Contacts of the strand formed by residues 84 - 89 (chain A) in PDB entry 1LPB
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 PHE 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A CYS 3.5 15.0 - - - +
50A SER* 4.2 9.9 - - - -
59A TYR* 3.8 26.7 - + + -
60A LYS* 3.6 43.3 - - + +
69A CYS* 4.6 0.7 - - - -
71A GLY* 3.5 16.3 - - - -
72A ASP 3.8 9.1 + - - +
81A ASN 4.0 7.4 - - - -
82A THR* 2.8 47.3 + - + +
83A ASN* 1.3 79.3 - - - +
85A GLY* 1.3 58.1 + - - +
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Residues in contact with GLY 85 (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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48A GLU* 3.5 9.0 - - - +
49A CYS* 3.0 29.9 + - - +
69A CYS* 3.7 5.6 - - - -
70A GLU 2.9 20.2 - - - -
71A GLY* 3.8 2.5 - - - -
84A PHE* 1.3 76.6 - - - +
86A ILE* 1.3 63.1 + - - +
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Residues in contact with ILE 86 (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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46A ASN* 3.3 37.5 - - - +
47A SER 3.3 9.0 - - - +
48A GLU* 4.7 9.4 - - + -
49A CYS* 3.4 5.4 - - - -
70A GLU* 2.8 28.8 + - - +
85A GLY* 1.3 77.4 - - - +
87A CYS* 1.3 66.7 + - - +
88A HIS* 3.3 31.2 + - + +
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Residues in contact with CYS 87 (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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43A ALA* 3.4 28.9 - - - -
44A ARG 3.3 20.4 - - - +
45A GLU* 3.7 9.7 - - - +
46A ASN* 2.7 26.0 + - - +
47A SER 3.0 9.9 + - - +
49A CYS* 3.5 5.2 - - - -
63A CYS* 2.0 53.8 - - + -
67A LEU* 4.1 4.3 - - + -
68A THR 3.6 0.2 - - - -
86A ILE* 1.3 71.7 - - - +
88A HIS* 1.3 65.0 + - - +
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Residues in contact with HIS 88 (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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45A GLU* 4.8 0.7 - - + -
46A ASN* 3.7 16.5 + - - -
67A LEU* 3.7 5.6 - - - -
68A THR* 2.8 37.2 + - - +
70A GLU* 2.9 43.2 + - + +
86A ILE* 3.8 34.0 + - + +
87A CYS* 1.3 83.0 - - - +
89A ASN* 1.3 64.3 + - - +
90A VAL 3.1 5.0 + - - -
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Residues in contact with ASN 89 (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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45A GLU* 3.9 11.9 + - - +
66A GLY 4.1 2.8 + - - -
67A LEU* 4.1 7.9 - - - +
88A HIS* 1.3 71.8 - - - +
90A VAL* 1.3 82.6 + - - +
399B LYS* 3.0 34.3 + - - +
442B VAL* 6.1 0.8 - - - +
443B LEU* 3.5 41.5 + - - +
445B THR* 3.7 7.4 + - - -
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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