Contacts of the strand formed by residues 163 - 167 (chain A) in PDB entry 1LII
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 ILE 163 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ARG 3.4 11.4 + - - +
15A VAL* 3.3 16.9 - - + +
16A PHE* 2.9 26.2 + - - +
161A ALA* 4.4 1.2 - - - +
162A LEU* 1.3 87.6 - - + +
164A PHE* 1.3 66.2 + - - +
192A ILE* 3.8 20.4 - - + -
194A THR* 4.7 4.0 - - + +
325A LEU* 4.2 27.6 - - + +
328A LEU* 4.0 19.5 - - + +
329A SER* 4.1 31.4 - - - +
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Residues in contact with PHE 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A PHE* 3.3 31.6 - + + -
154A TRP* 4.0 18.6 - + - -
158A ALA* 4.4 8.7 - - + -
161A ALA* 3.5 30.3 - - + -
162A LEU 4.1 8.1 - - - -
163A ILE* 1.3 72.7 - - - +
165A TYR* 1.3 61.6 + - - +
181A VAL* 3.7 24.0 - - + -
184A TYR* 3.8 23.8 - + - -
185A ALA* 3.8 16.4 - - + -
188A ILE* 5.6 1.3 - - + -
191A ALA* 4.2 13.0 - - + -
192A ILE 3.0 17.6 + - - +
193A PHE* 3.6 8.8 - - + -
194A THR* 2.8 30.2 + - - -
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Residues in contact with TYR 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A VAL* 4.9 4.7 - - + -
16A PHE 2.8 13.9 + - - +
17A ALA* 3.2 36.6 - - + +
18A ILE* 3.3 6.2 + - - +
70A SER* 4.9 2.4 + - - -
71A ALA* 4.1 16.4 - - + -
74A SER* 4.2 16.0 + - - -
75A VAL* 6.0 1.3 - - + -
163A ILE* 5.5 0.2 - - + -
164A PHE* 1.3 75.7 - - - +
166A ALA* 1.3 72.7 + - - +
167A THR* 3.8 23.5 - - + +
181A VAL* 5.2 3.5 - - - +
193A PHE* 4.6 1.6 - - - -
194A THR* 3.1 26.2 - - - +
196A ASN* 3.1 37.5 + - + +
221A PHE* 4.3 8.7 - + - -
318A ASP* 5.6 0.3 + - - -
321A VAL* 3.6 22.9 - - + +
325A LEU* 4.2 19.1 - - + -
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Residues in contact with ALA 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 3.9 24.5 - - + -
165A TYR* 1.3 80.7 - - - +
167A THR* 1.3 66.7 + - - +
178A ALA* 4.2 17.0 - - + -
181A VAL* 5.7 0.7 - - + -
193A PHE* 3.9 23.3 - - + -
194A THR 3.1 6.3 + - - +
195A LEU* 3.4 9.3 - - + +
196A ASN 3.2 20.3 + - - -
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Residues in contact with THR 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ILE 4.4 0.8 + - - -
70A SER* 4.0 8.3 - - - +
71A ALA* 3.7 32.2 - - + +
165A TYR* 3.8 20.0 - - + +
166A ALA* 1.3 79.7 - - - +
168A ALA* 1.3 61.4 + - - +
169A TYR* 3.7 7.3 + - - +
170A THR* 2.9 33.4 + - - +
171A LEU* 4.8 0.9 - - - +
178A ALA* 5.4 0.3 - - - +
195A LEU* 4.4 3.2 - - - +
196A ASN* 4.0 5.6 - - + -
198A SER* 3.3 13.5 - - - +
899A CL 3.2 20.3 - - + +
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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