Contacts of the strand formed by residues 30 - 39 (chain E) in PDB entry 5IXM
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 PHE 30 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26E ILE* 3.3 16.0 + - + -
27E ALA* 2.7 50.0 + - + +
28E PRO 3.6 0.2 - - - -
29E ASN* 1.3 117.0 - - - +
31E ASP* 1.3 68.0 + - - +
50E PHE* 3.4 30.3 - + + -
51E ARG 3.5 3.4 - - - -
52E TYR* 3.9 16.8 - - + -
54E LEU* 3.5 28.7 - - + -
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Residues in contact with ASP 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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23E TYR* 3.0 29.8 + - + +
25E ASN* 3.8 9.6 - - - +
26E ILE* 4.5 4.9 - - - +
27E ALA 3.9 5.6 - - - +
28E PRO 5.6 1.8 - - - +
29E ASN 5.8 0.2 - - - -
30E PHE* 1.3 89.4 - - - +
32E ALA* 1.3 62.0 + - - +
50E PHE* 3.0 12.4 - - - -
51E ARG* 2.9 72.0 + - + +
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Residues in contact with ALA 32 (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 TYR* 3.7 5.4 - - - -
24E TRP* 3.2 55.4 + - + -
25E ASN 4.5 5.7 - - - +
26E ILE* 3.9 10.5 - - + +
31E ASP* 1.3 77.0 - - - +
33E THR* 1.3 67.7 + - - +
34E ILE* 4.6 4.5 - - + -
49E GLU 3.2 9.6 - - - +
50E PHE* 4.5 6.3 - - + -
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Residues in contact with THR 33 (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 LEU* 5.3 7.3 - - + +
21E PRO* 4.9 5.8 - - + -
22E TYR 3.4 14.4 - - - +
23E TYR* 3.7 16.5 - - - -
32E ALA* 1.3 79.2 + - - +
34E ILE* 1.3 63.9 + - - +
35E THR* 3.8 16.6 - - - +
47E GLN 3.5 4.0 - - - +
48E ASN* 3.5 1.6 - - - -
49E GLU* 2.9 48.8 + - + +
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Residues in contact with ILE 34 (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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21E PRO 3.7 0.2 - - - -
22E TYR* 2.8 62.8 + - + +
24E TRP* 4.1 29.8 - - + -
32E ALA* 4.6 2.7 - - + -
33E THR* 1.3 83.5 - - - +
35E THR* 1.3 64.7 + - - +
36E PRO* 3.8 3.5 - - + +
46E TRP* 4.1 24.9 - - + -
47E GLN 3.5 2.5 - - - -
48E ASN* 3.6 26.2 - - + +
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Residues in contact with THR 35 (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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19E LEU* 3.7 24.9 - - + -
20E LEU 3.9 3.8 - - - +
21E PRO* 3.6 27.2 - - + +
33E THR* 3.8 12.3 - - - +
34E ILE* 1.3 81.7 + - - +
36E PRO* 1.3 74.7 - - - +
37E HIS 3.5 2.3 + - - -
46E TRP* 3.6 2.9 - - - -
47E GLN* 2.9 52.5 + - - +
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Residues in contact with PRO 36 (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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3E PHE* 6.3 1.1 - - + -
18E PHE 3.7 2.5 - - - +
20E LEU* 3.0 65.7 + - + +
22E TYR* 5.4 2.9 - - + -
34E ILE* 3.8 5.2 - - + +
35E THR* 1.3 87.8 - - - +
37E HIS* 1.3 58.8 + - - +
38E TYR 4.0 1.6 - - - -
44E LEU* 4.2 13.7 - - + -
45E GLN 3.5 7.4 - - - +
46E TRP* 3.9 31.0 - - + -
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Residues in contact with HIS 37 (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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17E GLU* 3.0 29.8 + - + +
18E PHE 3.5 4.7 - - - -
19E LEU* 3.4 30.4 - - + +
35E THR 4.3 4.3 - - - +
36E PRO* 1.3 73.7 - - - +
38E TYR* 1.3 71.4 + - - +
39E MET* 3.3 29.4 - - + +
44E LEU* 3.8 1.9 - - - +
45E GLN* 2.9 59.8 + - + +
47E GLN* 3.6 13.6 + - + +
117E LEU* 5.5 0.2 - - + -
118E THR* 5.1 15.3 - - - -
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Residues in contact with TYR 38 (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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16E PHE* 4.5 11.7 - + + -
17E GLU* 3.2 5.5 - - - -
18E PHE* 2.9 51.6 + - + +
36E PRO 4.0 0.4 - - - -
37E HIS* 1.3 74.0 - - - +
39E MET* 1.3 71.0 + - - +
40E GLU* 3.9 34.2 + - + +
43E GLY* 3.8 13.5 - - - -
44E LEU* 4.0 15.3 - - + +
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Residues in contact with MET 39 (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 ASN* 4.0 11.7 - - + +
16E PHE 3.7 3.4 - - - -
17E GLU* 3.6 19.7 - - + +
37E HIS* 3.3 39.5 - - - +
38E TYR* 1.3 86.4 - - - +
40E GLU* 1.3 66.4 + - - +
41E ARG 3.4 1.3 - - - -
42E ARG* 3.0 9.7 + - + -
43E GLY* 2.8 44.0 + - - +
45E GLN* 3.5 32.8 - - + +
66E LEU* 4.2 8.5 - - + -
70E ARG* 5.4 0.2 + - - -
117E LEU* 3.8 28.3 - - + -
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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