Contacts of the helix formed by residues 153 - 157 (chain D) in PDB entry 1LWU
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 153 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D VAL 3.7 2.8 + - - +
150D ALA* 2.5 29.1 + - - +
152D ARG* 1.3 72.2 - - - +
154D CYS* 1.3 58.9 + - - +
155D LYS 3.2 0.3 + - - -
156D GLY 3.3 1.4 + - - -
157D SER* 3.8 3.8 + - - -
279E GLY 2.9 14.2 + - - +
280E SER 2.8 23.0 - - - +
281E SER 4.8 0.7 - - - -
282E ASN* 4.7 19.7 - - + +
131F ARG* 6.0 2.7 - - - +
134F CYS* 3.9 23.1 - - + +
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Residues in contact with CYS 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D ALA 4.1 0.7 - - - -
151D LEU* 3.0 23.1 + - - +
153D ALA* 1.3 73.8 - - - +
155D LYS* 1.3 60.3 + - - +
156D GLY 3.2 0.2 - - - -
157D SER* 3.4 2.7 - - - -
158D CYS* 2.7 34.6 + - - +
161D TYR* 4.1 2.1 - - - +
210E GLN* 3.2 28.7 - - - +
130F ILE* 3.9 16.6 - - - -
134F CYS* 2.0 49.4 - - - -
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Residues in contact with LYS 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D ARG* 3.3 16.8 + - + +
153D ALA 3.2 0.6 + - - -
154D CYS* 1.3 79.6 - - - +
156D GLY* 1.3 59.6 + - - +
157D SER 3.2 2.4 + - - -
158D CYS 3.8 11.3 - - - +
161D TYR* 3.6 47.4 - - + +
218E CYS* 4.3 4.0 - - - +
278E ASP* 3.0 36.7 + - + +
280E SER* 4.1 8.5 - - - -
299E PHE* 4.6 18.2 - - + -
308E ILE* 6.4 0.2 - - - +
138F CYS* 4.9 0.5 - - - -
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Residues in contact with GLY 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D ALA 3.3 5.3 + - - -
154D CYS 3.2 0.6 - - - -
155D LYS* 1.3 79.0 - - - +
157D SER* 1.3 56.2 + - - +
218E CYS* 3.2 13.8 - - - -
280E SER* 3.3 19.0 + - - +
296E ASN* 2.9 29.9 + - - -
299E PHE* 4.0 12.6 - - - -
136F ARG 3.7 0.4 - - - +
137F PRO* 3.7 4.9 - - - +
138F CYS 3.3 5.5 + - - -
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Residues in contact with SER 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D ALA 4.0 0.9 - - - -
154D CYS* 2.8 12.3 + - - -
155D LYS 3.1 0.2 - - - -
156D GLY* 1.3 78.4 - - - +
158D CYS* 1.3 61.8 + - - +
217E PRO* 3.5 10.4 - - - +
218E CYS* 3.3 19.6 + - - -
133F THR 3.3 8.8 + - - -
134F CYS* 3.2 39.6 - - - -
136F ARG* 2.8 26.4 + - - +
137F PRO 5.3 0.7 - - - -
138F CYS 5.2 0.5 + - - -
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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