Contacts of the strand formed by residues 44 - 49 (chain G) 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 THR 44 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G PHE* 3.4 3.5 - - - +
41G ASP* 2.7 56.8 + - - +
42G ASN 3.8 0.2 - - - -
43G PHE* 1.3 81.0 - - - +
45G VAL* 1.3 66.5 + - - +
55G LEU* 3.8 18.6 - - + -
56G VAL 3.3 8.5 - - - +
57G PHE* 3.8 23.6 - - + -
58G LYS* 4.1 1.0 - - - +
8J LEU* 3.2 16.0 - - - +
9J GLN* 3.4 29.3 - - + +
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Residues in contact with VAL 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G LEU* 4.3 11.0 - - + -
37G VAL* 4.3 11.0 - - + -
39G SER 3.6 10.1 - - - +
40G PHE* 4.0 9.2 - - + -
44G THR* 1.3 80.0 - - - +
46G LEU* 1.3 62.4 + - - +
47G LEU* 3.6 24.4 + - + +
54G GLN 3.3 2.8 - - - +
55G LEU* 4.2 3.4 - - - -
56G VAL* 2.8 42.4 + - + +
58G LYS* 4.0 19.7 - - + -
61G ILE* 4.0 23.1 - - + -
64G PHE* 4.4 12.6 - - + -
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Residues in contact with LEU 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G VAL* 3.9 0.2 - - - -
38G VAL* 2.9 50.4 + - + -
39G SER* 2.8 23.0 + - - +
45G VAL* 1.3 71.1 - - - +
47G LEU* 1.3 69.6 + - - +
53G GLN* 4.1 14.4 - - + +
54G GLN 3.5 22.9 - - - +
55G LEU* 4.1 7.0 - - + +
8J LEU* 4.2 23.8 - - + +
12J TYR* 3.7 26.5 - - + -
72J LEU* 4.1 24.9 - - + -
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Residues in contact with LEU 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G VAL* 3.9 32.1 - - + -
33G LEU* 4.4 10.1 - - + -
35G GLY* 5.2 2.9 - - - +
36G ARG 3.4 14.6 - - - +
37G VAL* 4.0 13.5 - - + -
38G VAL* 4.1 3.6 - - - +
45G VAL* 3.6 21.3 - - + +
46G LEU* 1.3 83.9 - - - +
48G ASP* 1.3 59.0 + - - +
49G VAL* 3.8 9.4 - - + -
52G LYS 3.5 0.2 - - - +
53G GLN* 3.3 7.6 - - - +
54G GLN* 2.7 46.7 + - + +
56G VAL* 3.5 32.1 - - + -
61G ILE* 5.8 0.2 - - + -
64G PHE* 5.0 0.9 - - + -
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Residues in contact with ASP 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G LYS* 6.2 2.7 - - - +
35G GLY* 3.3 2.8 - - - -
36G ARG* 2.7 43.7 + - + +
38G VAL* 3.6 20.1 - - + +
47G LEU* 1.3 72.2 - - - +
49G VAL* 1.3 60.6 + - - +
50G GLU* 3.6 2.9 + - - -
51G GLY* 3.6 34.2 + - - +
52G LYS 3.4 3.2 - - - +
53G GLN* 4.8 3.4 - - + +
69J ASN* 5.2 1.7 + - - -
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Residues in contact with VAL 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G LEU* 4.1 15.7 - - + -
34G ARG 3.4 29.8 - - - +
35G GLY* 4.3 2.0 - - - -
47G LEU* 4.4 7.2 - - + -
48G ASP* 1.3 74.6 - - - +
50G GLU* 1.3 75.4 + - + +
51G GLY 3.4 0.2 - - - -
52G LYS* 2.6 29.7 + - + +
54G GLN* 3.5 29.8 - - + +
1K MET* 4.1 25.8 - - + +
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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