Contacts of the helix formed by residues 133 - 144 (chain C) in PDB entry 5T5W
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 SER 133 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C ASP* 4.1 20.5 + - - -
38C CYS* 3.9 10.7 - - - +
132C GLU* 1.3 76.4 - - - +
134C PRO* 1.3 76.5 - - - +
135C GLY 4.6 0.9 - - - -
136C CYS* 3.2 22.7 + - - +
137C LEU* 3.1 20.5 + - - +
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Residues in contact with PRO 134 (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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35C ASP* 5.7 2.2 - - - +
132C GLU 3.9 2.0 - - - +
133C SER* 1.3 87.1 - - - +
135C GLY* 1.3 53.7 + - - +
137C LEU* 3.1 9.7 + - + +
138C GLU* 2.7 50.2 + - + +
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Residues in contact with GLY 135 (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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31C LEU* 5.3 2.6 - - - +
34C LYS* 4.8 14.1 - - - +
35C ASP* 4.1 17.4 + - - -
36C CYS* 4.0 5.6 - - - +
133C SER* 3.5 1.8 - - - -
134C PRO* 1.3 82.2 - - - +
136C CYS* 1.3 56.3 + - - +
138C GLU* 3.7 17.2 + - - +
139C ALA* 3.0 28.1 + - - +
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Residues in contact with CYS 136 (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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35C ASP 3.9 2.2 + - - -
36C CYS* 4.3 8.3 - - - +
37C LYS* 4.2 5.4 - - - +
38C CYS* 2.0 64.4 - - + +
41C ARG* 6.1 3.6 - - - -
132C GLU* 5.1 0.2 - - - -
133C SER* 3.2 20.4 + - - +
134C PRO 3.1 0.6 - - - -
135C GLY* 1.3 75.1 - - - +
137C LEU* 1.3 56.3 + - - +
139C ALA* 3.0 4.0 + - - +
140C SER* 2.6 41.1 + - - -
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Residues in contact with LEU 137 (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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42C LEU* 4.0 27.4 - - + -
67C LEU* 5.1 7.6 - - + -
71C VAL* 3.9 24.5 - - + -
128C ALA* 4.2 6.7 - - + +
129C PRO* 3.7 34.1 - - + +
132C GLU* 4.1 21.3 - - + +
133C SER 3.1 12.2 + - - +
134C PRO* 3.1 10.2 + - + +
136C CYS* 1.3 80.0 - - - +
138C GLU* 1.3 63.8 + - - +
140C SER* 4.1 6.1 - - - -
141C VAL* 3.0 31.4 + - + +
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Residues in contact with GLU 138 (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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27C LEU* 6.1 2.5 - - + -
30C SER* 5.3 4.3 + - - -
31C LEU* 5.7 5.8 - - + -
71C VAL* 3.7 13.7 - - + -
72C LEU* 5.6 2.5 - - + -
74C ALA* 5.0 1.0 - - - +
75C THR* 3.0 45.8 + - + +
78C THR* 5.0 7.8 + - - +
134C PRO* 2.7 36.7 + - + +
135C GLY* 3.7 12.7 - - - +
137C LEU* 1.3 72.7 - - - +
139C ALA* 1.3 58.0 + - - +
141C VAL* 3.6 2.4 - - - +
142C THR* 2.6 35.6 + - - +
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Residues in contact with ALA 139 (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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31C LEU* 4.3 16.6 - - + +
36C CYS* 3.9 21.5 - - + -
37C LYS 5.0 1.8 - - - +
135C GLY 3.0 19.3 + - - +
136C CYS* 3.0 4.0 + - - +
138C GLU* 1.3 77.5 - - - +
140C SER* 1.3 62.9 + - - +
142C THR* 3.8 4.8 - - - -
143C PHE* 3.2 45.7 + - + -
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Residues in contact with SER 140 (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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41C ARG* 5.8 1.3 - - - +
42C LEU* 3.7 11.6 + - - +
43C PHE* 3.3 47.3 + - - +
136C CYS* 2.6 24.9 + - - -
137C LEU* 3.2 11.2 + - - -
139C ALA* 1.3 76.2 - - - +
141C VAL* 1.3 61.3 + - - +
143C PHE* 3.9 4.1 + - - +
144C ASN* 3.4 13.2 + - - +
147C ARG* 4.5 0.2 + - - -
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Residues in contact with VAL 141 (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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42C LEU* 5.6 0.2 - - + -
43C PHE* 3.9 23.1 - - + -
67C LEU* 4.7 7.6 - - + -
68C THR* 4.1 34.4 - - + +
71C VAL* 3.9 27.6 - - + -
72C LEU* 4.0 18.6 - - + +
137C LEU* 3.0 21.1 + - + +
138C GLU 3.6 5.2 - - - +
140C SER* 1.3 76.4 - - - +
142C THR* 1.3 66.5 + - - +
144C ASN* 3.7 3.2 + - - -
145C LEU* 3.2 25.3 + - - +
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Residues in contact with THR 142 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24C LYS* 4.0 29.5 - - + +
27C LEU* 3.4 47.0 - - + +
28C GLU* 4.3 13.5 - - + +
72C LEU* 4.7 1.5 - - - +
138C GLU* 2.6 24.0 + - - +
139C ALA* 3.8 7.8 - - - -
140C SER 3.3 0.4 - - - -
141C VAL* 1.3 80.3 - - - +
143C PHE* 1.3 65.4 + - + +
145C LEU* 3.2 21.6 + - + +
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Residues in contact with PHE 143 (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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42B SER* 4.4 11.7 - - - -
43B PRO* 3.6 39.5 - - + -
73B TYR 4.6 1.9 - - - +
74B ASN* 2.9 47.4 + - - +
24C LYS* 4.9 0.9 + - - -
28C GLU* 3.6 34.3 - - + -
31C LEU* 5.5 7.4 - - + -
32C LEU* 5.6 8.1 - - + -
36C CYS* 6.6 0.2 - - - -
139C ALA* 3.2 35.5 + - + +
140C SER* 4.5 2.5 - - - +
142C THR* 1.3 81.7 - - + +
144C ASN* 1.3 57.8 + - - +
145C LEU 3.3 1.3 - - - -
146C PHE 4.8 1.3 + - - -
147C ARG* 3.5 19.3 + - - +
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Residues in contact with ASN 144 (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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43C PHE* 3.5 43.7 - - + +
44C PRO* 4.6 2.3 - - - +
45C ARG* 5.4 2.4 + - - -
64C GLU* 4.5 6.0 + - - +
68C THR* 5.0 1.4 + - - -
140C SER 3.4 17.7 + - - +
141C VAL 3.7 4.3 - - - +
142C THR 3.2 0.8 - - - -
143C PHE* 1.3 77.2 - - - +
145C LEU* 1.3 64.3 + - - +
146C PHE 3.4 2.0 - - - -
147C ARG* 2.9 36.3 + - - +
148C LEU* 3.0 33.9 + - - +
151C ARG* 5.0 1.2 + - - -
152C ASP* 4.9 2.5 + - - +
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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