Contacts of the strand formed by residues 32 - 38 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B ILE* 3.6 28.3 - - + -
23B GLY 3.3 5.8 - - - +
24B LEU* 4.3 5.1 - - + +
31B ARG* 1.3 88.5 - - - +
33B HIS* 1.3 62.9 + - - +
34B HIS* 3.6 18.4 - - - -
35B SER* 4.3 20.6 - - - -
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Residues in contact with HIS 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLY 5.0 1.8 - - - -
28A ALA* 4.5 10.4 + - - +
30A THR* 4.0 12.9 + - - -
101A TRP* 4.0 15.0 - + - -
23B GLY 2.9 28.3 + - - -
24B LEU 4.0 6.1 - - - -
25B THR* 3.7 17.3 - - + -
31B ARG* 6.3 0.2 - - - -
32B PHE* 1.3 78.9 - - - +
34B HIS* 1.3 80.5 + - + +
51B HIS* 3.6 24.6 + - + +
52B THR* 2.7 27.9 + - - -
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Residues in contact with HIS 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 5.3 0.4 - - + -
30A THR* 3.4 45.0 + - + +
31A ARG* 5.8 0.2 - - - -
101A TRP* 3.8 16.6 - + + -
21B VAL 3.9 0.7 - - - +
22B ILE* 3.5 2.6 - - - -
23B GLY 2.9 27.3 + - - +
32B PHE* 3.6 8.7 - - - -
33B HIS* 1.3 104.9 + - + +
35B SER* 1.3 77.8 + - - +
36B GLU* 2.6 33.2 + - + -
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Residues in contact with SER 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ASN* 2.6 34.3 + - - -
21B VAL 3.4 4.0 - - - -
22B ILE* 4.4 6.5 - - - -
32B PHE* 4.3 17.8 - - - -
34B HIS* 1.3 89.4 + - - +
36B GLU* 1.3 59.0 + - - +
37B LYS* 4.0 9.7 + - - +
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Residues in contact with GLU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 3.7 17.6 - - + +
30A THR* 4.7 0.2 - - - +
32A PHE* 3.3 27.0 - - - -
56A LYS* 3.5 20.5 + - - -
101A TRP* 5.4 2.0 - - + -
19B VAL 3.8 0.2 - - - +
20B ASN* 3.8 0.6 + - - -
21B VAL* 2.7 43.4 + - + +
34B HIS* 2.6 39.7 + - + +
35B SER* 1.3 73.6 - - - +
37B LYS* 1.3 67.8 + - - +
38B LEU* 4.8 0.7 - - + -
44B LEU* 4.1 26.0 - - + -
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Residues in contact with LYS 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LYS* 3.1 24.8 + - - -
18B GLY* 4.7 18.6 - - - +
19B VAL 3.1 9.6 - - - +
20B ASN* 4.3 24.9 - - - +
35B SER* 4.0 7.0 + - - +
36B GLU* 1.3 78.2 - - - +
38B LEU* 1.3 61.1 + - - +
39B ASP* 5.8 1.1 - - - +
42B GLU* 4.3 0.2 - - - +
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Residues in contact with LEU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LYS* 3.8 22.0 - - + -
12B ILE* 3.8 40.8 - - + +
14B ALA* 3.7 15.9 - - + +
16B GLU 3.8 0.3 - - - +
17B ASP 3.8 0.3 - - - -
18B GLY* 3.1 20.1 + - - -
19B VAL* 2.7 23.1 + - + +
21B VAL* 3.9 18.2 - - + -
36B GLU* 4.8 1.3 - - + -
37B LYS* 1.3 83.4 - - - +
39B ASP* 1.3 64.9 + - - +
42B GLU* 3.4 20.6 - - + +
44B LEU* 4.0 23.3 - - + +
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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