Contacts of the helix formed by residues 153 - 159 (chain L) 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 ASP 153 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151L GLY 3.0 1.9 - - - -
152L LYS* 1.3 81.5 - - - +
154L CYS* 1.3 62.9 + - - +
155L GLN* 2.6 22.2 + - - +
156L GLN* 2.9 12.0 + - - +
157L VAL* 3.2 25.0 + - - +
170L ILE* 4.1 13.7 - - - -
192L THR* 3.9 8.7 - - + -
236L LEU* 3.7 11.7 - - + -
239L GLN* 4.4 0.2 - - - +
240L GLN* 3.5 10.7 + - - -
242L TYR* 2.4 40.2 + - - +
386L PRO* 3.6 4.6 - - - +
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Residues in contact with CYS 154 (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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153L ASP* 1.3 76.2 - - - +
155L GLN* 1.3 59.7 + - - +
157L VAL* 3.1 17.5 - - - +
158L VAL* 3.1 8.0 + - - +
170L ILE* 4.2 0.6 - - - +
181L VAL* 4.0 11.2 - - - -
183L CYS* 2.0 59.3 - - + +
190L GLY* 3.2 31.1 - - - +
192L THR* 3.1 29.7 - - - +
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Residues in contact with GLN 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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153L ASP* 2.6 15.8 + - - +
154L CYS* 1.3 69.2 - - - +
156L GLN* 1.3 67.7 + - - +
157L VAL 2.9 1.1 - - - -
158L VAL* 2.7 20.3 + - - +
159L ASP* 2.7 44.7 + - - +
188L GLY 3.6 15.0 + - - -
189L ASN* 3.3 7.3 - - - +
190L GLY* 2.6 33.2 + - - +
385L LEU* 4.5 3.3 - - - +
386L PRO* 3.6 29.4 - - + -
389L ARG* 3.7 29.7 + - - +
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Residues in contact with GLN 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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151L GLY* 3.2 22.1 - - - -
152L LYS* 2.9 56.2 - - + +
153L ASP* 2.9 10.6 + - - +
155L GLN* 1.3 76.3 - - - +
157L VAL* 1.3 56.1 + - - +
159L ASP* 3.0 17.1 + - + +
160L ASN* 2.9 42.5 + - - +
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Residues in contact with VAL 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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149L ILE* 3.6 7.2 - - + +
150L THR* 3.3 32.1 - - - +
151L GLY 4.0 0.4 - - - +
153L ASP 3.2 17.0 + - - +
154L CYS* 3.1 18.4 - - - +
155L GLN 2.9 0.2 + - - -
156L GLN* 1.3 76.7 - - - +
158L VAL* 1.3 60.5 + - + +
160L ASN* 3.0 9.9 + - - +
161L GLY 3.3 0.7 + - - -
162L GLY* 2.8 24.9 + - - -
168L TYR* 3.4 41.3 - - + -
170L ILE* 4.1 11.4 - - + -
183L CYS* 4.5 5.6 - - - -
185L ILE* 5.2 1.1 - - + -
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Residues in contact with VAL 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 CYS 3.5 12.3 - - - +
155L GLN* 2.7 16.1 + - - +
157L VAL* 1.3 67.6 - - - +
159L ASP* 1.3 60.2 + - - +
160L ASN 2.9 9.7 + - - -
161L GLY* 3.1 11.3 + - - -
162L GLY 3.5 16.6 + - - +
185L ILE* 3.7 31.4 - - + -
188L GLY* 3.6 28.3 - - - +
190L GLY* 3.7 21.1 - - - +
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Residues in contact with ASP 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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155L GLN* 2.7 44.6 + - - +
156L GLN* 3.1 20.8 - - + +
158L VAL* 1.3 77.0 - - - +
160L ASN* 1.3 66.9 + - - +
161L GLY 3.5 0.4 - - - -
389L ARG* 4.8 2.9 + - - -
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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