Contacts of the strand formed by residues 30 - 36 (chain C) in PDB entry 1LNU
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 ASP 30 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C GLU* 3.3 2.3 - - - -
27C PHE* 2.6 41.4 + - - +
28C ASP* 3.3 5.7 - - - +
29C GLY* 1.3 78.2 - - - +
31C GLU* 1.3 61.5 + - - +
32C LEU 3.4 0.9 + - - -
139C PHE* 4.1 3.8 - - - -
150D TYR* 3.6 19.6 + - - -
176D ARG* 2.7 38.1 + - - +
178D GLY 4.1 4.9 - - - +
180D TRP* 3.4 52.1 + - + +
182D PHE* 5.1 0.2 - - - -
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Residues in contact with GLU 31 (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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24C THR* 4.9 5.4 - - - -
25C PHE 3.8 6.5 - - - +
26C GLU* 4.4 3.8 - - + -
30C ASP* 1.3 70.5 - - - +
32C LEU* 1.3 63.5 + - - +
33C PHE* 3.7 19.8 - - - +
34C TYR* 3.2 22.2 - - - +
45C MET* 3.8 29.0 - - - +
134C TYR* 5.4 1.0 + - - -
136C THR* 4.5 2.3 - - - -
137C SER* 2.6 48.9 + - - -
139C PHE* 3.5 27.3 - - + -
178D GLY 5.0 1.8 + - - -
180D TRP* 2.8 24.0 + - - +
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Residues in contact with LEU 32 (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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9C TYR* 3.9 18.6 - - + -
25C PHE* 2.9 27.5 + - + +
26C GLU 4.4 1.6 - - - +
27C PHE* 4.0 11.4 - - + -
30C ASP 3.4 0.8 + - - -
31C GLU* 1.3 73.7 - - - +
33C PHE* 1.3 72.7 + - + +
44C TRP* 3.0 26.1 - - + -
45C MET 3.6 9.9 + - - -
46C LEU 4.8 1.2 + - - -
49C PHE* 4.1 13.3 - - + -
112D PRO* 6.5 0.9 - - + -
113D GLU* 3.2 24.9 - - - +
116D THR* 5.1 1.3 - - + -
117D SER* 3.7 15.3 - - - +
180D TRP* 2.9 36.8 - - + -
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Residues in contact with PHE 33 (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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23C TYR* 4.7 2.0 - + - -
24C THR* 3.7 1.6 - - - -
25C PHE* 3.3 65.9 + + + +
31C GLU* 3.3 15.1 - - - +
32C LEU* 1.3 87.7 - - + +
34C TYR* 1.3 67.2 + - - +
35C VAL* 3.9 19.5 - - + -
42C THR* 3.5 13.2 - - + -
43C VAL 2.9 20.9 - - - +
44C TRP* 3.5 37.2 - + + +
45C MET 4.4 0.9 - - - +
55C PHE* 3.5 34.3 - + + -
3D ALA* 5.1 4.5 - - + -
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Residues in contact with TYR 34 (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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22C GLN* 5.8 0.7 - - + -
23C TYR 3.4 12.8 - - - +
24C THR* 3.9 8.1 - - + -
31C GLU* 3.2 18.8 - - - +
33C PHE* 1.3 78.7 - - - +
35C VAL* 1.3 72.4 + - - +
36C ASP* 3.9 24.1 + - + -
42C THR* 3.8 0.2 - - - -
43C VAL* 2.8 67.4 + - + +
44C TRP 6.0 0.2 - - - -
45C MET* 6.6 0.2 - - - -
134C TYR* 5.3 10.3 - + - -
137C SER* 3.7 21.3 - - - +
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Residues in contact with VAL 35 (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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22C GLN* 5.8 0.3 - - - -
23C TYR* 3.0 43.1 + - + +
33C PHE* 3.9 14.8 - - + -
34C TYR* 1.3 80.6 - - - +
36C ASP* 1.3 79.2 + - - +
37C LEU* 3.0 21.4 + - + +
40C LYS* 4.8 1.3 - - - -
41C GLU 3.5 17.7 - - - +
42C THR* 4.6 3.4 - - - +
55C PHE* 4.1 15.9 - - + -
57C PRO* 3.9 21.8 - - + +
60C GLY* 4.6 2.9 - - - -
61C LEU* 5.2 1.8 - - + +
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Residues in contact with ASP 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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34C TYR* 3.8 24.1 + - + -
35C VAL* 1.3 75.9 - - - +
37C LEU* 1.3 60.4 + - - +
38C ASP* 2.8 16.9 + - - +
39C LYS* 2.2 59.6 + - + +
40C LYS* 3.1 21.1 + - - -
41C GLU* 2.9 20.7 + - + +
43C VAL* 4.9 3.6 - - + -
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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