Contacts of the strand formed by residues 155 - 160 (chain F) in PDB entry 1LNU
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 155 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163D GLN* 5.1 3.8 - - - +
164D GLU* 3.0 49.3 + - - +
166D THR* 3.7 19.7 - - + +
153F LYS* 5.8 7.2 - - - +
154F ILE* 1.3 80.8 + - - +
156F VAL* 1.3 64.8 + - - +
157F ARG* 3.0 38.9 + - - +
201F HIS* 3.6 1.7 - - - +
202F VAL* 3.4 3.3 - - - -
203F GLU* 3.0 51.7 + - + +
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Residues in contact with VAL 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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166D THR* 3.2 32.4 + - - +
167D VAL* 6.1 1.6 - - + -
146F VAL* 3.7 23.6 - - + -
154F ILE* 4.0 17.7 - - + -
155F LYS* 1.3 78.6 - - - +
157F ARG* 1.3 67.6 + - - +
184F VAL* 4.4 9.9 - - + -
186F VAL* 4.0 31.2 - - + +
200F CYS* 3.7 24.7 - - - -
201F HIS 3.3 8.7 - - - +
202F VAL* 4.1 6.5 - - + -
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Residues in contact with ARG 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D GLU* 4.7 14.8 + - - +
166D THR* 5.1 2.2 - - + -
155F LYS* 3.0 32.4 + - - +
156F VAL* 1.3 80.8 - - - +
158F TRP* 1.3 63.5 + - - +
159F PHE* 3.8 18.8 - - + -
164F GLU* 3.0 44.4 + - + +
165F GLU 5.8 0.7 - - - +
186F VAL* 6.1 0.7 - - - -
200F CYS* 3.6 4.2 - - - -
201F HIS* 2.8 58.5 + - + +
203F GLU* 2.8 28.1 + - - -
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Residues in contact with TRP 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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128F ILE* 4.1 17.5 - - + -
142F LEU* 3.3 41.3 - - + -
144F CYS* 3.4 30.5 - - + -
157F ARG* 1.3 72.6 - - - +
159F PHE* 1.3 82.6 + - - +
164F GLU* 3.7 4.0 - - - +
165F GLU* 3.6 32.6 + - + +
169F VAL* 4.8 9.2 - - + -
186F VAL* 3.3 30.3 + - + +
187F MET 3.5 9.2 + - - -
188F LEU* 3.2 41.6 - - + +
198F TYR* 4.4 2.2 - - + -
199F THR* 3.2 41.3 - - - -
200F CYS* 4.0 6.3 - - + -
215F TRP* 5.8 0.7 - - + -
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Residues in contact with PHE 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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157F ARG* 3.8 24.7 - - + -
158F TRP* 1.3 91.1 - - - +
160F ARG* 1.3 60.2 + - - +
161F ASN 3.7 0.4 + - - -
162F GLY 3.7 14.4 - - - +
163F GLN* 3.2 25.1 - - - -
164F GLU* 3.4 35.4 - - + -
165F GLU* 4.6 2.4 - - - +
188F LEU* 6.0 0.2 - - - -
197F VAL 4.0 0.4 - - - +
198F TYR* 3.2 14.0 - - - +
199F THR* 3.1 46.8 + - - +
201F HIS* 3.7 31.2 - + + -
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Residues in contact with ARG 160 (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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159F PHE* 1.3 69.2 - - - +
161F ASN* 1.3 72.4 - - - +
162F GLY* 2.3 25.7 + - - -
163F GLN* 3.0 16.9 + - - +
165F GLU* 4.8 25.0 + - + +
188F LEU* 5.8 0.6 - - - +
190F MET* 4.4 7.3 - - - +
191F THR* 3.2 11.3 + - - +
193F ARG* 4.1 16.8 - - - +
196F GLU* 2.5 29.7 + - - -
198F TYR* 2.5 48.4 + - + -
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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