Contacts of the strand formed by residues 155 - 160 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D LYS* 5.3 12.4 - - - +
154D ILE* 1.3 80.2 + - - +
156D VAL* 1.3 64.0 + - - +
157D ARG* 3.3 35.4 - - - +
201D HIS* 3.6 1.4 - - - +
202D VAL* 3.4 4.0 - - - -
203D GLU* 3.0 53.0 + - + +
163F GLN* 5.2 3.6 - - - +
164F GLU* 2.8 45.8 + - - +
166F THR* 3.5 21.8 - - + +
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Residues in contact with VAL 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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146D VAL* 3.6 26.2 - - + -
154D ILE* 4.3 13.7 - - + -
155D LYS* 1.3 79.7 - - - +
157D ARG* 1.3 66.9 - - - +
158D TRP* 5.7 0.2 - - - +
184D VAL* 4.5 6.1 - - + -
186D VAL* 3.4 41.0 - - + +
200D CYS* 4.1 18.4 - - - -
201D HIS 3.3 5.4 - - - +
202D VAL* 3.7 9.6 - - + -
166F THR* 3.2 32.1 + - - +
167F VAL* 6.3 1.6 - - + -
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Residues in contact with ARG 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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155D LYS* 3.3 36.4 - - - +
156D VAL* 1.3 83.2 - - - +
158D TRP* 1.3 68.1 + - - +
159D PHE* 4.5 15.6 - - + -
164D GLU* 2.8 43.4 + - + +
165D GLU 5.8 0.7 - - - +
186D VAL* 5.9 0.4 - - - -
200D CYS* 3.6 3.8 - - - -
201D HIS* 2.8 63.0 + - + +
203D GLU* 3.5 17.8 + - - -
164F GLU* 4.4 11.2 + - - -
166F THR* 4.6 6.1 - - + -
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Residues in contact with TRP 158 (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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128D ILE* 3.9 20.6 - - + -
142D LEU* 3.4 30.1 - - + -
144D CYS* 3.2 32.3 - - + -
156D VAL* 5.7 0.2 - - + -
157D ARG* 1.3 78.5 - - - +
159D PHE* 1.3 78.1 + - - +
164D GLU* 3.7 5.5 - - - +
165D GLU* 3.6 28.3 + - + +
169D VAL* 5.1 6.7 - - + -
186D VAL* 3.1 39.4 + - + +
187D MET 3.8 4.2 + - - -
188D LEU* 3.3 47.0 - - + +
198D TYR* 4.3 15.7 - - + -
199D THR* 3.4 31.4 - - - -
200D CYS* 4.2 3.6 - - + -
215D TRP* 5.7 0.9 - - + -
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Residues in contact with PHE 159 (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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157D ARG* 4.3 19.3 - - + -
158D TRP* 1.3 83.5 - - - +
160D ARG* 1.3 60.1 + - - +
161D ASN 3.7 0.4 + - - -
162D GLY 3.8 12.3 - - - +
163D GLN* 2.9 26.9 - - - -
164D GLU* 3.1 34.1 - - + +
165D GLU* 4.6 2.0 - - - +
188D LEU* 5.8 0.9 - - - -
197D VAL 3.9 0.2 - - - +
198D TYR* 3.2 12.2 - - - +
199D THR* 3.1 47.9 + - - +
201D HIS* 3.8 37.9 - + + -
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Residues in contact with ARG 160 (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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159D PHE* 1.3 68.9 - - - +
161D ASN* 1.3 71.3 - - - +
162D GLY* 2.2 25.2 + - - -
163D GLN* 3.0 17.9 + - - +
165D GLU* 4.9 17.0 - - + +
188D LEU* 6.5 0.2 - - + -
190D MET* 4.3 7.3 - - - +
191D THR* 2.9 16.4 + - - +
193D ARG* 4.0 13.9 - - - +
196D GLU* 2.6 37.5 + - - -
198D TYR* 2.7 43.4 + - + -
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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