Contacts of the helix formed by residues 56 - 65 (chain C) in PDB entry 3LUE
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 56 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54C VAL 3.4 2.1 + - - +
55C GLY* 1.3 68.2 - - - -
57C GLU* 1.3 63.1 + - - +
58C ALA 2.9 4.9 - - - -
59C GLN* 2.9 26.7 + - + +
60C SER* 3.1 19.8 + - - +
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Residues in contact with GLU 57 (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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50C LYS* 3.6 1.2 + - - -
54C VAL 3.3 20.8 + - - +
56C ASP* 1.3 81.1 + - - +
58C ALA* 1.3 46.3 - - - +
60C SER* 4.4 3.1 - - - +
61C LYS* 4.4 0.9 + - - +
149E THR* 5.2 7.8 + - + +
166E TYR* 2.1 37.5 + - - -
167E GLU* 2.7 24.7 - - - +
292E ASP* 4.7 17.9 - - - +
127L GLU* 5.2 2.9 - - - +
128L GLU* 2.7 35.1 - - - +
136L MET* 6.2 0.2 - - - -
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Residues in contact with ALA 58 (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 ILE* 4.9 2.5 - - - +
36C GLY 4.5 1.1 - - - +
53C TYR* 3.6 32.8 - - + +
54C VAL 4.0 1.3 - - - +
55C GLY 3.5 12.7 + - - +
56C ASP 2.9 0.6 - - - -
57C GLU* 1.3 69.2 - - - +
59C GLN* 1.3 65.0 + - - +
62C ARG* 3.3 17.2 + - - +
65C LEU* 4.5 1.1 - - + -
67C LEU* 3.7 21.8 - - + +
166E TYR* 1.5 42.9 + - - +
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Residues in contact with GLN 59 (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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33C SER 5.1 6.8 - - - +
34C ILE* 4.4 12.3 - - + +
55C GLY 3.5 4.3 + - - +
56C ASP* 3.2 23.2 - - + +
58C ALA* 1.3 79.2 - - - +
60C SER* 1.3 56.8 + - - +
61C LYS 2.9 0.4 + - - -
62C ARG* 2.8 70.7 + - - +
67C LEU* 5.4 0.2 - - - +
70C PRO* 5.8 2.9 - - - +
203C THR* 3.4 9.2 - - - +
207C GLU* 4.9 14.0 - - + +
288E ASP* 3.8 21.8 - - + +
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Residues in contact with SER 60 (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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56C ASP* 3.1 15.5 + - - +
57C GLU 5.1 0.2 - - - -
58C ALA 3.3 0.4 - - - +
59C GLN* 1.3 73.0 - - - +
61C LYS* 1.3 46.2 - - - +
204C ALA* 3.6 1.7 - - - +
166E TYR* 4.2 0.2 - - - -
286E ASP* 3.8 4.9 - - - -
288E ASP* 1.6 62.9 + - - +
289E ILE* 1.2 99.3 - - - +
291E LYS* 4.8 0.2 - - - +
292E ASP* 4.6 2.9 - - - -
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Residues in contact with LYS 61 (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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59C GLN 3.1 0.4 - - - -
60C SER* 1.3 72.4 - - - +
62C ARG* 1.4 56.6 + - - +
63C GLY 3.2 2.7 - - - -
64C ILE* 2.8 25.1 + - + -
65C LEU 2.9 8.5 + - - -
149E THR* 1.5 46.0 - - - +
165E ILE 3.1 2.2 - - - -
166E TYR* 0.8 329.6 - - + +
286E ASP* 3.8 3.8 + - - -
289E ILE* 2.9 30.3 - - + +
293E LEU* 5.2 0.9 - - - +
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Residues in contact with ARG 62 (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 ILE* 4.8 4.4 - - - +
58C ALA 3.3 14.0 + - - +
59C GLN* 2.8 55.3 + - - +
61C LYS* 1.4 73.6 - - - +
63C GLY* 1.3 63.3 + - - +
65C LEU* 2.9 26.7 - - - +
67C LEU* 3.9 29.7 - - + +
69C TYR* 3.9 15.1 + - - -
70C PRO* 4.9 13.5 - - - +
77C THR* 5.7 1.6 + - - -
78C ASN* 4.4 25.3 - - - +
203C THR* 4.2 13.2 - - + -
166E TYR* 4.5 0.4 - - - -
286E ASP* 3.5 0.8 + - - +
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Residues in contact with GLY 63 (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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61C LYS 3.2 0.8 - - - -
62C ARG* 1.3 84.4 - - - +
64C ILE* 1.3 60.2 + - - +
65C LEU 3.6 0.9 + - - +
203C THR* 5.7 0.2 - - - -
286E ASP* 3.2 14.1 + - - -
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Residues in contact with ILE 64 (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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38C PRO 4.1 9.2 - - - +
61C LYS* 2.8 27.3 + - + +
63C GLY* 1.3 72.8 - - - +
65C LEU* 1.4 60.6 + - + +
166E TYR* 3.0 29.8 - - + +
169E TYR* 4.4 2.1 - - - +
171E LEU* 1.5 92.4 - - + +
172E PRO* 5.9 0.9 - - + -
173E HIS* 3.5 27.4 - - + -
286E ASP* 4.8 4.2 + - + +
289E ILE* 4.1 0.7 - - + -
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Residues in contact with LEU 65 (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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36C GLY* 3.9 16.4 - - - +
37C ARG 4.2 3.1 - - - +
38C PRO* 3.6 38.1 - - + -
39C ARG* 6.1 0.2 - - - -
53C TYR* 3.8 12.8 - - + -
58C ALA* 4.4 2.0 - - + +
61C LYS 2.9 5.9 + - - +
62C ARG* 2.9 18.1 + - - +
63C GLY 3.4 1.3 - - - +
64C ILE* 1.4 84.2 - - + +
66C THR* 1.3 67.2 + - - +
67C LEU* 3.8 4.9 + - + +
166E TYR* 2.3 64.6 - - + +
169E TYR* 3.8 6.3 - - + -
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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