Contacts of the strand formed by residues 32 - 38 (chain D) in PDB entry 3U8Z
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 GLU 32 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B MET* 3.6 0.7 - - - +
34B GLU* 2.7 62.5 + - + +
25D ARG* 2.9 55.3 + - + +
26D ILE 3.9 2.5 - - - -
27D VAL* 4.5 14.3 - - + +
31D ALA* 1.3 70.4 - - - +
33D MET* 1.3 59.0 + - - +
34D GLU* 5.7 1.1 - - + +
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Residues in contact with MET 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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31B ALA* 5.2 0.7 - - + -
32B GLU 3.7 7.2 - - - +
33B MET* 4.0 27.1 - - + +
53B THR* 3.9 19.1 - - + -
25D ARG* 3.3 8.7 - - - +
26D ILE* 2.7 39.7 + - - +
28D THR* 3.8 31.4 - - + +
31D ALA* 4.3 7.0 - - + +
32D GLU* 1.3 77.4 - - - +
34D GLU* 1.3 63.7 + - - +
35D PHE* 3.8 30.7 - - + -
50D VAL* 5.4 0.7 - - - -
53D THR* 4.8 1.1 - - - -
54D LEU* 3.7 31.6 - - + -
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Residues in contact with GLU 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ALA* 3.7 8.5 - - - +
32B GLU* 2.8 59.7 + - + +
34B GLU* 5.4 7.6 - - - +
23D THR* 3.8 28.2 - - + +
24D VAL 3.3 6.1 - - - +
25D ARG* 3.0 41.5 + - + -
32D GLU* 6.1 0.9 - - + -
33D MET* 1.3 78.7 - - - +
35D PHE* 1.3 61.1 + - - +
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Residues in contact with PHE 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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30B ASP 4.8 6.5 - - - -
31B ALA* 3.7 21.1 - - + -
23D THR* 3.4 6.0 - - - +
24D VAL* 2.9 33.8 + - + +
26D ILE* 3.6 37.7 - - + -
33D MET* 3.8 21.3 - - + -
34D GLU* 1.3 75.4 - - - +
36D ASN* 1.3 65.0 + - - +
37D CYS 3.6 1.0 + - - -
46D LEU* 4.6 10.1 - - + -
49D LEU* 3.7 35.9 - - + -
50D VAL* 3.8 16.8 - - + -
53D THR* 3.2 39.5 - - + -
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Residues in contact with ASN 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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21D THR* 4.0 29.5 + - + +
22D PHE 3.7 5.4 - - - +
23D THR* 3.9 15.9 + - - -
35D PHE* 1.3 73.2 - - - +
37D CYS* 1.3 61.1 + - - +
38D GLU* 3.9 2.8 + - - +
41D TRP* 4.3 10.4 - - - -
49D LEU* 4.6 5.3 - - - +
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Residues in contact with CYS 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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21D THR* 3.2 1.5 - - - -
22D PHE* 2.8 53.7 + - + +
24D VAL* 3.5 25.6 - - + -
35D PHE 3.6 1.6 + - - -
36D ASN* 1.3 71.8 - - - +
38D GLU* 1.3 76.2 + - - +
41D TRP* 3.8 26.2 - - + -
46D LEU* 4.4 17.0 - - + -
81D VAL* 4.2 15.9 - - - -
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Residues in contact with GLU 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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20D LYS* 3.5 8.7 - - - +
21D THR* 3.9 16.6 - - + -
22D PHE* 3.6 2.4 - - - -
36D ASN 3.9 1.9 + - - +
37D CYS* 1.3 81.0 - - - +
39D MET* 1.3 64.7 + - - +
40D LYS 3.3 2.0 - - - +
41D TRP* 3.2 65.4 + - + +
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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