Contacts of the helix formed by residues 154 - 159 (chain L) in PDB entry 4XLR
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 ALA 154 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153L THR* 1.3 81.0 - - + +
155L ARG* 1.3 56.0 + - - +
156L ILE* 3.0 9.2 + - - -
157L GLN* 3.5 3.9 + - - +
158L LYS* 3.1 46.7 + - - +
167L ASP* 4.6 11.4 - - - +
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Residues in contact with ARG 155 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158J TYR* 5.4 6.3 + - - -
453J ASP* 5.2 1.6 + - - -
455J ARG* 4.1 29.8 - - - +
459J GLU* 4.6 16.2 + - - +
564J GLU* 4.0 23.0 + - - +
571J LYS* 4.1 14.3 - - - +
151L LEU 4.7 3.1 - - - -
152L GLY* 4.6 4.9 - - - -
153L THR* 2.7 28.1 + - - +
154L ALA* 1.3 73.1 - - - +
156L ILE* 1.3 78.8 + - + +
158L LYS* 3.9 14.7 + - - +
159L ILE* 4.7 7.1 + - - +
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Residues in contact with ILE 156 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558J LEU* 4.4 19.8 - - - +
559J ALA* 5.1 9.2 - - - +
561J GLY* 5.5 0.2 - - - -
144L GLU* 6.5 1.1 - - + -
147L ARG* 4.0 18.2 - - + +
148L ALA* 4.8 5.8 - - - +
151L LEU* 3.5 60.3 - - + +
152L GLY 4.1 3.8 - - - +
153L THR 3.7 11.4 - - - +
154L ALA 3.0 3.2 + - - -
155L ARG* 1.3 94.0 - - + +
157L GLN* 1.3 70.5 + - + +
158L LYS 3.4 0.4 + - - -
159L ILE 4.7 1.9 + - - -
160L PRO* 4.3 9.4 - - - +
164L GLU* 5.4 0.3 - - - +
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Residues in contact with GLN 157 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559J ALA* 6.4 0.7 - - - -
144L GLU* 4.5 15.2 + - - +
145L VAL* 5.7 0.2 - - - +
148L ALA* 4.2 20.8 - - - +
154L ALA 3.5 4.1 + - - +
156L ILE* 1.3 87.7 - - + +
158L LYS* 1.3 65.1 + - - +
159L ILE 3.4 2.2 - - - -
160L PRO* 3.1 18.3 - - + +
164L GLU* 3.8 16.8 - - - +
165L LYS* 3.5 31.2 - - + +
167L ASP* 3.7 30.1 - - + +
171L VAL* 3.2 32.1 - - - +
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Residues in contact with LYS 158 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154L ALA* 3.1 46.9 + - - +
155L ARG* 4.0 13.7 - - - +
156L ILE 3.4 1.4 - - - -
157L GLN* 1.3 80.4 - - - +
159L ILE* 1.3 74.7 + - + +
160L PRO* 4.0 1.0 - - - +
161L GLY 5.1 1.0 - - - +
167L ASP* 4.2 11.9 + - - +
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Residues in contact with ILE 159 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96J ALA* 3.6 38.0 - - - +
97J THR* 4.7 4.3 - - + -
98J PRO* 4.1 14.1 - - + -
459J GLU* 3.6 24.7 - - - +
515J GLU* 5.6 6.3 - - - +
558J LEU* 5.0 4.3 - - - +
155L ARG 4.7 7.5 + - - +
156L ILE 4.7 2.6 + - - -
158L LYS* 1.3 98.4 - - + +
160L PRO* 1.4 56.2 - - - +
161L GLY 3.3 13.5 + - - +
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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