Contacts of the strand formed by residues 35 - 41 (chain C) in PDB entry 1XZ0
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 LEU 35 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31C TRP* 3.6 1.7 - - - -
32C LEU* 2.9 40.1 + - + +
34C ASP* 1.3 78.2 - - + +
36C GLN* 1.3 73.5 + - - +
37C THR* 3.8 3.9 + - + +
51C TRP* 3.9 22.9 - - + +
53C TRP* 3.7 30.3 - - + -
180C HIS* 3.8 21.8 - - + +
181C LEU* 4.1 14.1 - - + -
212C TYR* 6.1 0.2 - - - +
241C GLY* 6.4 1.6 - - - -
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Residues in contact with GLN 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C SER* 3.9 9.3 - - - -
30C GLY 3.8 10.3 - - - +
31C TRP* 3.5 34.5 - - + +
34C ASP 3.5 1.2 + - - -
35C LEU* 1.3 78.0 - - - +
37C THR* 1.3 62.8 + - - +
38C HIS 3.4 16.6 + - - +
39C THR* 3.7 11.7 - - - +
50C LEU* 3.4 21.8 - - + +
51C TRP* 3.2 21.0 + - - -
53D ASP* 3.2 44.0 + - - +
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Residues in contact with THR 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C PHE* 3.8 7.6 - - - -
30C GLY 3.0 13.5 + - - -
32C LEU* 4.1 15.9 - - + -
35C LEU* 3.8 11.7 - - + +
36C GLN* 1.3 80.1 - - - +
38C HIS* 1.3 91.0 + - - +
50C LEU* 3.2 22.5 + - - -
51C TRP* 4.2 4.9 - - + +
53C TRP* 4.2 26.9 - - + -
54C SER* 3.1 22.8 + - - -
173C LEU* 5.0 3.9 - - + +
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Residues in contact with HIS 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C PHE* 4.2 10.0 - + - -
29C SER* 3.4 2.0 - - - -
30C GLY* 3.1 24.9 + - - +
36C GLN* 3.4 16.7 + - - -
37C THR* 1.3 111.4 + - - +
39C THR* 1.3 62.7 + - - +
47C ILE* 4.3 6.7 - - + -
48C VAL 3.5 6.5 - - - +
49C PHE* 4.0 22.2 - + - -
50C LEU* 3.9 1.0 - - - +
54C SER* 3.1 25.7 + - - -
63C TRP* 3.8 11.4 - + - -
169C PHE* 3.6 26.2 - + - -
173C LEU* 4.7 1.8 - - + -
602C JH0 3.6 31.0 - - + -
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Residues in contact with THR 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C VAL 3.9 10.1 - - - +
29C SER* 4.7 1.6 - - - -
36C GLN* 3.7 18.8 - - - +
38C HIS* 1.3 75.2 - - - +
40C TRP* 1.3 66.6 + - - +
41C ASP* 6.1 0.2 - - - -
47C ILE* 3.6 5.9 - - - +
48C VAL* 2.8 52.5 + - - +
50C LEU* 3.9 14.3 - - + +
602C JH0 5.2 2.7 - - - -
53D ASP* 3.9 11.4 - - - +
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Residues in contact with TRP 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ASN* 5.9 2.5 - - - -
28C VAL* 3.3 44.6 + - + +
39C THR* 1.3 78.3 - - - +
41C ASP* 1.3 58.6 + - - +
42C SER* 3.8 25.9 + - - +
45C SER* 3.6 30.7 - - - -
46C THR* 3.4 24.5 - - - -
47C ILE* 3.6 26.5 - - + -
67C GLU* 3.5 14.8 - - - -
70C PHE* 3.6 25.1 - + + -
71C ARG* 3.4 35.7 - - + -
74C THR* 4.2 15.2 + - + -
602C JH0 5.4 3.6 - - + -
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Residues in contact with ASP 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C THR* 4.1 0.8 - - - -
40C TRP* 1.3 72.2 - - - +
42C SER* 1.3 54.1 + - - +
43C ASN* 4.2 17.5 + - - +
44C SER* 2.6 30.6 + - - +
45C SER* 2.7 31.6 + - - -
46C THR* 2.9 19.0 + - - +
48C VAL* 4.0 20.0 - - + -
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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