Contacts of the strand formed by residues 32 - 38 (chain D) 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 PHE 32 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D ILE* 3.4 35.4 - - + -
23D GLY 3.4 4.0 - - - -
24D LEU* 3.9 22.9 - - + -
31D ARG* 1.3 86.7 - - - +
33D HIS* 1.3 59.7 + - - +
34D HIS 4.7 3.4 - - - +
35D SER* 6.4 0.2 - - - -
56D LYS* 4.3 15.3 - - + -
58D ARG* 4.5 15.0 - - - -
36E GLU* 3.6 28.3 - - - -
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Residues in contact with HIS 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ALA 4.5 15.0 + - - +
30C THR* 4.2 8.7 + - - -
101C TRP* 3.9 18.8 - + - -
23D GLY* 3.0 29.7 + - - -
24D LEU 4.0 1.8 - - - -
25D THR* 3.7 22.9 - - + -
31D ARG* 5.3 1.8 - - + +
32D PHE* 1.3 75.0 - - - +
34D HIS* 1.3 79.0 + - + +
51D HIS* 3.7 22.3 + - + -
52D THR* 2.8 27.5 + - - -
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Residues in contact with HIS 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C LEU* 5.4 0.2 - - + -
30C THR* 3.5 46.3 + - + +
101C TRP* 4.1 12.3 - + + -
21D VAL 3.8 0.7 - - - +
22D ILE* 3.4 5.7 - - - +
23D GLY 3.0 26.3 + - - -
32D PHE* 3.7 2.5 - - - +
33D HIS* 1.3 102.8 + - + +
35D SER* 1.3 80.4 + - - +
36D GLU* 2.7 41.5 + - + -
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Residues in contact with SER 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D ASN* 3.3 32.4 + - - +
21D VAL 3.6 3.6 - - - -
22D ILE* 3.7 12.7 - - - +
32D PHE* 6.4 0.9 - - - -
34D HIS* 1.3 88.0 + - - +
36D GLU* 1.3 59.5 + - - +
37D LYS* 3.8 2.3 + - - +
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Residues in contact with GLU 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C LEU* 3.7 21.5 - - + +
30C THR* 4.5 0.2 - - - +
32C PHE* 3.5 22.0 - - - -
56C LYS* 3.1 28.4 + - - +
101C TRP* 5.6 1.3 - - + -
19D VAL 3.5 1.7 - - - +
20D ASN* 3.6 1.5 - - - -
21D VAL* 2.9 40.7 + - - +
34D HIS* 2.7 36.8 + - + +
35D SER* 1.3 69.7 + - - +
37D LYS* 1.3 64.9 + - - +
38D LEU* 3.7 3.2 + - + +
44D LEU* 4.1 28.5 - - + -
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Residues in contact with LYS 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C LYS* 2.8 27.0 + - - -
58C ARG* 5.3 0.5 + - - -
18D GLY* 4.0 18.6 - - - -
19D VAL 3.2 9.9 - - - +
20D ASN* 4.1 10.8 - - - +
35D SER 3.8 4.0 + - - +
36D GLU* 1.3 73.5 - - - +
38D LEU* 1.3 56.2 + - - +
39D ASP* 3.5 30.2 + - - +
42D GLU* 4.3 1.0 - - - +
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Residues in contact with LEU 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C LYS* 3.7 28.7 - - + +
12D ILE* 3.9 24.9 - - + +
14D ALA* 3.7 14.6 - - + +
16D GLU 3.8 1.0 - - - +
18D GLY 3.1 4.2 + - - -
19D VAL* 2.8 43.2 + - + +
21D VAL* 3.6 29.8 - - + -
36D GLU* 4.4 4.7 - - + +
37D LYS* 1.3 73.6 - - - +
39D ASP* 1.3 65.1 + - - +
42D GLU* 3.4 17.5 - - + +
43D VAL 4.5 0.4 - - - -
44D LEU* 3.8 27.6 - - + +
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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