Contacts of the strand formed by residues 33 - 39 (chain D) in PDB entry 2W2X
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 LYS 33 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ALA 3.8 0.5 - - - +
29D ILE* 3.4 2.6 - - - -
30D ALA* 2.9 31.8 + - - +
31D ASP* 5.9 0.2 - - + -
32D ALA* 1.3 80.9 - - - +
34D LEU* 1.3 60.8 + - - +
35D SER 4.0 0.7 + - - -
57D ILE* 3.5 25.4 - - + -
58D LEU 3.2 6.7 - - - +
59D ASP* 4.9 3.8 - - + +
60D LEU* 4.7 1.3 - - - -
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Residues in contact with LEU 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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12D LEU* 5.2 2.2 - - + -
27D CYS* 4.5 5.2 - - + -
28D ALA 3.2 10.8 - - - +
29D ILE* 4.3 6.1 - - + +
33D LYS* 1.3 71.0 - - - +
35D SER* 1.3 72.4 + - - +
36D PHE* 4.3 6.3 - - + -
56D GLY 3.8 0.5 - - - +
57D ILE* 3.2 3.8 - - - -
58D LEU* 2.7 49.2 + - + +
60D LEU* 4.1 19.6 - - + +
79D PHE* 5.4 0.4 - - + -
81D LEU* 4.6 11.9 - - + -
93D PHE* 4.0 28.7 - - + -
104D TRP* 3.9 26.0 - - + -
108D ILE* 4.3 19.1 - - + -
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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
----------------------------------------------------------
26D PHE* 3.9 0.9 - - - +
27D CYS* 3.0 6.2 - - - +
28D ALA* 2.8 47.1 + - - +
33D LYS 4.0 1.6 + - - -
34D LEU* 1.3 76.8 - - - +
36D PHE* 1.3 61.5 + - - +
53D LEU 4.9 3.3 + - - -
54D CYS* 3.9 24.2 - - - -
56D GLY 3.3 9.0 - - - -
57D ILE* 4.1 7.9 - - - +
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Residues in contact with PHE 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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14D MET* 3.7 35.9 - - + -
25D HIS* 4.3 4.3 - + + -
26D PHE 3.5 3.6 - - - -
27D CYS* 3.6 20.2 - - - -
34D LEU* 4.3 12.6 - - + -
35D SER* 1.3 76.8 - - - +
37D SER* 1.3 69.1 + - - +
53D LEU 3.5 3.6 - - - -
54D CYS* 3.8 0.2 - - - -
55D ARG* 3.0 29.8 + - + -
56D GLY* 3.0 40.5 + - - +
58D LEU* 3.9 25.6 - - + -
91D VAL* 5.7 0.2 - - + -
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Residues in contact with SER 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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25D HIS* 3.0 19.5 + - - +
26D PHE* 2.7 44.3 + - - +
36D PHE* 1.3 84.7 - - - +
38D ASP* 1.3 76.7 + - - +
40D ILE* 4.3 3.5 - - - +
52D SER 3.2 11.9 - - - -
53D LEU* 2.9 25.0 + - - -
54D CYS 4.0 0.2 - - - +
55D ARG* 3.9 4.3 - - - +
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Residues in contact with ASP 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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24D ARG 3.7 1.6 - - - +
25D HIS* 3.5 5.7 + - - -
37D SER* 1.3 94.8 + - - +
39D ASP* 1.3 66.4 + - - +
40D ILE* 3.4 3.5 + - - +
42D GLN* 5.8 0.4 - - - +
43D THR* 3.6 20.6 - - + -
51D GLY* 3.8 3.4 - - - -
52D SER* 2.6 40.7 + - - +
55D ARG* 2.7 52.0 + - - +
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Residues in contact with ASP 39 (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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23D THR* 3.6 27.7 - - + +
24D ARG 3.4 10.4 + - - +
25D HIS* 3.7 14.3 + - + -
38D ASP* 1.3 74.0 + - - +
40D ILE* 1.3 51.9 + - - +
41D GLU* 2.6 27.1 + - - +
42D GLN* 2.6 32.9 + - + +
43D THR* 2.8 42.3 + - - +
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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