Contacts of the strand formed by residues 189 - 195 (chain A) in PDB entry 1LHA
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 ARG 189 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ASP* 3.6 12.6 - - + -
184A TRP* 3.2 54.3 - - + +
187A VAL* 3.1 39.1 - - + +
188A THR* 1.3 70.9 - - - +
190A LEU* 1.3 68.9 + - - +
246A ASN* 2.4 58.8 + - - +
247A ASN* 3.1 18.4 + - - +
248A ILE* 3.2 22.7 - - + +
249A GLN* 3.2 22.3 - - - +
368A THR* 5.4 2.6 - - - +
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Residues in contact with LEU 190 (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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60A ILE* 3.8 18.6 - - + -
61A ASP 2.7 16.7 + - - +
62A LEU* 3.6 27.8 - - + -
63A TYR* 3.0 26.2 + - - +
188A THR* 3.4 15.7 - - - +
189A ARG* 1.3 96.7 - - - +
191A LEU* 1.3 62.7 + - - +
192A VAL* 4.0 3.4 - - + -
248A ILE* 4.7 3.9 - - - +
249A GLN* 3.5 7.4 - - + +
251A ILE* 4.8 8.7 - - + -
288A ILE* 4.4 12.3 - - + +
291A ALA* 5.7 0.7 - - + -
292A TYR* 4.5 8.7 - - + +
295A LEU* 3.3 34.5 - - + -
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Residues in contact with LEU 191 (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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63A TYR* 3.5 39.0 - - + +
65A LEU* 4.4 6.5 - - + -
172A ILE* 4.0 21.8 - - + +
175A VAL* 3.5 38.6 - - + +
190A LEU* 1.3 75.4 - - - +
192A VAL* 1.3 63.4 + - - +
193A PHE* 3.5 3.5 + - + +
243A LEU* 5.4 1.1 - - + -
248A ILE* 3.7 18.4 - - + -
249A GLN 2.7 15.5 + - - +
250A THR* 3.6 19.0 - - + -
251A ILE* 2.9 25.5 + - - +
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Residues in contact with VAL 192 (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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62A LEU* 5.1 5.8 - - + -
63A TYR 3.1 13.1 + - - +
64A TYR* 4.5 20.8 - - + -
65A LEU* 3.0 30.5 + - - +
190A LEU* 5.1 6.7 - - + -
191A LEU* 1.3 73.2 - - - +
193A PHE* 1.3 62.8 + - - +
194A SER* 3.9 1.3 - - - +
251A ILE* 3.9 20.0 - - + -
253A ALA* 4.1 22.4 - - + -
284A VAL* 4.8 0.9 - - + -
288A ILE* 3.8 45.5 - - + -
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Residues in contact with PHE 193 (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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65A LEU* 3.5 13.5 - - + -
104A PHE* 3.6 32.8 - + - -
168A GLY* 4.2 16.4 - - - -
169A PHE* 5.3 3.6 - + - -
172A ILE* 3.3 36.1 - - + -
191A LEU* 4.5 4.7 - - + +
192A VAL* 1.3 72.7 - - - +
194A SER* 1.3 56.3 + - - +
195A THR* 3.5 24.9 + - + -
199A PHE* 5.8 2.2 - - + -
250A THR* 6.1 0.9 - - - -
251A ILE 2.7 18.3 + - - +
252A PHE* 3.2 29.1 - + + -
253A ALA* 2.7 31.2 + - - +
254A VAL* 4.2 1.1 - - + +
262A TYR* 3.9 20.6 - + - -
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Residues in contact with SER 194 (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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64A TYR* 4.3 16.4 - - - -
65A LEU 3.1 6.9 + - - +
66A MET* 2.8 38.9 - - - +
67A ASP* 3.0 18.0 + - - +
72A MET* 4.0 5.3 - - - +
104A PHE* 3.9 4.2 - - - -
192A VAL* 3.9 2.2 - - - -
193A PHE* 1.3 74.4 - - - +
195A THR* 1.3 66.2 + - - +
253A ALA* 2.9 17.3 - - - -
277A LEU* 3.9 14.1 - - - -
281A SER* 5.4 0.2 - - - -
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Residues in contact with THR 195 (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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67A ASP* 3.5 24.5 + - - +
72A MET* 4.6 4.0 - - - +
104A PHE* 4.4 4.6 - - - -
166A GLU* 4.1 6.9 - - - +
193A PHE* 3.5 25.1 - - + -
194A SER* 1.3 76.4 - - - +
196A ASP* 1.3 67.2 + - - +
197A ALA 3.4 12.3 + - - +
198A GLY 4.8 0.2 + - - -
253A ALA 3.1 4.0 + - - -
254A VAL* 3.1 46.4 - - + +
255A THR* 3.2 5.7 + - - +
262A TYR* 3.6 19.0 + - + +
277A LEU* 4.3 4.3 - - - +
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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