Contacts of the strand formed by residues 84 - 90 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A VAL* 3.8 19.5 - - + -
98A IOD 4.0 5.6 - - + -
10E GLU* 4.3 20.0 - - + +
12E ALA* 3.4 27.1 + - + +
49E ASP* 4.2 14.9 - - - +
51E ARG* 4.6 1.7 + - - -
84E VAL* 3.6 18.6 - - + -
10F GLU* 3.3 34.5 - - + +
11F LEU 3.5 8.7 - - - +
12F ALA* 4.1 2.7 - - + +
62F ASN* 4.6 0.3 + - - +
82F GLY 4.2 3.8 + - - +
83F GLN* 1.3 78.4 - - - +
85F VAL* 1.3 66.3 + - - +
86F HIS 4.3 0.5 + - - -
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Residues in contact with VAL 85 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9F VAL 3.5 2.3 - - - +
10F GLU* 3.6 3.4 - - - -
11F LEU* 2.9 31.9 + - - +
13F LYS* 3.8 3.1 - - + -
18F LEU* 3.8 31.6 - - + -
61F VAL* 3.8 24.7 - - + -
62F ASN* 3.6 11.4 - - - +
78F LEU 5.4 0.2 - - - +
81F THR* 3.5 30.3 - - + +
82F GLY 3.6 11.7 - - - +
84F VAL* 1.3 79.2 - - - +
86F HIS* 1.3 66.3 + - - +
87F LEU* 3.5 12.0 + - + +
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Residues in contact with HIS 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E ARG* 4.2 17.5 + - - +
8F GLU* 2.8 33.5 + - + +
9F VAL 3.4 16.6 - - - -
10F GLU* 3.5 28.1 + - + +
61F VAL* 3.5 3.6 - - - -
62F ASN* 2.8 45.8 + - - +
63F GLY* 4.8 2.0 + - - -
84F VAL 4.3 0.2 + - - -
85F VAL* 1.3 72.5 - - - +
87F LEU* 1.3 66.5 + - - +
100F SCN 3.3 28.3 - - - -
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Residues in contact with LEU 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F GLU* 3.2 7.4 - - - +
9F VAL* 2.8 37.6 + - + +
11F LEU* 4.1 26.0 - - + -
18F LEU* 4.7 10.1 - - + -
20F ILE* 4.9 8.5 - - + -
52F ILE* 4.1 21.5 - - + -
58F VAL* 4.5 7.6 - - + -
60F ALA 3.7 2.5 - - - +
61F VAL* 3.8 27.6 - - + -
78F LEU* 3.8 15.9 - - + -
85F VAL* 4.1 11.9 - - + +
86F HIS* 1.3 79.5 - - - +
88F LEU* 1.3 59.4 + - - +
89F LEU* 3.8 16.6 - - + +
100F SCN 3.9 2.7 - - - -
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Residues in contact with LEU 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ILE* 4.0 40.4 - - + -
59D LEU* 5.0 0.4 - - + -
88D LEU* 4.0 20.2 - - + -
6F ILE* 3.7 26.9 - - + -
7F PHE 3.8 5.6 - - - +
8F GLU* 4.3 16.4 - - + -
58F VAL* 3.7 1.4 - - - +
59F LEU* 2.7 45.6 + - + -
60F ALA* 3.1 17.1 + - + +
87F LEU* 1.3 73.4 - - - +
89F LEU* 1.3 57.1 + - - +
100F SCN 3.6 21.5 - - - +
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Residues in contact with LEU 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F ILE* 3.4 9.5 - - - +
7F PHE* 2.8 67.9 + - + +
9F VAL* 4.4 3.8 - - + -
20F ILE* 6.4 0.4 - - + -
37F VAL* 4.6 0.9 - - + -
52F ILE* 4.1 30.3 - - + -
56F ASP* 4.0 19.3 - - + -
57F ARG 3.1 13.9 - - - +
58F VAL* 4.3 17.3 - - + -
59F LEU* 4.0 5.8 - - - +
87F LEU* 3.8 29.6 - - + +
88F LEU* 1.3 79.7 - - - +
90F GLU* 1.3 61.3 + - - +
91F LYS 4.2 0.2 - - - -
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Residues in contact with GLU 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D SER* 3.4 35.0 + - - -
67D GLU* 2.6 40.8 - - - +
4F GLY* 3.7 18.4 + - - +
5F ASP 3.4 3.8 - - - -
6F ILE* 4.4 0.7 - - + -
7F PHE* 4.0 2.2 - - - -
56F ASP* 3.4 3.1 - - - +
57F ARG* 2.9 44.3 + - + +
59F LEU* 4.1 16.1 - - + +
89F LEU* 1.3 74.8 - - - +
91F LYS* 1.3 74.3 + - - +
92F GLY* 3.3 1.4 + - - -
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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