Contacts of the helix formed by residues 165 - 170 (chain H) 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 LYS 165 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163H ALA* 3.0 4.9 + - + -
164H GLN* 1.3 81.0 - - - +
166H GLU* 1.3 60.6 + - - +
167H ILE 3.2 1.6 - - - -
168H GLU* 3.0 6.4 + - - +
169H ASN* 2.7 57.2 + - - +
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Residues in contact with GLU 166 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105G LEU* 5.5 5.3 - - - +
109G GLU* 4.7 23.4 - - - +
163H ALA 3.2 25.0 - - - +
165H LYS* 1.3 78.5 - - - +
167H ILE* 1.3 84.2 + - + +
168H GLU 3.1 2.6 + - - -
169H ASN* 3.7 8.6 + - - +
170H ARG* 3.6 38.8 + - - +
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Residues in contact with ILE 167 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105G LEU* 5.4 10.5 - - + -
108G LEU* 4.9 18.8 - - + +
109G GLU* 5.8 1.1 - - - -
112G ILE* 4.7 25.8 - - + -
163H ALA* 3.9 14.1 + - - +
165H LYS 3.2 0.6 - - - -
166H GLU* 1.3 103.6 - - + +
168H GLU* 1.3 59.1 + - - +
170H ARG* 4.9 2.7 - - - +
171H TYR* 3.1 25.6 - - + +
85I VAL* 6.0 0.4 - - + -
88I ILE* 3.2 48.3 - - + +
91I GLU* 4.2 6.9 - - + +
92I VAL* 5.7 0.4 - - + -
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Residues in contact with GLU 168 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164H GLN* 3.2 43.0 + - - +
165H LYS* 3.0 9.8 + - - +
167H ILE* 1.3 78.7 - - - +
169H ASN* 1.3 63.4 + - - +
170H ARG 3.5 0.9 - - - -
171H TYR* 3.9 27.1 - - - -
172H LYS* 3.2 27.6 + - + +
88I ILE* 5.7 3.3 - - - +
91I GLU* 4.9 6.9 - - - +
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Residues in contact with ASN 169 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190G GLU* 5.9 1.8 - - - +
165H LYS* 2.7 52.1 + - - +
166H GLU* 3.7 8.5 + - - +
168H GLU* 1.3 81.4 - - - +
170H ARG* 1.3 54.7 + - + +
172H LYS* 4.1 3.6 - - - +
173H GLU* 2.5 36.0 + - - +
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Residues in contact with ARG 170 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109G GLU* 5.5 4.4 + - - +
112G ILE* 5.0 19.4 - - + +
113G ILE* 3.1 34.5 - - - +
116G GLN* 5.9 5.3 + - - +
188G ARG* 6.4 0.2 - - + -
190G GLU* 3.7 38.4 + - + +
191G GLU* 6.0 0.2 - - - -
166H GLU* 3.6 25.5 + - - +
167H ILE* 5.2 1.3 - - - -
169H ASN* 1.3 77.2 - - + +
171H TYR* 1.3 61.1 + - - +
172H LYS 3.3 0.7 - - - -
173H GLU* 2.9 23.3 - - - +
174H VAL* 2.9 32.0 + - - +
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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