Contacts of the helix formed by residues 3 - 19 (chain E) in PDB entry 4IVZ
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 3 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E GLU* 1.3 73.8 - - - +
4E PHE* 1.3 66.8 + - - +
6E LEU* 3.3 26.7 + - - +
7E SER* 3.2 17.2 + - - -
45E SER* 4.7 1.0 + - - -
50F ILE* 5.6 0.5 - - - +
51F LYS* 3.8 35.5 - - - +
54F GLU* 2.6 26.8 + - - +
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Residues in contact with PHE 4 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E GLU 3.3 5.4 + - - -
3E SER* 1.3 70.2 + - - +
5E LEU* 1.3 64.4 + - - +
7E SER* 2.5 40.7 + - - -
8E LYS* 3.2 30.7 + - + -
75E ILE* 3.2 29.8 - - + -
54F GLU* 3.7 13.4 + - - +
64F ASP* 3.1 27.6 - - - -
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Residues in contact with LEU 5 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E PHE* 1.3 83.3 - - - +
6E LEU* 1.3 64.1 + - - +
8E LYS* 3.1 15.4 + - + -
9E VAL* 3.0 33.5 + - + +
71E LEU* 4.2 9.0 - - + -
75E ILE* 5.7 2.9 - - + -
50F ILE* 3.9 20.9 - - + -
53F LEU* 5.4 2.7 - - + -
54F GLU* 3.3 35.6 + - + +
57F MET* 3.7 23.1 - - + -
64F ASP* 4.2 16.2 - - + +
68F PHE* 3.8 30.7 - - + -
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Residues in contact with LEU 6 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E SER* 3.3 21.3 + - - +
4E PHE 3.0 1.0 + - - -
5E LEU* 1.3 78.5 - - - +
7E SER* 1.3 61.4 + - - +
9E VAL* 3.1 17.7 + - + +
10E SER* 3.2 10.4 + - - -
41E ILE* 5.9 0.5 - - - +
45E SER* 3.0 36.1 + - - +
46E ARG 3.5 13.5 - - - +
47E ASN* 3.6 15.0 - - + +
48E LEU* 4.6 4.9 - - + +
50F ILE* 3.6 34.9 - - + +
51F LYS* 3.6 38.6 - - + +
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Residues in contact with SER 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E GLU 5.4 1.5 + - - -
3E SER 3.2 6.6 + - - -
4E PHE* 2.5 31.4 + - - -
6E LEU* 1.3 68.1 - - - +
8E LYS* 1.3 63.0 + - - +
9E VAL 3.0 9.4 + - - -
10E SER* 2.8 20.3 + - - -
11E PHE* 3.1 13.0 + - - +
45E SER* 3.0 18.3 + - - -
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Residues in contact with LYS 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E PHE* 3.2 39.4 + - + +
5E LEU* 3.1 14.6 + - + +
7E SER* 1.3 83.6 + - - +
9E VAL* 1.3 52.9 + - - +
11E PHE* 4.3 26.6 - - + +
12E VAL* 3.7 10.7 - - - +
71E LEU* 2.6 37.7 - - + +
74E GLU* 3.2 37.5 + - + +
75E ILE* 4.5 8.1 - - + -
77E LYS* 5.2 8.9 - - - +
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Residues in contact with VAL 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E LEU* 3.0 35.4 - - + +
6E LEU* 3.5 8.3 - - + +
7E SER 3.0 0.8 - - - -
8E LYS* 1.3 81.3 - - - +
10E SER* 1.3 63.6 + - - +
11E PHE 2.9 5.6 + - - -
12E VAL* 3.2 2.3 + - - +
13E ILE* 3.1 42.0 + - + +
41E ILE* 6.1 0.7 - - + -
48E LEU* 5.0 13.5 - - + -
53E LEU* 4.6 7.9 - - + -
67E PHE* 3.9 21.1 - - + -
71E LEU* 4.4 7.0 - - + -
50F ILE* 4.8 13.7 - - + -
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Residues in contact with SER 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E LEU 3.2 4.7 + - - -
7E SER* 2.8 21.8 + - - -
9E VAL* 1.3 77.5 - - - +
11E PHE* 1.3 58.1 + - - +
13E ILE* 4.3 4.4 - - - +
14E LYS* 3.4 23.4 + - - +
41E ILE* 3.0 42.0 - - - +
42E GLU* 4.0 18.5 + - - +
43E ARG 5.3 0.3 + - - -
45E SER* 3.7 15.5 + - - -
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Residues in contact with PHE 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E SER 3.1 15.5 + - - +
8E LYS* 4.4 22.0 - - + +
9E VAL 2.9 0.8 + - - -
10E SER* 1.3 75.2 + - - +
12E VAL* 1.3 62.4 + - + +
13E ILE 3.1 1.4 + - - -
14E LYS* 3.2 8.7 + - + +
15E LYS* 2.9 45.2 + - + +
74E GLU* 3.4 44.4 - - + -
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Residues in contact with VAL 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E LYS 3.7 17.5 - - - +
9E VAL 3.2 4.8 + - - +
11E PHE* 1.3 81.4 - - + +
13E ILE* 1.3 60.8 + - - +
15E LYS* 3.8 7.4 - - + +
16E ILE* 3.1 31.6 + - + +
67E PHE* 3.7 40.8 - - + +
70E MET* 4.3 12.8 - - + +
71E LEU* 3.9 24.5 - - + +
74E GLU* 4.2 21.8 - - + -
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Residues in contact with ILE 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E VAL* 3.1 35.3 + - + +
10E SER* 4.4 4.7 - - - +
12E VAL* 1.3 72.7 - - - +
14E LYS* 1.3 54.1 + - - +
15E LYS 3.0 3.8 - - - -
16E ILE* 2.8 23.9 + - - +
17E ARG* 2.8 17.2 + - + +
27E LEU* 4.5 11.4 - - + -
38E ILE* 6.0 1.6 - - + -
41E ILE* 4.9 12.6 - - + -
42E GLU* 4.4 13.7 - - + +
48E LEU* 5.0 3.4 - - + -
53E LEU* 4.5 6.3 - - + -
56E ILE* 4.2 37.0 - - + -
60E LEU* 4.3 10.2 - - + +
67E PHE* 3.6 21.8 - - + -
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Residues in contact with LYS 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E SER 3.4 17.7 + - - +
11E PHE* 3.2 7.7 + - + +
13E ILE* 1.3 79.0 - - - +
15E LYS* 1.3 66.0 + - - +
17E ARG* 3.4 32.7 + - - +
18E LEU* 3.3 35.2 + - + +
24E GLN* 4.8 0.4 - - - +
42E GLU* 3.2 33.0 + - + +
43E ARG* 3.8 12.6 - - - +
2G T 5.1 3.4 + - - -
3G G 3.5 23.2 + - - -
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Residues in contact with LYS 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E PHE* 2.9 36.6 + - + +
12E VAL* 3.8 8.1 - - + +
13E ILE 2.9 0.4 + - - -
14E LYS* 1.3 74.7 - - - +
16E ILE* 1.3 66.0 + - + +
17E ARG 2.7 5.3 + - - -
18E LEU* 2.8 17.5 + - - +
19E GLU* 3.1 20.7 + - + +
70E MET* 4.1 27.6 - - + +
74E GLU* 4.1 15.5 + - + +
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Residues in contact with ILE 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E VAL* 3.1 21.1 + - + +
13E ILE 2.8 6.1 + - - -
15E LYS* 1.3 72.8 - - + +
17E ARG* 1.3 65.8 + - - +
19E GLU* 3.5 23.0 - - - +
20E LYS* 3.2 44.5 + - - +
60E LEU* 3.9 17.8 - - + +
62E VAL* 4.0 22.2 - - + -
67E PHE* 3.8 28.3 - - + -
70E MET* 4.1 24.5 - - - -
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Residues in contact with ARG 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E ILE* 2.8 13.1 + - + +
14E LYS* 3.4 36.9 + - - +
15E LYS 2.7 0.8 + - - -
16E ILE* 1.3 78.6 - - - +
18E LEU* 1.3 69.5 + - - +
20E LYS* 2.8 23.7 + - - +
21E GLY 3.0 8.3 + - - -
22E MET* 2.6 53.9 + - + +
23E THR* 3.6 6.0 - - - +
24E GLN* 3.3 20.6 - - - +
27E LEU* 4.9 15.0 - - + -
38E ILE* 5.6 0.7 - - - -
42E GLU* 2.9 28.2 + - - -
60E LEU* 3.6 16.5 - - + +
2G T 2.9 32.8 + - - -
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Residues in contact with LEU 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E LYS* 3.3 28.5 - - + +
15E LYS* 2.8 8.0 + - - +
17E ARG* 1.3 109.9 - - - +
19E GLU* 1.3 56.5 + - - +
20E LYS 3.0 0.2 + - - -
21E GLY* 2.8 24.5 + - - +
22E MET 4.2 4.5 - - - +
2G T 4.6 3.1 - - - +
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Residues in contact with GLU 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E LYS* 3.1 24.2 + - + +
16E ILE* 3.5 31.3 - - - +
18E LEU* 1.3 76.2 - - - +
20E LYS* 1.3 70.7 + - - +
70E MET* 4.8 12.5 - - - +
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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