Contacts of the strand formed by residues 91 - 94 (chain A) in PDB entry 1LUA
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 SER 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A THR 4.3 2.8 + - - -
62A ALA* 3.5 4.1 - - - -
63A ILE 3.0 22.3 + - - -
90A VAL* 1.3 79.5 - - - +
92A CYS* 1.3 58.8 + - - +
266A LYS 4.9 0.3 + - - -
267A LEU* 3.3 37.8 + - - -
270A SER* 2.6 25.1 + - - -
271A SER* 3.5 4.4 + - - +
272A GLU 3.4 0.2 + - - -
273A GLY* 2.9 31.4 + - - +
275A PHE* 5.5 0.2 - - - -
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Residues in contact with CYS 92 (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 ILE* 3.1 24.9 - - + +
77A PHE* 3.6 25.6 - - + -
80A VAL* 4.5 8.3 - - + -
81A LYS* 4.3 12.3 - - - -
84A PHE* 4.2 20.2 - - + -
90A VAL 4.6 1.6 - - - +
91A SER* 1.3 76.0 - - - +
93A MET* 1.3 62.3 + - - +
267A LEU* 3.8 6.6 - - - +
273A GLY 3.0 14.9 + - - +
274A VAL* 4.4 8.5 - - - -
275A PHE 3.0 22.5 + - - -
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Residues in contact with MET 93 (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 ILE 2.9 7.2 + - - +
64A PHE* 3.5 19.6 - - + -
65A VAL* 2.8 30.5 + - - +
77A PHE* 3.5 10.5 - - - -
92A CYS* 1.3 76.2 - - - +
94A LEU* 1.3 59.0 + - - +
95A ASP* 4.1 19.5 - - + -
101A THR* 4.1 13.2 - - + -
260A HIS* 4.0 22.7 - - + -
263A CYS* 3.7 34.5 - - + -
264A ILE* 4.2 11.4 - - - -
267A LEU* 4.0 17.3 - - + -
275A PHE* 3.4 22.4 - - + +
280A ILE* 4.3 4.3 - - + -
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Residues in contact with LEU 94 (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 VAL* 3.6 24.7 - - + +
70A MET* 4.2 4.9 - - - -
73A GLY 3.9 11.0 - - - +
74A GLU* 3.8 27.6 - - + -
77A PHE* 3.7 28.9 - - + -
93A MET* 1.3 73.7 - - - +
95A ASP* 1.3 66.6 + - - +
96A SER* 3.7 24.7 - - - +
100A ASN* 2.9 25.1 + - - +
135A ARG* 4.1 4.7 - - - +
275A PHE 3.0 8.7 + - - +
276A ASP* 3.8 24.0 - - - +
280A ILE* 3.8 8.8 - - - +
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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