Contacts of the helix formed by residues 41 - 58 (chain D) in PDB entry 3IZ0
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 LYS 41 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D ASN* 3.7 21.1 + - - +
35D ASP* 2.9 45.4 + - + +
39D ASN 4.4 3.4 - - - +
40D PRO* 1.3 71.4 - - - +
42D PRO* 1.3 60.7 - - - +
43D GLU* 3.0 21.8 - - - +
44D VAL* 2.6 42.1 + - + +
45D LEU* 3.2 8.7 + - - +
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Residues in contact with PRO 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C ASP* 4.5 22.7 - - + +
40D PRO 2.9 11.6 - - - +
41D LYS* 1.3 82.4 - - + +
43D GLU* 1.3 63.9 + - + +
45D LEU* 3.5 5.8 + - + +
46D HIS* 2.9 28.8 + - - +
109D ILE* 3.5 24.4 - - - +
110D LEU* 4.7 5.2 - - - +
112D PRO* 4.0 22.0 - - + -
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Residues in contact with GLU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C ASP* 6.0 0.9 - - - +
41D LYS* 2.8 25.8 + - - +
42D PRO* 1.3 79.7 - - + +
44D VAL* 1.3 73.9 + - - +
46D HIS* 3.6 9.1 - - + +
47D MET* 3.4 24.3 + - - +
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Residues in contact with VAL 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU* 5.7 1.1 - - + -
31D LEU* 3.9 18.2 - - + -
35D ASP* 3.5 34.8 - - - +
36D LEU* 4.9 2.5 - - + -
41D LYS* 2.6 38.7 + - + +
43D GLU* 1.3 80.6 - - - +
45D LEU* 1.3 62.4 + - - +
47D MET* 3.2 16.3 + - + +
48D ILE* 3.1 30.8 + - + +
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Residues in contact with LEU 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D LEU* 3.5 29.2 - - + -
40D PRO* 4.1 6.1 - - + -
41D LYS 3.2 9.2 + - - +
42D PRO* 3.7 8.3 - - + +
44D VAL* 1.3 73.3 - - - +
46D HIS* 1.3 57.1 - - - +
48D ILE* 3.7 4.2 - - + +
49D TYR* 2.8 67.0 + - + +
108D ASP 4.4 1.8 - - - +
109D ILE* 5.7 2.5 - - + +
112D PRO* 3.6 38.6 - - + -
117D THR* 3.7 18.6 - - + -
121D LEU* 4.2 18.8 - - + -
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Residues in contact with HIS 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D PRO 2.9 17.8 + - - +
43D GLU* 3.6 13.2 - - + +
45D LEU* 1.3 76.6 - - - +
47D MET* 1.3 55.9 + - - +
49D TYR* 3.9 1.3 - - - +
50D MET* 2.9 71.4 + - + +
84D PRO* 3.8 18.9 + - + +
85D PHE* 4.0 30.5 - - + -
88D LEU* 4.1 19.6 - - + +
109D ILE* 4.2 16.7 - - + +
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Residues in contact with MET 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LEU* 4.0 22.9 - - + -
27D ASP* 3.4 36.3 - - - +
43D GLU* 3.4 12.5 + - - +
44D VAL* 3.2 19.0 + - + +
45D LEU 3.2 0.2 - - - -
46D HIS* 1.3 77.3 - - - +
48D ILE* 1.3 56.9 + - - +
50D MET* 3.4 6.4 + - - +
51D ARG* 2.8 45.6 + - + +
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Residues in contact with ILE 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ILE* 4.3 25.1 - - + -
22D ILE* 3.8 19.7 - - + +
23D LEU* 4.2 25.6 - - + -
31D LEU* 4.6 6.7 - - + -
36D LEU* 4.3 13.7 - - + -
44D VAL* 3.1 34.9 + - + +
45D LEU* 3.7 12.1 - - + +
47D MET* 1.3 73.2 - - - +
49D TYR* 1.3 63.6 + - + +
50D MET 3.1 0.3 + - - -
51D ARG* 3.1 3.1 + - - +
52D ALA* 2.8 31.3 + - + +
121D LEU* 3.7 25.4 - - + -
124D ILE* 6.1 0.7 - - + -
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Residues in contact with TYR 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D LEU* 2.8 52.6 + - + +
46D HIS 4.1 2.7 - - - +
48D ILE* 1.3 72.5 - - - +
50D MET* 1.3 60.8 + - - +
52D ALA* 3.6 5.7 + - - +
53D LEU* 3.2 27.9 + - - +
88D LEU* 4.1 7.2 - - + -
92D LEU* 3.8 25.3 - - + +
96D LEU* 5.2 2.9 - - + -
104D PHE* 4.9 4.0 - + - -
108D ASP* 5.2 1.3 - - - +
109D ILE* 3.6 31.4 - - + -
117D THR* 3.8 17.7 + - + +
120D PHE* 3.5 34.5 - + + +
121D LEU* 4.0 14.1 - - + +
124D ILE* 3.8 29.6 - - + -
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Residues in contact with MET 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D HIS* 2.9 63.9 + - + +
47D MET* 3.7 6.1 - - - +
49D TYR* 1.3 75.2 - - - +
51D ARG* 1.3 66.7 + - + +
53D LEU* 3.2 4.7 + - - +
54D GLN* 3.0 33.0 + - + +
61D LEU* 4.0 24.0 - - + -
64D PHE* 3.5 44.1 - - + -
65D TYR* 6.6 0.2 - - + -
84D PRO* 4.8 9.9 - - + -
88D LEU* 4.2 8.3 - - + +
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Residues in contact with ARG 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C GLU* 3.2 26.9 + - - -
22D ILE* 3.0 38.7 + - + -
23D LEU* 4.0 15.5 - - + +
24D THR* 4.3 19.6 + - - +
47D MET* 2.8 29.5 + - + +
50D MET* 1.3 73.5 - - + +
52D ALA* 1.3 63.7 + - - +
54D GLN* 3.0 28.5 + - - +
55D ILE* 2.9 50.8 + - - +
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Residues in contact with ALA 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ILE* 3.9 15.4 - - + +
48D ILE* 2.8 17.0 + - + +
49D TYR* 3.7 9.0 - - - +
51D ARG* 1.3 77.8 - - - +
53D LEU* 1.3 63.4 + - - +
55D ILE* 3.2 5.9 + - - +
56D VAL* 3.0 29.7 + - - +
92D LEU* 6.4 0.2 - - + -
95D PHE* 4.5 9.6 - - + -
124D ILE* 4.2 27.4 - - + -
128D ILE* 4.9 3.6 - - + -
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Residues in contact with LEU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D TYR 3.2 9.5 + - - +
50D MET 3.2 6.5 + - - +
52D ALA* 1.3 75.9 - - - +
54D GLN* 1.3 59.9 + - - +
56D VAL* 4.9 0.9 - - - -
57D TYR* 2.8 67.5 + - + +
59D ILE* 4.3 5.4 - - + -
64D PHE* 4.2 14.6 - - + -
88D LEU* 3.5 31.4 - - + -
91D HIS* 3.7 28.0 - - + +
92D LEU* 3.9 10.3 - - + -
95D PHE* 3.7 24.5 - - + -
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Residues in contact with GLN 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C THR* 5.2 0.3 - - - +
216C GLU* 5.1 7.1 + - - +
50D MET* 3.0 27.1 + - - +
51D ARG* 3.0 39.2 + - - +
53D LEU* 1.3 74.4 - - - +
55D ILE* 1.3 57.8 + - - +
58D GLY* 2.7 34.0 + - - -
59D ILE* 3.2 30.0 + - + +
60D ARG* 3.3 5.6 - - - +
61D LEU* 3.0 40.4 - - - +
64D PHE* 4.3 5.0 - - + -
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Residues in contact with ILE 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C THR* 3.1 30.4 - - + +
216C GLU* 4.1 17.5 + - - +
217C ASP* 5.3 4.5 - - + +
21D LYS 3.5 24.9 - - - +
22D ILE* 3.9 18.8 - - + +
51D ARG* 2.9 42.8 + - - +
52D ALA* 3.5 7.6 - - - +
54D GLN* 1.3 75.6 - - - +
56D VAL* 1.3 66.8 + - + +
58D GLY 4.1 0.2 + - - -
128D ILE* 5.0 10.1 - - + -
131D ARG* 3.5 17.7 + - - +
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Residues in contact with VAL 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C ASN* 3.3 16.3 + - - +
226C LEU* 3.7 25.0 - - + +
52D ALA 3.0 17.2 + - - +
53D LEU 4.2 1.1 - - - +
55D ILE* 1.3 83.4 - - + +
57D TYR* 1.3 66.6 + - + +
58D GLY 3.4 0.2 - - - -
95D PHE* 3.8 32.8 - - + -
98D ILE* 6.3 0.2 - - + -
127D PHE* 3.7 27.8 - - + -
128D ILE* 4.4 13.7 - - + -
131D ARG* 3.6 20.9 + - - +
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Residues in contact with TYR 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C GLY* 3.6 12.3 + - - +
222C ASN* 3.5 14.4 + - - +
226C LEU* 3.5 26.7 - - + -
230C ILE* 6.1 0.9 - - + -
53D LEU* 2.8 50.1 + - + +
56D VAL* 1.3 76.7 - - + +
58D GLY* 1.3 67.6 + - - +
59D ILE* 4.3 20.5 - - + +
91D HIS* 5.2 4.9 - + + -
94D SER* 3.2 22.9 + - - -
95D PHE* 3.6 20.5 - + + -
98D ILE* 3.3 24.6 - - + +
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Residues in contact with GLY 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C GLY* 3.1 20.8 - - - -
214C GLU 4.1 19.7 - - - +
215C THR* 4.4 8.1 - - - -
216C GLU 5.3 1.3 - - - -
222C ASN* 3.8 5.5 - - - +
54D GLN 2.7 19.7 + - - -
55D ILE 4.1 0.8 + - - -
56D VAL 3.4 2.8 + - - -
57D TYR* 1.3 76.6 - - - +
59D ILE* 1.3 58.0 + - - +
60D ARG* 5.1 7.3 + - - -
63D HIS* 5.6 1.0 + - - -
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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