Contacts of the helix formed by residues 153 - 161 (chain A) in PDB entry 5T14
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 PRO 153 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A SER 3.4 21.5 - - - +
135A MET* 4.4 0.8 - - + -
136A LEU* 4.2 0.6 - - - +
151A ALA 4.1 1.3 - - - +
152A MET* 1.3 100.0 - - + +
154A GLY* 1.3 68.2 + - - +
155A PHE* 3.5 18.6 - - + -
156A ILE* 3.5 29.8 - - + -
157A ALA* 3.3 15.4 + - - +
4D A 3.6 43.5 - - + +
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Residues in contact with GLY 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A SER 3.6 16.3 + - - -
133A MET* 2.7 29.3 + - - -
135A MET 3.9 1.4 - - - +
136A LEU* 4.0 7.3 - - - +
152A MET 3.9 0.4 + - - -
153A PRO* 1.3 71.2 - - - +
155A PHE* 1.3 52.8 - - - -
157A ALA* 2.8 25.5 + - - +
158A LYS* 2.9 14.5 + - - +
166A ILE* 3.9 10.3 - - - +
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Residues in contact with PHE 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ALA 4.5 8.3 - - - -
133A MET* 3.1 29.5 + - + +
153A PRO* 3.9 16.4 - - + -
154A GLY* 1.3 75.0 - - - +
156A ILE* 1.3 81.9 + - + +
158A LYS* 3.6 3.4 + - - +
159A ARG* 3.4 39.9 + - - +
3D T 3.4 83.2 - + + +
4D A 3.9 27.4 - + - -
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Residues in contact with ILE 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ILE 5.7 0.4 - - - -
40A ILE* 3.8 38.6 - - + +
43A ALA* 4.2 19.5 - - + -
44A THR 4.9 0.4 - - - +
152A MET* 4.1 9.6 - - + -
153A PRO* 3.5 21.5 + - + +
154A GLY 3.2 0.6 - - - -
155A PHE* 1.3 96.1 - - + +
157A ALA* 1.3 65.5 + - - +
158A LYS 3.2 0.2 - - - -
159A ARG* 3.3 7.6 + - - +
160A LEU* 3.1 23.7 + - + +
4D A 3.2 43.1 - - + +
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Residues in contact with ALA 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A LEU* 3.5 31.4 - - + -
148A VAL* 3.7 16.1 - - + +
152A MET* 3.9 16.3 - - - -
153A PRO 3.3 5.3 + - - +
154A GLY 2.8 15.7 + - - +
156A ILE* 1.3 75.2 - - - +
158A LYS* 1.3 53.9 + - - -
160A LEU* 3.6 4.5 + - - +
161A CYS* 3.2 23.2 + - - +
164A LEU* 3.6 14.9 - - + +
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Residues in contact with LYS 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A MET* 3.8 27.8 - - + -
154A GLY 2.9 15.8 + - - +
155A PHE* 3.8 8.5 - - - +
156A ILE 3.2 0.4 - - - -
157A ALA* 1.3 75.6 - - - +
159A ARG* 1.3 60.3 + - - +
161A CYS 3.9 3.4 - - - +
162A PRO* 3.1 49.6 + - + +
164A LEU* 2.9 34.6 + - + +
166A ILE* 4.1 18.1 - - + +
2T C 5.7 4.6 - - - +
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Residues in contact with ARG 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ILE* 4.0 33.1 - - + +
42A GLU* 6.2 0.4 - - - -
43A ALA* 3.3 38.2 + - + +
155A PHE* 3.4 34.6 + - - +
156A ILE* 3.3 9.5 + - - +
158A LYS* 1.3 77.3 - - - +
160A LEU* 1.3 62.4 + - - +
161A CYS 3.3 0.7 + - - -
162A PRO* 4.3 7.9 - - - +
3D T 4.1 13.3 + - - +
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Residues in contact with LEU 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 4.5 10.3 - - + +
36A ILE* 3.7 38.4 - - + +
39A ILE* 4.6 18.5 - - + +
40A ILE* 4.2 12.6 - - + -
146A PHE* 3.5 40.6 - - - +
147A GLY 4.2 5.4 - - - +
148A VAL* 4.3 3.4 - - + +
152A MET* 3.6 39.9 - - + -
156A ILE* 3.1 14.5 + - + +
157A ALA* 3.6 9.2 - - - +
158A LYS 3.3 0.2 - - - -
159A ARG* 1.3 75.7 - - - +
161A CYS* 1.3 60.0 + - - +
162A PRO* 4.3 1.3 - - - +
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Residues in contact with CYS 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A PRO* 4.0 16.2 - - - -
143A ALA 5.5 0.2 - - - -
146A PHE* 3.6 41.3 - - + -
148A VAL* 4.3 6.3 - - + -
157A ALA 3.2 11.0 + - - +
158A LYS* 3.2 7.5 - - - +
159A ARG 3.2 3.2 + - - -
160A LEU* 1.3 81.9 - - - +
162A PRO* 1.4 63.5 - - - +
163A GLN* 3.2 14.4 - - - -
164A LEU* 3.1 42.5 + - + +
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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