72.9 - - - +
24B PHE* 1.3 57.4 + - - +
26B ARG* 3.6 28.0 + - - +
27B ALA* 2.8 32.0 + - - +
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Residues in contact with PHE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ILE* 3.9 15.9 - - + -
10B ASN 4.2 4.0 - - - +
11B PHE* 3.6 47.3 - + + -
20B SER 3.0 15.7 + - - +
21B TYR* 3.2 19.5 - + - +
22B THR 3.1 0.2 - - - -
23B ASN* 1.3 75.2 - - - +
25B ILE* 1.3 85.0 + - + +
27B ALA* 3.0 8.5 + - - +
28B VAL* 2.9 40.5 + - + +
60B VAL* 3.6 33.4 - - + -
62B LEU* 5.0 0.9 - - + -
175B ILE* 4.4 23.1 - - + -
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Residues in contact with ILE 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B TYR* 2.9 44.8 + - + +
22B THR 3.7 2.9 - - - +
24B PHE* 1.3 93.0 - - + +
26B ARG* 1.3 57.6 + - - +
28B VAL* 3.1 9.3 + - + +
29B ARG* 2.8 59.2 + - - +
174B MET 3.9 6.7 - - - +
175B ILE* 4.1 9.9 - - + +
178B ALA* 3.6 31.6 - - + +
179B ALA* 3.8 7.9 - - + -
185B GLU* 4.3 7.9 - - + +
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Residues in contact with ARG 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLN* 5.9 1.0 - - - +
22B THR* 2.8 42.6 + - + +
23B ASN* 3.6 26.9 + - - +
25B ILE* 1.3 76.0 - - - +
27B ALA* 1.3 56.7 + - - +
29B ARG* 3.5 26.3 + - - +
30B GLY* 2.8 25.3 + - - -
185B GLU* 4.4 2.0 - - - +
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Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ILE* 4.2 25.7 - - + +
23B ASN 2.8 18.8 + - - +
24B PHE* 3.0 6.9 + - - +
26B ARG* 1.3 74.3 - - - +
28B VAL* 1.3 65.7 + - - +
30B GLY* 3.0 4.3 + - - -
31B ARG* 3.0 23.4 + - - +
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Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 4.3 13.9 - - + +
24B PHE* 2.9 48.9 + - + +
25B ILE* 3.4 11.7 - - + +
27B ALA* 1.3 75.6 - - - +
29B ARG* 1.3 57.3 + - - +
31B ARG* 3.1 7.3 + - - +
32B LEU* 2.9 54.3 + - + +
58B ILE* 6.1 2.7 - - + -
60B VAL* 4.9 5.6 - - + -
74B LEU* 4.0 19.7 - - + -
175B ILE* 5.2 4.7 - - + -
179B ALA* 4.4 12.3 - - + -
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Residues in contact with ARG 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ILE* 2.8 29.1 + - - +
26B ARG* 3.6 21.0 - - - +
28B VAL* 1.3 75.3 - - - +
30B GLY* 1.3 54.1 + - - +
31B ARG 3.0 0.2 + - - -
32B LEU* 4.5 4.9 - - - +
33B THR* 2.7 46.8 + - - +
178B ALA 2.9 24.7 + - - -
179B ALA* 3.1 30.9 + - + +
181B PHE 4.1 0.4 + - - -
182B GLN* 3.8 19.3 + - - +
185B GLU* 3.0 39.4 + - - +
253B ALA* 3.9 13.9 - - - +
254B LEU* 4.4 10.1 - - + -
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Residues in contact with GLY 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ARG 2.8 16.4 + - - -
27B ALA* 3.0 6.0 + - - -
29B ARG* 1.3 75.7 - - - +
31B ARG* 1.3 59.9 + - - +
33B THR* 4.1 13.3 - - - +
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Residues in contact with ARG 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B PRO* 3.8 34.7 - - + +
8B ILE 4.8 4.0 + - - -
9B ILE* 3.7 27.2 - - + +
27B ALA 3.0 10.0 + - - +
28B VAL* 3.6 8.7 - - - +
30B GLY* 1.3 79.6 - - - +
32B LEU* 1.3 62.9 + - - +
33B THR 3.5 4.0 - - - +
58B ILE* 3.5 33.7 - - + +
76B VAL* 5.1 1.7 - - - +
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B VAL* 2.9 39.1 + - + +
29B ARG 3.9 1.3 - - - +
31B ARG* 1.3 77.8 - - - +
33B THR* 1.3 66.1 - - - +
34B THR* 3.2 3.1 + - - -
45B LEU* 3.6 22.9 - - + +
46B PRO* 3.8 3.6 - - - +
58B ILE* 3.6 24.2 - - + -
74B LEU* 4.8 10.1 - - + -
76B VAL* 3.8 38.5 - - + +
79B ALA* 3.6 32.1 - - + -
179B ALA* 4.7 3.1 - - + -
254B LEU* 3.8 16.8 - - + -
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Residues in contact with THR 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ARG* 2.7 32.1 + - - +
30B GLY* 4.1 13.4 - - - +
31B ARG 4.1 3.6 - - - +
32B LEU* 1.3 72.9 - - - +
34B THR* 1.3 59.3 + - - +
35B GLY* 2.9 30.6 + - - +
36B ALA 5.3 0.7 - - - +
43B PRO* 3.8 28.0 - - + +
44B VAL 4.9 2.9 - - - +
45B LEU* 4.5 2.2 - - - +
254B LEU* 3.4 23.0 - - - +
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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