Contacts of the strand formed by residues 32 - 38 (chain U) in PDB entry 5EEY
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 32 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36T GLU* 4.4 1.1 - - - -
22U ILE* 3.4 49.8 - - + -
23U GLY 3.6 3.1 - - - -
24U LEU* 4.0 15.0 - - + -
25U THR* 4.5 0.9 - - - -
31U ARG* 1.3 80.7 + - - +
33U HIS* 1.3 60.3 + - - +
34U HIS 4.5 3.1 - - - +
56U LYS* 4.4 3.8 - - - -
58U ARG* 4.2 4.0 - - - -
148W G 2.6 85.4 + + + +
149W U 3.6 54.8 - + - +
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Residues in contact with HIS 33 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23U GLY* 3.0 30.8 + - - -
24U LEU 3.9 0.9 - - - -
25U THR* 3.7 20.2 - - + -
31U ARG* 3.6 4.4 + - - +
32U PHE* 1.3 75.6 - - - +
34U HIS* 1.3 76.1 + - + +
51U HIS* 3.5 26.9 + - + +
52U THR* 2.5 32.0 + - - -
27V GLY 5.1 0.2 - - - -
28V ALA* 4.7 15.5 + - - +
30V THR* 4.7 1.8 + - - -
101V TRP* 3.9 27.1 - + - -
149W U 5.6 3.5 - - - +
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Residues in contact with HIS 34 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21U VAL 4.0 0.3 - - - +
22U ILE* 3.5 6.0 - - - +
23U GLY 2.8 27.4 + - - -
32U PHE* 3.5 2.6 - - - +
33U HIS* 1.3 99.6 + - + +
35U SER* 1.3 80.7 + - - +
36U GLU* 2.8 35.9 + - + -
24V LEU* 5.8 0.4 - - + -
30V THR* 3.5 49.5 + - + +
101V TRP* 3.9 15.3 - + + -
149W U 5.5 5.2 - - - -
152W A 4.1 10.1 - + - -
153W G 3.8 3.8 - - - -
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Residues in contact with SER 35 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20U ASN* 2.8 31.2 + - - +
21U VAL 3.5 4.0 - - - -
22U ILE* 3.8 13.2 - - - +
34U HIS* 1.3 82.4 + - - +
36U GLU* 1.3 59.0 + - - +
37U LYS* 3.5 11.7 + - - -
149W U 3.1 29.4 + - - -
151W G 4.7 2.7 + - - -
152W A 3.4 17.2 - - - -
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Residues in contact with GLU 36 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19U VAL 3.5 0.5 - - - +
20U ASN* 3.5 2.4 - - - -
21U VAL* 2.8 44.6 + - - +
34U HIS* 2.8 18.8 + - + +
35U SER* 1.3 72.6 - - - +
37U LYS* 1.3 62.3 + - - +
38U LEU* 3.8 21.4 + - + +
44U LEU* 4.3 22.9 - - + -
24V LEU* 4.0 11.2 - - + +
32V PHE* 4.8 0.2 - - - -
56V LYS* 2.7 24.1 + - - +
101V TRP* 5.5 1.1 - - + -
152W A 3.5 6.1 - - - +
153W G 2.7 47.7 + - - +
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Residues in contact with LYS 37 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18U GLY 5.2 0.4 - - - +
19U VAL 3.2 3.1 - - - +
20U ASN* 2.7 42.8 + - - +
35U SER* 3.5 23.9 + - - -
36U GLU* 1.3 72.3 - - - +
38U LEU* 1.3 67.8 + - - +
42U GLU* 4.0 3.6 - - - +
56V LYS* 4.0 2.9 + - - -
149W U 3.8 9.9 + - - -
151W G 3.2 93.6 + - + +
152W A 3.0 32.3 + - - +
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Residues in contact with LEU 38 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12U ILE* 4.1 12.3 - - + +
14U ALA* 3.8 17.0 - - + -
16U GLU 3.9 1.6 - - - +
17U ASP 3.8 0.3 - - - -
18U GLY 3.1 20.7 + - - -
19U VAL* 2.7 21.5 + - + +
21U VAL* 4.0 27.1 - - + -
36U GLU* 3.9 18.8 - - + +
37U LYS* 1.3 84.1 - - - +
39U ASP* 1.3 66.1 + - - +
42U GLU* 3.2 26.7 - - + +
44U LEU* 4.1 23.6 - - + +
56V LYS* 3.9 21.3 - - + -
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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