Contacts of the helix formed by residues 19 - 31 (chain E) in PDB entry 5LEZ
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 ILE 19 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9E ASP 4.6 0.4 - - - +
10E VAL* 3.4 38.8 - - + +
12E VAL 4.4 10.5 - - - +
13E TRP* 3.7 40.8 - - + +
18E ARG* 1.3 79.2 - - - +
20E HIS* 1.3 66.2 + - - +
21E GLN 4.2 1.6 - - - +
22E ILE* 3.1 47.9 + - + +
23E GLU* 3.3 14.6 + - - +
120E THR* 4.8 4.9 - - - +
80F LEU* 4.4 8.7 - - + -
83F ASP* 5.9 0.2 - - - +
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Residues in contact with HIS 20 (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 ASN 4.4 6.5 + - - -
6E TYR* 3.4 30.1 + + + +
7E ASP* 3.5 30.0 - - + +
9E ASP 5.7 0.2 + - - -
12E VAL 4.9 0.6 + - - -
14E SER* 4.1 22.8 + - - -
16E GLN* 5.7 3.6 + - - -
18E ARG* 3.9 23.3 + - + -
19E ILE* 1.3 72.4 - - - +
21E GLN* 1.4 57.6 + - - +
23E GLU* 3.1 21.0 + - - +
24E TYR* 2.8 46.8 + + + -
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Residues in contact with GLN 21 (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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13D ASN 4.4 1.9 - - - +
14D THR* 3.6 8.9 - - - +
15D PHE* 2.8 59.9 + - - +
6E TYR 5.2 0.2 + - - -
7E ASP 2.5 24.9 + - - +
8E ASN 3.4 28.7 - - - +
9E ASP 3.7 5.9 + - - +
10E VAL* 3.7 29.4 - - + +
19E ILE* 3.3 2.2 + - + +
20E HIS* 1.4 76.1 - - - +
22E ILE* 1.3 57.2 + - - +
24E TYR* 3.4 7.6 + - - +
25E ALA* 3.0 27.7 + - - +
126E ARG* 5.6 0.3 - - - +
127E PRO* 3.9 8.3 - - + +
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Residues in contact with ILE 22 (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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10E VAL* 4.2 4.0 - - + -
19E ILE* 3.1 42.4 + - + +
21E GLN* 1.3 74.2 - - - +
23E GLU* 1.3 67.8 + - + +
25E ALA* 3.2 4.0 + - - +
26E MET* 3.1 35.5 + - + +
120E THR* 4.1 25.1 - - + +
127E PRO* 4.0 21.1 - - + -
149E PRO* 4.4 0.8 - - - +
150E SER* 3.7 35.4 - - - +
80F LEU* 5.0 12.3 - - + -
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Residues in contact with GLU 23 (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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18E ARG* 2.6 58.6 + - - +
19E ILE 3.3 11.0 + - - +
20E HIS* 3.1 16.5 + - - +
22E ILE* 1.3 78.1 - - + +
24E TYR* 1.3 68.3 + - + +
26E MET* 3.2 36.8 + - + +
27E GLU* 3.4 11.5 + - - +
30E LYS* 5.7 0.2 - - - -
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Residues in contact with TYR 24 (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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15D PHE* 3.7 16.2 - - + -
16D SER 3.3 19.3 - - - +
17D PRO* 3.7 38.0 - - + +
19D GLY* 3.3 12.3 - - - -
7E ASP* 3.2 47.3 + - + +
8E ASN* 5.8 0.4 - - - -
20E HIS* 2.8 33.5 + + + +
21E GLN* 3.6 22.9 - - - +
22E ILE 3.2 0.2 - - - -
23E GLU* 1.3 79.5 - - + +
25E ALA* 1.3 63.9 + - - +
27E GLU* 3.0 24.5 + - + +
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Residues in contact with ALA 25 (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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15D PHE* 3.6 37.3 - - + -
21E GLN 3.0 12.9 + - - +
22E ILE 3.2 8.3 + - - +
24E TYR* 1.3 75.0 - - - +
26E MET* 1.3 62.8 + - - +
28E ALA* 3.0 20.8 + - - +
29E VAL* 3.8 2.4 + - - +
127E PRO* 3.9 10.3 - - + -
128E TYR 4.0 3.1 - - - +
129E GLY* 4.2 1.6 - - - -
149E PRO* 3.7 24.7 - - + +
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Residues in contact with MET 26 (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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22E ILE* 3.1 25.4 + - + +
23E GLU* 3.3 51.4 - - + +
25E ALA* 1.3 76.6 - - - +
27E GLU* 1.3 60.5 + - - +
29E VAL* 3.1 15.7 + - - +
30E LYS* 3.2 27.1 + - - +
148E 6V1 4.1 28.2 - - - +
149E PRO* 4.0 25.1 - - + -
150E SER* 4.8 9.4 - - - +
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Residues in contact with GLU 27 (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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17D PRO 3.5 19.1 - - - +
18D GLU* 3.9 19.7 - - - +
23E GLU 3.4 11.4 + - - +
24E TYR* 3.0 15.7 + - + +
26E MET* 1.3 74.1 - - - +
28E ALA* 1.3 66.0 + - - +
30E LYS* 3.2 41.2 + - - +
31E GLN* 3.3 39.3 + - - +
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Residues in contact with ALA 28 (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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15D PHE* 4.8 1.1 - - + -
18D GLU 4.9 1.1 - - - -
19D GLY* 3.4 26.5 - - - +
24E TYR 3.6 3.0 + - - -
25E ALA* 3.0 14.8 + - - +
27E GLU* 1.3 78.1 - - - +
29E VAL* 1.3 60.7 + - - +
31E GLN* 3.5 5.3 + - - +
32E GLY 3.5 11.8 + - - -
76E GLY* 3.5 14.4 - - - -
77E LEU* 4.3 12.6 - - + -
129E GLY* 3.7 20.9 - - - +
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Residues in contact with VAL 29 (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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25E ALA 4.0 2.0 - - - +
26E MET 3.1 10.3 + - - +
28E ALA* 1.3 77.3 - - - +
30E LYS* 1.3 59.6 + - - +
32E GLY 3.1 10.6 + - - -
75E ALA* 3.4 33.7 - - + +
130E VAL* 4.1 3.4 - - - -
131E GLY* 3.8 11.9 - - - +
148E 6V1 3.2 29.8 - - + +
149E PRO* 3.7 35.0 - - + -
161E ILE* 4.4 18.6 - - + -
162E GLY* 3.4 12.0 - - - +
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Residues in contact with LYS 30 (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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23E GLU 5.7 0.2 - - - -
26E MET* 3.2 23.1 + - - +
27E GLU* 3.2 41.5 + - - +
29E VAL* 1.3 74.8 - - - +
31E GLN* 1.3 60.0 + - + +
32E GLY 3.5 0.2 - - - -
148E 6V1 4.1 22.4 - - + -
162E GLY* 3.3 8.1 - - - +
163E ALA* 3.1 28.5 + - - +
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Residues in contact with GLN 31 (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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18D GLU* 3.2 38.0 + - - +
20D ARG* 4.5 17.9 + - - +
27E GLU* 3.3 25.2 + - - +
28E ALA* 4.0 5.6 - - - +
29E VAL 3.1 0.6 - - - -
30E LYS* 1.3 81.2 - - + +
32E GLY* 1.3 63.5 + - - +
163E ALA* 4.6 7.5 - - - +
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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
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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