Contacts of the strand formed by residues 19 - 25 (chain E) in PDB entry 5EEZ
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 VAL 19 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12E ILE* 4.5 0.2 - - + -
14E ALA* 3.5 16.6 - - + -
16E GLU* 3.5 18.8 - - + +
17E ASP 3.4 1.2 + - - -
18E GLY* 1.3 76.1 - - - +
20E ASN* 1.3 64.4 + - - +
21E VAL* 4.3 9.6 - - + -
36E GLU 3.8 0.5 - - - +
37E LYS* 3.1 6.4 - - - -
38E LEU* 2.8 37.9 + - + +
57E VAL* 4.1 20.0 - - + -
58E ARG 3.5 11.9 - - - +
59E GLY* 4.7 2.0 - - - -
60E LYS 3.2 37.7 - - - +
61E ALA* 4.2 7.0 - - + -
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Residues in contact with ASN 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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18E GLY 3.4 5.8 + - - +
19E VAL* 1.3 72.7 - - - +
21E VAL* 1.3 63.5 + - - +
22E ILE* 3.7 21.3 + - + +
35E SER* 2.8 34.6 + - - -
36E GLU 3.9 3.9 - - - +
37E LYS* 4.0 18.4 - - + +
56E LYS 3.4 5.5 - - - +
57E VAL* 3.5 1.4 - - - -
58E ARG* 2.9 53.3 + - + +
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Residues in contact with VAL 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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101D TRP* 4.4 13.4 - - + -
12E ILE* 3.8 43.5 - - + -
19E VAL* 4.3 4.0 - - + -
20E ASN* 1.3 73.3 - - - +
22E ILE* 1.3 63.0 + - - +
23E GLY 4.0 0.5 + - - -
34E HIS 3.9 0.7 - - - +
35E SER* 3.4 2.1 - - - -
36E GLU* 2.8 42.1 + - - +
38E LEU* 4.0 17.3 - - + -
44E LEU* 4.0 18.6 - - + -
46E ALA* 5.4 0.2 - - + -
55E ILE* 3.8 23.8 - - + -
56E LYS 3.6 2.7 - - - +
57E VAL* 4.7 4.5 - - + +
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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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101D TRP* 4.2 2.9 - - - -
20E ASN* 3.8 22.9 - - - +
21E VAL* 1.3 77.2 - - - +
23E GLY* 1.4 61.9 + - - +
24E LEU* 3.8 11.2 + - + +
32E PHE* 3.6 33.4 - - + -
34E HIS 3.6 4.3 - - - +
35E SER* 4.9 3.1 - - - -
55E ILE* 3.2 6.4 - - - -
56E LYS* 2.8 68.0 + - + +
58E ARG* 3.9 36.6 - - + +
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Residues in contact with GLY 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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101D TRP* 3.5 28.2 - - - -
22E ILE* 1.4 70.6 - - - +
24E LEU* 1.3 63.0 + - - -
32E PHE* 3.3 3.8 - - - -
33E HIS* 2.9 35.3 + - - -
34E HIS 3.0 12.8 + - - -
52E THR* 3.9 6.5 - - - -
54E ALA 3.8 3.8 - - - -
55E ILE* 4.7 0.2 - - - -
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Residues in contact with LEU 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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22E ILE* 4.1 12.8 - - + +
23E GLY* 1.3 73.9 - - - -
25E THR* 1.3 66.9 + - - +
30E THR* 4.2 17.3 - - + -
31E ARG* 3.5 5.8 - - - +
32E PHE* 3.8 28.5 - - + +
33E HIS* 3.8 1.8 - - - -
52E THR* 3.5 3.8 - - - -
53E SER 3.2 21.0 + - - -
54E ALA* 2.8 40.8 + - + +
55E ILE 5.0 0.4 - - - +
56E LYS* 5.2 5.2 - - + +
101E TRP* 5.1 3.6 - - + -
34F HIS* 5.8 0.2 - - + -
36F GLU* 4.0 33.9 - - + +
44F LEU* 4.2 12.8 - - + -
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Residues in contact with THR 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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24E LEU* 1.3 71.9 - - - +
26E ARG* 1.3 64.7 + - - +
29E ASP* 2.9 19.1 + - - +
30E THR* 4.5 0.5 - - - -
31E ARG* 2.9 41.5 + - + +
33E HIS* 3.6 27.3 - - + -
51E HIS 3.3 7.4 - - - +
53E SER* 4.1 0.2 - - - -
101E TRP* 2.9 24.6 + - - +
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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