Contacts of the helix formed by residues 153 - 159 (chain F) in PDB entry 4XLN
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 THR 153 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148F ALA* 3.2 16.9 - - - +
149F LYS* 4.9 14.1 - - + +
152F GLY* 1.3 78.3 - - - +
154F ALA* 1.3 74.9 + - - +
155F ARG* 3.3 2.4 + - - +
156F ILE* 4.1 2.6 + - - +
157F GLN* 4.0 17.0 - - - +
167F ASP* 4.5 1.7 - - - +
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Residues in contact with ALA 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F THR* 1.3 85.8 + - - +
155F ARG* 1.3 59.0 + - - +
156F ILE 3.3 0.3 + - - -
157F GLN* 3.4 2.8 + - - +
158F LYS* 3.0 54.9 + - - +
167F ASP* 4.5 6.1 - - - -
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Residues in contact with ARG 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D THR* 6.1 0.4 - - - -
459D GLU* 4.6 19.0 + - - +
558D LEU* 4.7 18.7 - - - +
564D GLU* 3.3 27.1 + - - +
567D ILE* 5.6 0.9 - - - +
571D LYS* 2.9 29.9 - - - +
151F LEU* 4.1 14.4 - - - -
152F GLY* 4.2 13.0 - - - -
153F THR 4.6 0.4 - - - +
154F ALA* 1.3 79.2 - - - +
156F ILE* 1.3 79.3 + - + +
158F LYS* 3.7 11.7 + - - -
159F ILE* 3.7 26.1 + - + +
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Residues in contact with ILE 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558D LEU* 4.9 17.7 - - + +
559D ALA* 4.8 17.6 - - - +
561D GLY* 5.7 1.8 - - - -
144F GLU 6.1 0.4 - - - +
147F ARG* 4.7 3.4 - - + +
148F ALA* 4.8 8.1 - - + +
151F LEU* 3.5 42.2 - - + +
152F GLY 3.2 24.2 - - - +
153F THR 4.1 1.3 + - - +
154F ALA 3.3 1.2 - - - -
155F ARG* 1.3 98.0 - - + +
157F GLN* 1.3 76.7 + - + +
159F ILE 4.7 0.7 - - - -
160F PRO* 3.5 18.7 - - - +
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Residues in contact with GLN 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F GLU 5.5 0.4 + - - -
145F VAL* 5.8 0.6 - - - +
148F ALA* 3.3 28.8 - - + +
153F THR 4.0 12.6 - - - +
154F ALA 3.4 1.0 + - - +
156F ILE* 1.3 89.6 - - + +
158F LYS* 1.3 64.9 + - - +
160F PRO* 3.4 14.7 - - - +
165F LYS* 4.4 29.2 + - - +
167F ASP* 3.3 41.9 + - + +
171F VAL* 3.3 32.8 - - - +
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Residues in contact with LYS 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154F ALA* 3.0 41.5 + - - +
155F ARG* 4.1 4.3 - - - +
156F ILE 3.3 0.8 - - - -
157F GLN* 1.3 80.9 - - - +
159F ILE* 1.3 73.2 + - + +
160F PRO* 3.4 3.7 - - - +
161F GLY 4.8 3.3 - - - +
167F ASP* 4.1 18.7 + - - +
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Residues in contact with ILE 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D LEU 5.2 2.0 - - - +
96D ALA* 3.5 42.3 - - + +
97D THR* 5.4 1.8 - - - -
98D PRO* 5.1 4.5 - - + -
459D GLU* 3.8 21.8 - - - +
555D LYS* 6.0 0.3 - - - +
558D LEU* 5.0 12.5 - - + +
559D ALA 5.9 0.2 + - - -
155F ARG* 3.7 21.4 + - + +
156F ILE 4.7 2.5 - - - -
158F LYS* 1.3 92.8 - - + +
160F PRO* 1.3 58.8 - - - +
161F GLY* 3.0 14.5 + - - +
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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