Contacts of the helix formed by residues 41 - 58 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F ASN* 3.7 21.3 + - - +
35F ASP* 2.9 45.0 + - + +
39F ASN 4.4 3.4 - - - +
40F PRO* 1.3 71.4 - - - +
42F PRO* 1.3 60.7 - - - +
43F GLU* 3.0 21.5 - - - +
44F VAL* 2.6 42.1 + - + +
45F LEU* 3.2 8.7 + - - +
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Residues in contact with PRO 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157E ASP* 4.5 22.7 - - + +
40F PRO 2.9 11.6 - - - +
41F LYS* 1.3 82.1 - - + +
43F GLU* 1.3 63.7 + - + +
45F LEU* 3.5 5.8 + - + +
46F HIS* 2.9 28.8 + - - +
109F ILE* 3.5 24.4 - - - +
110F LEU* 4.7 5.2 - - - +
112F PRO* 4.0 22.0 - - + -
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Residues in contact with GLU 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157E ASP* 6.0 0.9 - - - +
41F LYS* 2.8 25.8 + - - +
42F PRO* 1.3 79.7 - - + +
44F VAL* 1.3 73.9 + - - +
46F HIS* 3.6 9.1 - - + +
47F MET* 3.4 24.5 + - - +
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Residues in contact with VAL 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F LEU* 5.7 1.1 - - + -
31F LEU* 3.9 18.2 - - + -
35F ASP* 3.5 34.8 - - - +
36F LEU* 4.9 2.5 - - + -
41F LYS* 2.6 38.7 + - + +
43F GLU* 1.3 80.6 - - - +
45F LEU* 1.3 62.4 + - - +
47F MET* 3.2 16.3 + - + +
48F ILE* 3.1 31.0 + - + +
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Residues in contact with LEU 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F LEU* 3.5 29.2 - - + -
40F PRO* 4.1 6.1 - - + -
41F LYS 3.2 9.0 + - - +
42F PRO* 3.7 8.3 - - + +
44F VAL* 1.3 73.7 - - - +
46F HIS* 1.3 56.9 - - - +
48F ILE* 3.7 4.4 - - + +
49F TYR* 2.8 66.8 + - + +
108F ASP 4.4 1.8 - - - +
109F ILE* 5.7 2.5 - - + +
112F PRO* 3.6 38.6 - - + -
117F THR* 3.7 18.6 - - + -
121F LEU* 4.2 18.8 - - + -
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Residues in contact with HIS 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F PRO 2.9 17.8 + - - +
43F GLU* 3.6 13.2 - - + +
45F LEU* 1.3 76.6 - - - +
47F MET* 1.3 55.7 + - - +
49F TYR* 3.9 1.3 - - - +
50F MET* 2.9 71.2 + - + +
84F PRO* 3.8 18.9 + - + +
85F PHE* 4.0 30.5 - - + -
88F LEU* 4.1 19.6 - - + +
109F ILE* 4.2 16.5 - - + +
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Residues in contact with MET 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F LEU* 4.0 22.9 - - + -
27F ASP* 3.4 36.3 - - - +
43F GLU* 3.4 12.7 + - - +
44F VAL* 3.2 19.0 + - + +
45F LEU 3.2 0.2 - - - -
46F HIS* 1.3 77.5 - - - +
48F ILE* 1.3 56.9 + - - +
50F MET* 3.4 6.4 + - - +
51F ARG* 2.8 45.6 + - + +
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Residues in contact with ILE 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F ILE* 4.3 25.4 - - + -
22F ILE* 3.8 19.7 - - + +
23F LEU* 4.2 25.8 - - + -
31F LEU* 4.6 6.7 - - + -
36F LEU* 4.3 13.7 - - + -
44F VAL* 3.1 34.9 + - + +
45F LEU* 3.7 12.1 - - + +
47F MET* 1.3 73.4 - - - +
49F TYR* 1.3 63.4 + - + +
50F MET 3.1 0.3 + - - -
51F ARG* 3.1 3.1 + - - +
52F ALA* 2.8 31.4 + - + +
121F LEU* 3.7 25.4 - - + -
124F ILE* 6.1 0.7 - - + -
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Residues in contact with TYR 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F LEU* 2.8 52.6 + - + +
46F HIS 4.1 2.5 - - - +
48F ILE* 1.3 72.8 - - - +
50F MET* 1.3 60.8 + - - +
52F ALA* 3.6 5.7 + - - +
53F LEU* 3.2 27.9 + - - +
88F LEU* 4.1 7.4 - - + -
92F LEU* 3.8 25.0 - - + +
96F LEU* 5.2 2.9 - - + -
104F PHE* 4.9 4.0 - + - -
108F ASP* 5.2 1.3 - - - +
109F ILE* 3.6 31.4 - - + -
117F THR* 3.8 17.7 + - + +
120F PHE* 3.5 34.5 - + + +
121F LEU* 4.0 14.1 - - + +
124F ILE* 3.8 29.6 - - + -
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Residues in contact with MET 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F HIS* 2.9 63.7 + - + +
47F MET* 3.7 6.1 - - - +
49F TYR* 1.3 75.4 - - - +
51F ARG* 1.3 66.6 + - + +
53F LEU* 3.2 4.7 + - - +
54F GLN* 3.0 33.0 + - + +
61F LEU* 4.0 23.8 - - + -
64F PHE* 3.5 43.9 - - + -
65F TYR* 6.2 0.4 - - + -
84F PRO* 4.8 9.9 - - + -
88F LEU* 4.2 8.3 - - + +
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Residues in contact with ARG 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216E GLU* 3.2 26.9 + - - -
22F ILE* 3.0 38.7 + - + -
23F LEU* 4.0 15.7 - - + +
24F THR* 4.3 19.6 + - - +
47F MET* 2.8 29.5 + - + +
50F MET* 1.3 73.5 - - + +
52F ALA* 1.3 63.7 + - - +
54F GLN* 3.0 28.5 + - - +
55F ILE* 2.9 50.8 + - - +
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Residues in contact with ALA 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F ILE* 3.9 15.4 - - + +
48F ILE* 2.8 17.2 + - + +
49F TYR* 3.7 9.0 - - - +
51F ARG* 1.3 77.4 - - - +
53F LEU* 1.3 63.4 + - - +
55F ILE* 3.2 5.9 + - - +
56F VAL* 3.0 29.7 + - - +
92F LEU* 6.4 0.2 - - + -
95F PHE* 4.5 9.9 - - + -
124F ILE* 4.2 27.4 - - + -
128F ILE* 4.9 3.6 - - + -
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Residues in contact with LEU 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F TYR 3.2 9.5 + - - +
50F MET 3.2 6.5 + - - +
52F ALA* 1.3 76.3 - - - +
54F GLN* 1.3 59.9 + - - +
56F VAL* 4.9 0.7 - - - -
57F TYR* 2.8 67.5 + - + +
59F ILE* 4.3 5.4 - - + -
64F PHE* 4.2 14.8 - - + -
88F LEU* 3.5 31.4 - - + -
91F HIS* 3.7 28.0 - - + +
92F LEU* 3.9 10.5 - - + -
95F PHE* 3.7 24.5 - - + -
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Residues in contact with GLN 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E THR* 5.2 0.3 - - - +
216E GLU* 5.1 7.1 + - - +
50F MET* 3.0 27.1 + - - +
51F ARG* 3.0 39.3 + - - +
53F LEU* 1.3 74.4 - - - +
55F ILE* 1.3 57.6 + - - +
58F GLY* 2.7 34.0 + - - -
59F ILE* 3.2 29.8 + - + +
60F ARG* 3.3 5.8 - - - +
61F LEU* 3.0 40.2 - - - +
64F PHE* 4.3 5.0 - - + -
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Residues in contact with ILE 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E THR* 3.1 30.2 - - + +
216E GLU* 4.1 17.5 + - - +
217E ASP* 5.3 4.5 - - + +
21F LYS 3.5 24.9 - - - +
22F ILE* 3.9 18.8 - - + +
51F ARG* 2.9 42.8 + - - +
52F ALA* 3.5 7.6 - - - +
54F GLN* 1.3 75.4 - - - +
56F VAL* 1.3 66.6 + - + +
58F GLY 4.1 0.2 + - - -
128F ILE* 5.0 10.3 - - + -
131F ARG* 3.5 17.7 + - - +
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Residues in contact with VAL 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222E ASN* 3.3 16.3 + - - +
226E LEU* 3.7 24.8 - - + +
52F ALA 3.0 17.4 + - - +
53F LEU 4.2 1.1 - - - +
55F ILE* 1.3 83.5 - - + +
57F TYR* 1.3 66.6 + - + +
58F GLY 3.4 0.2 - - - -
95F PHE* 3.8 32.5 - - + -
98F ILE* 6.3 0.2 - - + -
127F PHE* 3.7 27.8 - - + -
128F ILE* 4.4 13.2 - - + -
131F ARG* 3.6 20.9 + - - +
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Residues in contact with TYR 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212E GLY* 3.6 12.5 + - - +
222E ASN* 3.5 14.4 + - - +
226E LEU* 3.5 26.7 - - + -
230E ILE* 6.1 0.9 - - + -
53F LEU* 2.8 50.1 + - + +
56F VAL* 1.3 76.5 - - + +
58F GLY* 1.3 67.6 + - - +
59F ILE* 4.3 20.5 - - + +
91F HIS* 5.2 4.9 - + + -
94F SER* 3.2 22.9 + - - -
95F PHE* 3.6 20.3 - + + -
98F ILE* 3.3 24.6 - - + +
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Residues in contact with GLY 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212E GLY* 3.1 20.8 - - - -
214E GLU 4.1 19.7 - - - +
215E THR* 4.4 8.1 - - - -
216E GLU 5.3 1.3 - - - -
222E ASN* 3.8 5.5 - - - +
54F GLN 2.7 19.9 + - - -
55F ILE 4.1 0.8 + - - -
56F VAL 3.4 2.8 + - - -
57F TYR* 1.3 76.6 - - - +
59F ILE* 1.3 58.2 + - - +
60F ARG* 5.1 7.3 + - - -
63F 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