Contacts of the strand formed by residues 57 - 61 (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 ARG 57 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A HIS* 6.1 1.6 - - - +
57A ARG* 4.6 5.5 - - - +
67A GLU* 3.2 24.4 + - - +
32B HIS* 5.4 9.1 + - - +
33B GLY 5.1 0.2 - - - -
34B GLY* 3.5 25.5 - - - +
35B ILE 3.3 16.5 - - - +
36B TYR* 3.5 31.7 + - + -
55B GLY 3.6 0.8 + - - -
56B ASP* 1.3 73.5 - - - +
58B VAL* 1.3 62.8 + - - +
59B LEU* 3.5 17.1 + - + +
89B LEU* 3.1 9.3 - - - +
90B GLU* 2.9 53.5 + - + +
102B SCN 3.0 31.5 + - - -
103B SCN 3.4 19.3 + - - -
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Residues in contact with VAL 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ILE* 4.7 8.7 - - + -
22B VAL* 4.7 9.2 - - + -
35B ILE* 2.8 33.5 + - + +
37B VAL* 4.2 17.3 - - + -
57B ARG* 1.3 76.7 + - - +
59B LEU* 1.3 62.2 + - - +
60B ALA 4.0 15.7 - - - +
61B VAL* 4.3 8.5 - - + -
66B LEU* 3.4 32.7 - - + +
78B LEU* 4.9 5.6 - - + -
87B LEU* 4.6 11.4 - - + -
88B LEU 3.8 4.7 - - - +
89B LEU* 4.1 16.2 - - + -
102B SCN 5.1 1.7 + - - -
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Residues in contact with LEU 59 (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* 4.9 1.0 - - - +
59A LEU* 5.1 11.1 - - + +
65A SER* 5.3 1.3 - - - +
88A LEU* 5.0 2.7 - - + -
6B ILE* 3.6 31.0 - - + -
57B ARG* 3.8 20.2 - - + +
58B VAL* 1.3 74.2 - - - +
60B ALA* 1.3 59.6 + - - +
65B SER* 3.5 7.1 + - - -
66B LEU* 3.0 22.1 + - - +
88B LEU* 2.8 33.5 + - + +
89B LEU 4.1 11.0 - - - -
90B GLU* 4.2 13.5 - - + +
102B SCN 4.0 13.9 - - - -
103B SCN 2.9 34.3 - - - +
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Residues in contact with ALA 60 (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* 3.5 31.6 - - + -
58B VAL* 3.6 4.5 - - - +
59B LEU* 1.3 82.5 - - - +
61B VAL* 1.3 69.8 + - - +
64B VAL 3.2 16.2 - - - +
65B SER* 4.2 0.2 - - - +
66B LEU* 4.3 3.1 - - - +
87B LEU* 3.6 3.1 - - - -
88B LEU* 3.1 30.3 + - + +
101B SCN 3.8 13.5 - - - -
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Residues in contact with VAL 61 (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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58B VAL* 4.3 6.3 - - + -
60B ALA* 1.3 78.1 - - - +
62B ASN* 1.3 74.2 + - + +
63B GLY 3.1 1.3 + - - -
64B VAL* 3.0 22.0 + - - +
66B LEU* 4.2 11.4 - - + -
77B THR* 4.0 28.3 - - + +
78B LEU* 3.7 26.5 - - + -
81B THR* 3.8 29.6 - - + -
85B VAL* 3.8 13.7 - - + -
86B HIS 3.5 3.4 - - - -
87B LEU* 3.9 4.5 - - + -
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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