Contacts of the strand formed by residues 84 - 90 (chain B) in PDB entry 3LNX
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 VAL 84 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLU* 3.3 32.8 - - + +
11B LEU 3.4 7.6 - - - +
12B ALA* 4.0 4.3 - - - -
62B ASN* 4.6 0.7 + - - +
82B GLY* 4.2 5.7 + - - -
83B GLN* 1.3 81.8 + - - +
85B VAL* 1.3 67.3 + - - +
86B HIS 4.4 0.2 + - - -
98B IOD 4.0 4.7 - - + -
10C GLU* 4.0 22.1 - - + +
12C ALA* 3.5 27.2 + - + +
49C ASP* 4.2 13.7 - - - +
51C ARG* 4.6 1.9 + - - -
84C VAL* 3.6 18.6 - - + -
84D VAL* 3.8 17.7 - - + -
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL 3.5 1.2 - - - +
10B GLU* 3.5 5.0 - - - -
11B LEU* 2.9 36.1 + - - +
13B LYS* 3.6 18.4 - - - -
18B LEU* 3.9 20.2 - - + -
61B VAL* 3.8 17.7 - - + -
62B ASN* 3.8 6.3 - - - +
81B THR* 3.3 33.9 - - + +
82B GLY 3.6 1.3 - - - +
84B VAL* 1.3 79.2 - - - +
86B HIS* 1.3 73.2 + - - +
87B LEU* 3.6 20.2 + - + +
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Residues in contact with HIS 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLU* 2.7 33.9 + - + +
9B VAL 3.4 13.9 - - - -
10B GLU* 3.5 28.3 + - + +
61B VAL* 3.5 3.3 - - - -
62B ASN* 2.8 46.0 + - - +
63B GLY* 4.8 2.6 + - - -
84B VAL 4.4 0.4 + - - -
85B VAL* 1.3 72.0 - - - +
87B LEU* 1.3 70.7 + - - +
101B SCN 3.4 28.9 - - - -
51C ARG* 4.2 13.6 + - - +
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Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLU* 3.2 6.8 - - - +
9B VAL* 2.9 49.2 + - + -
11B LEU* 4.1 23.6 - - + -
18B LEU* 4.6 10.5 - - + -
20B ILE* 5.4 7.4 - - + -
52B ILE* 4.1 9.9 - - + -
58B VAL* 4.6 7.4 - - + -
60B ALA 3.6 3.1 - - - +
61B VAL* 3.9 11.7 - - + -
78B LEU* 3.9 24.0 - - + -
85B VAL* 3.7 21.5 - - + +
86B HIS* 1.3 82.6 - - - +
88B LEU* 1.3 61.2 + - - +
89B LEU* 3.8 16.5 - - + +
101B SCN 4.0 2.9 - - - -
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ILE* 4.0 26.9 - - + -
59A LEU* 4.8 0.7 - - + -
88A LEU* 3.9 22.9 - - + -
6B ILE* 3.7 27.1 - - + -
7B PHE 3.7 6.5 - - - +
8B GLU* 4.4 14.1 - - + +
58B VAL* 3.7 1.4 - - - +
59B LEU* 2.8 48.1 + - + -
60B ALA* 3.1 23.7 + - + +
87B LEU* 1.3 73.3 - - - +
89B LEU* 1.3 57.6 + - - +
101B SCN 3.7 21.0 - - - +
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Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 3.4 9.2 - - - +
7B PHE* 2.8 69.0 + - + +
9B VAL* 4.2 9.9 - - + -
37B VAL* 4.6 0.2 - - + -
52B ILE* 4.2 20.6 - - + -
56B ASP* 3.9 20.4 - - + -
57B ARG 3.1 13.9 - - - +
58B VAL* 4.1 19.1 - - + -
59B LEU* 4.1 6.1 - - - +
87B LEU* 3.8 29.4 - - + +
88B LEU* 1.3 80.1 - - - +
90B GLU* 1.3 61.4 + - - +
91B LYS 4.1 0.2 - - - -
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Residues in contact with GLU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A SER* 3.3 28.5 + - - +
67A GLU* 2.6 49.0 - - - +
4B GLY* 3.6 21.2 - - - +
5B ASP 3.4 4.0 - - - +
6B ILE* 4.5 0.7 - - + -
7B PHE* 4.1 2.5 - - - -
56B ASP* 3.4 2.8 - - - +
57B ARG* 2.9 46.8 + - + +
59B LEU* 4.2 11.6 - - + +
89B LEU* 1.3 73.9 - - - +
91B LYS* 1.3 73.2 + - - +
92B GLY* 3.4 1.8 + - - -
93B GLN* 5.7 1.9 + - - -
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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