Contacts of the helix formed by residues 22 - 41 (chain A) in PDB entry 1IL6
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 SER 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A THR* 1.3 80.1 + - - +
23A SER* 1.3 60.6 + - - -
25A ARG* 3.2 14.3 + - - +
26A ILE* 3.0 23.7 + - - +
126A PHE* 5.7 2.0 - - - -
130A LYS* 3.5 35.1 - - - +
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Residues in contact with SER 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A THR* 2.9 13.9 + - - +
22A SER* 1.3 80.3 - - - +
24A GLU* 1.3 64.1 + - - +
26A ILE* 2.8 26.4 + - - +
27A ASP* 3.2 6.1 + - - +
130A LYS* 3.8 18.3 + - - +
182A LEU* 3.3 33.9 + - - +
185A MET* 5.1 5.0 - - - +
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Residues in contact with GLU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU* 3.7 33.0 - - + +
21A THR* 2.9 25.9 + - + +
23A SER* 1.3 79.1 - - - +
25A ARG* 1.3 62.2 + - - +
27A ASP* 3.4 7.1 + - - +
28A LYS* 3.1 22.5 + - - +
183A ARG* 5.9 5.9 + - - -
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Residues in contact with ARG 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU* 4.2 25.4 - - + +
21A THR 3.2 5.2 + - - +
22A SER* 3.2 14.1 + - - +
23A SER 3.0 0.6 - - - -
24A GLU* 1.3 78.1 - - - +
26A ILE* 1.3 67.6 + - - +
28A LYS* 3.8 7.7 - - + +
29A GLN* 2.9 36.5 + - + +
126A PHE* 4.8 23.1 - - + -
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Residues in contact with ILE 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A SER 3.0 16.4 + - - +
23A SER* 2.8 13.3 + - - +
25A ARG* 1.3 78.2 - - + +
27A ASP* 1.3 61.5 + - - +
30A ILE* 3.1 31.3 + - + +
88A ILE* 6.1 1.1 - - + -
123A LEU* 3.2 19.0 - - + +
126A PHE* 3.5 33.0 - - + +
127A LEU* 3.3 44.4 - - + -
130A LYS* 4.0 7.0 - - + -
182A LEU* 3.1 27.8 - - + -
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Residues in contact with ASP 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A SER 3.2 7.2 + - - +
24A GLU* 3.8 10.5 - - - +
26A ILE* 1.3 78.7 - - - +
28A LYS* 1.3 67.2 + - - +
29A GLN 2.9 6.3 + - - -
30A ILE* 3.0 12.4 + - - -
31A ARG* 3.1 10.6 + - - +
179A LEU* 2.7 62.7 - - - +
182A LEU* 4.0 13.6 - - + +
183A ARG* 5.0 10.7 - - + +
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Residues in contact with LYS 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLU 3.1 15.3 + - - +
25A ARG* 3.8 9.9 - - + +
27A ASP* 1.3 83.5 + - - +
29A GLN* 1.3 64.1 + - + +
31A ARG* 3.7 31.5 - - + +
32A TYR* 3.8 21.8 + - + +
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Residues in contact with GLN 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ARG* 2.9 29.4 + - + +
27A ASP 2.9 1.0 - - - -
28A LYS* 1.3 79.2 - - + +
30A ILE* 1.3 63.2 + - - +
31A ARG 3.1 0.2 - - - -
32A TYR* 3.0 24.8 + - - +
33A ILE* 3.2 12.3 + - - +
119A SER* 3.4 20.3 + - - -
122A VAL* 4.1 23.0 - - + +
123A LEU* 3.1 34.8 - - + -
126A PHE* 5.1 8.5 - - + -
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Residues in contact with ILE 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ILE* 3.1 22.2 - - + +
27A ASP* 3.0 5.7 + - - +
29A GLN* 1.3 76.7 - - - +
31A ARG* 1.3 58.9 + - - +
33A ILE* 2.7 38.3 + - + +
34A LEU* 3.1 7.0 + - + +
88A ILE* 5.3 0.7 - - + -
92A LEU* 4.6 8.3 - - + -
123A LEU* 3.5 24.9 - - + -
175A LEU* 3.3 38.6 - - + +
178A SER* 4.3 15.3 - - - +
179A LEU* 3.0 30.7 - - + -
182A LEU* 6.0 0.4 - - + -
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Residues in contact with ARG 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ASP* 3.1 11.0 + - - +
28A LYS* 3.7 30.5 - - + +
30A ILE* 1.3 76.7 - - - +
32A TYR* 1.3 60.8 + - - +
34A LEU* 3.6 8.3 + - + +
35A ASP* 3.2 24.2 + - - +
179A LEU* 3.8 16.5 - - + +
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Residues in contact with TYR 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LYS* 3.8 19.2 + - - +
29A GLN* 3.0 21.6 + - - +
30A ILE 3.0 0.6 - - - -
31A ARG* 1.3 78.8 - - - +
33A ILE* 1.3 65.5 + - - +
35A ASP* 3.1 25.9 + - + -
36A GLY* 3.1 10.9 + - - -
115A ALA* 4.8 14.7 - - + +
119A SER* 3.7 17.5 - - - +
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Residues in contact with ILE 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A GLN 3.5 11.2 - - - +
30A ILE* 2.7 39.5 + - + +
32A TYR* 1.3 80.3 - - - +
34A LEU* 1.3 61.5 + - - +
36A GLY 3.3 0.3 + - - -
37A ILE* 3.2 7.6 + - - +
92A LEU* 4.6 2.2 - - + -
116A VAL* 3.1 27.3 - - + +
119A SER* 3.9 7.6 - - - -
120A THR* 3.1 53.4 - - + +
123A LEU* 3.7 5.4 - - + -
171A PHE* 3.7 6.5 - - + -
175A LEU* 3.1 32.3 - - + -
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ILE* 3.1 9.9 + - + +
31A ARG* 3.9 9.2 - - + +
33A ILE* 1.3 75.0 - - - +
35A ASP* 1.3 68.7 + - - +
36A GLY 3.0 2.2 - - - -
37A ILE* 2.9 18.2 + - + +
38A SER* 3.0 12.0 + - - -
171A PHE 3.1 26.5 - - - +
172A LYS* 3.6 46.2 + - + +
175A LEU* 3.2 23.3 - - + -
176A GLN* 4.1 16.8 - - + +
179A LEU* 5.3 2.2 - - + -
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Residues in contact with ASP 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ARG* 3.2 16.0 + - - +
32A TYR* 3.1 28.5 + - + +
34A LEU* 1.3 78.7 - - - +
36A GLY* 1.3 63.1 + - - +
38A SER* 3.4 19.2 - - - -
39A ALA* 3.9 4.2 + - - +
112A GLN* 4.9 0.7 - - - +
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Residues in contact with GLY 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A TYR* 3.1 11.5 + - - -
33A ILE 3.3 3.6 + - - -
34A LEU 3.0 1.0 - - - -
35A ASP* 1.3 75.0 - - - +
37A ILE* 1.3 63.0 + - - +
38A SER 2.7 6.3 + - - -
39A ALA* 2.7 14.9 + - - +
40A LEU* 2.9 24.6 + - - +
112A GLN* 4.5 12.6 - - - -
115A ALA* 5.1 5.2 - - - -
116A VAL* 4.3 9.0 - - - -
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Residues in contact with ILE 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE 3.2 16.0 + - - +
34A LEU* 2.9 13.2 + - + +
36A GLY* 1.3 74.7 - - - +
38A SER* 1.3 53.3 + - - +
40A LEU* 3.4 7.8 - - + +
41A ARG* 2.6 36.5 + - + +
99A LEU* 5.7 0.2 - - + -
102A LEU* 5.6 3.4 - - + -
116A VAL* 3.4 21.8 - - + -
168A LEU* 3.5 50.5 - - + +
171A PHE* 3.7 30.5 - - + -
172A LYS* 4.2 14.6 - - + -
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Residues in contact with SER 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU 3.0 8.2 + - - -
35A ASP* 3.4 17.7 - - - -
36A GLY 2.7 4.9 + - - -
37A ILE* 1.3 74.8 - - - +
39A ALA* 1.3 57.3 + - - -
40A LEU 3.0 0.2 - - - -
41A ARG* 4.9 1.1 - - - -
42A LYS* 3.0 36.6 + - - +
172A LYS* 4.0 17.3 + - - +
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Residues in contact with ALA 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ASP 3.9 2.8 + - - +
36A GLY 2.7 9.2 + - - +
38A SER* 1.3 76.5 - - - +
40A LEU* 1.3 63.0 + - - +
41A ARG 3.4 0.2 - - - -
42A LYS* 4.4 7.3 + - - +
43A GLU* 4.8 8.3 + - - +
106A PHE* 4.5 7.4 - - - -
109A SER* 4.6 7.4 + - - +
112A GLN* 3.0 46.7 - - + +
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Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLY 2.9 18.3 + - - +
37A ILE* 3.3 6.7 - - + +
39A ALA* 1.3 81.4 - - - +
41A ARG* 1.3 49.4 + - - +
42A LYS 3.7 0.7 - - - -
44A THR* 2.6 29.9 - - - +
102A LEU* 5.4 3.1 - - + -
106A PHE* 3.5 32.1 - - + -
112A GLN* 3.4 14.4 - - + +
113A ALA* 3.2 31.4 - - - +
116A VAL* 2.9 47.6 - - + -
168A LEU* 2.9 25.0 - - + +
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Residues in contact with ARG 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ILE* 2.6 24.1 + - + +
38A SER* 3.8 1.8 - - - +
40A LEU* 1.3 76.9 - - - +
42A LYS* 1.3 55.0 + - - +
43A GLU 3.5 1.1 - - - -
44A THR* 3.5 6.7 - - + +
45A CYS* 2.7 44.2 - - + +
51A CYS* 3.7 24.1 - - - -
52A GLU* 6.2 0.6 - - - +
165A HIS* 4.6 6.5 + - + +
168A LEU* 3.5 41.3 - - + -
169A ARG* 4.4 18.4 - - - +
172A LYS* 4.2 27.9 - - - +
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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