Contacts of the strand formed by residues 52 - 57 (chain J) in PDB entry 4NL3
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 LYS 52 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B SER* 3.6 18.8 - - - -
66B PRO 2.4 31.3 + - - -
67B GLN* 3.7 14.7 + - - +
69B ASN* 4.0 10.3 + - - +
1C MET* 5.1 13.5 - - + -
47J LEU 3.5 0.9 - - - +
48J ASP* 3.5 2.4 - - - -
49J VAL* 2.7 43.8 + - - +
50J GLU 3.1 4.1 + - - +
51J GLY* 1.3 79.8 - - - +
53J GLN* 1.3 67.3 + - - +
54J GLN* 3.8 13.0 - - - +
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Residues in contact with GLN 53 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B TYR* 2.8 35.5 + - - +
66B PRO* 3.5 16.7 - - + +
69B ASN* 3.4 27.0 + - - +
70B VAL 3.0 38.4 + - - +
72B LEU* 3.5 27.7 - - - +
38J VAL* 5.4 4.7 - - + +
46J LEU* 4.0 13.8 - - + +
47J LEU 3.2 7.0 - - - +
48J ASP* 5.5 2.5 - - + +
52J LYS* 1.3 74.8 - - - +
54J GLN* 1.3 75.5 + - - +
55J LEU 4.2 0.4 - - - -
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Residues in contact with GLN 54 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B PHE* 5.1 1.9 - - - -
63B THR* 3.2 24.3 - - + +
64B PHE 3.7 2.5 - - - -
65B SER* 2.9 30.1 + - - -
1C MET* 5.2 15.2 - - - +
33J LEU* 3.9 19.3 - - + +
45J VAL 3.3 0.7 - - - +
46J LEU* 3.9 2.0 - - - +
47J LEU* 2.9 42.8 + - + +
49J VAL* 3.8 26.2 - - + +
52J LYS* 3.8 20.0 - - - +
53J GLN* 1.3 84.4 + - - +
55J LEU* 1.3 60.9 + - - +
56J VAL* 3.3 7.9 + - + +
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Residues in contact with LEU 55 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 3.8 28.5 - - + -
9B GLN* 4.9 4.5 - - + -
12B TYR* 3.6 42.5 + - + -
13B LEU* 4.6 10.5 - - + -
63B THR* 3.2 2.1 - - - -
64B PHE* 2.6 64.9 + - + +
44J THR* 3.8 25.4 - - + -
45J VAL 3.9 9.2 - - - +
46J LEU* 4.1 12.2 - - + +
53J GLN 4.2 0.4 - - - -
54J GLN* 1.3 70.1 - - - +
56J VAL* 1.3 59.3 + - - +
57J PHE* 4.1 2.4 + - + -
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Residues in contact with VAL 56 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B SER 3.4 13.0 - - - +
63B THR* 3.8 20.6 - - + +
25J VAL* 5.6 0.4 - - + -
27J LEU* 3.8 14.1 - - + -
33J LEU* 4.8 6.5 - - + -
44J THR* 3.3 3.2 - - - -
45J VAL* 2.7 42.3 + - - +
47J LEU* 4.2 19.3 - - + -
54J GLN* 3.7 14.4 - - + +
55J LEU* 1.3 76.1 - - - +
57J PHE* 1.3 66.6 + - - +
58J LYS 3.7 0.2 + - - -
60J ALA* 4.6 1.1 - - + -
61J ILE* 3.6 33.0 - - + -
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Residues in contact with PHE 57 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B GLN* 3.9 21.8 - - + -
13B LEU* 5.0 2.2 - - + -
45B VAL* 5.7 0.2 - - + -
58B LYS* 4.0 21.5 - - + -
61B ILE* 3.6 39.7 - - + +
62B SER 3.1 12.2 + - - +
64B PHE* 3.8 22.2 - + - -
43J PHE* 3.4 7.9 - - + -
44J THR* 3.7 23.1 - - + +
55J LEU* 4.8 4.0 - - + -
56J VAL* 1.3 73.3 - - - +
58J LYS* 1.3 59.4 + - - +
59J HIS* 3.3 35.0 - + + +
60J ALA* 2.9 24.6 + - - +
61J ILE* 3.4 7.4 + - - +
19R U 3.9 14.1 - - - -
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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