Contacts of the helix formed by residues 41 - 50 (chain J) in PDB entry 6NMY
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 ASN 41 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54F LYS* 5.3 6.9 + - - +
58F TYR* 3.2 43.3 - - + +
39J ASN 3.4 6.2 + - - +
40J LEU* 1.3 77.3 - - - +
42J GLY* 1.3 70.2 + - - +
43J GLU* 3.5 21.6 + - - +
44J ASP* 3.0 26.8 + - - +
45J GLN* 3.0 10.0 + - - +
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Residues in contact with GLY 42 (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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72F ALA* 3.8 17.6 - - - +
199F PHE* 6.0 3.8 - - - -
40J LEU 3.5 2.0 + - - -
41J ASN* 1.3 78.4 + - - +
43J GLU* 1.3 57.4 + - - +
45J GLN* 3.3 17.0 + - - +
46J ASP* 2.9 27.7 + - - +
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Residues in contact with GLU 43 (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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54F LYS* 2.9 32.5 + - + +
58F TYR* 3.3 27.8 - - + +
60F MET* 5.7 1.1 - - - +
70F PHE* 3.5 21.6 - - + +
71F GLY 2.5 29.0 + - - -
72F ALA* 3.0 24.3 + - - -
73F ILE 3.6 1.2 + - - -
41J ASN* 3.1 18.2 + - - +
42J GLY* 1.3 75.0 - - - +
44J ASP* 1.3 60.0 + - - +
46J ASP* 3.3 3.7 + - - +
47J ILE* 2.9 35.0 + - + +
94J ARG* 4.9 0.7 + - - -
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Residues in contact with ASP 44 (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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58F TYR* 2.9 35.4 + - - -
40J LEU* 3.9 18.8 - - + +
41J ASN* 3.0 17.0 + - - +
43J GLU* 1.3 75.7 - - - +
45J GLN* 1.3 57.2 + - - +
47J ILE* 3.3 5.6 + - - +
48J LEU* 2.9 38.3 + - + +
97J ILE* 3.3 26.5 - - + +
110J LYS* 3.6 17.7 + - - -
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Residues in contact with GLN 45 (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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201F VAL* 3.4 25.8 - - - +
37J PHE* 3.6 20.6 + - - +
38J ASN* 5.6 0.2 - - - +
40J LEU* 2.9 37.1 + - + +
41J ASN 3.0 11.1 + - - +
42J GLY* 3.4 14.7 - - - +
43J GLU 3.2 0.2 - - - -
44J ASP* 1.3 77.0 - - - +
46J ASP* 1.3 57.4 + - - +
48J LEU 3.3 1.0 + - - -
49J MET* 2.9 39.5 + - + +
113J PHE* 3.6 27.6 - - + -
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Residues in contact with ASP 46 (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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71F GLY* 3.5 32.5 - - - +
72F ALA* 5.1 0.7 - - + -
144F ASN* 4.4 12.4 - - - +
179F SER* 5.1 7.1 + - - -
42J GLY 2.9 16.0 + - - +
43J GLU 3.8 4.3 - - - +
45J GLN* 1.3 76.7 - - - +
47J ILE* 1.3 61.5 + - - +
49J MET* 3.4 12.8 + - + +
50J GLU* 3.1 21.8 + - - +
94J ARG* 2.7 37.9 + - - +
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Residues in contact with ILE 47 (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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58F TYR* 3.7 17.5 - - - +
60F MET* 4.3 16.4 - - + -
43J GLU* 2.9 22.6 + - + +
44J ASP* 3.6 8.5 - - - +
45J GLN 3.2 0.2 - - - -
46J ASP* 1.3 75.9 - - - +
48J LEU* 1.3 63.5 + - - +
50J GLU* 3.3 17.2 + - - +
53J LEU* 4.0 12.6 - - + +
57J ASN* 3.1 20.3 + - - +
94J ARG* 3.8 26.0 - - - +
95J HIS 4.3 10.1 - - - +
96J PRO 4.1 5.4 - - - +
97J ILE* 3.8 32.5 - - + +
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Residues in contact with LEU 48 (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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40J LEU* 4.2 7.4 - - + -
44J ASP 2.9 22.7 + - - +
45J GLN 3.9 2.9 - - - +
47J ILE* 1.3 76.4 - - - +
49J MET* 1.3 62.2 + - - +
50J GLU 4.1 0.5 - - - +
54J ARG* 3.5 22.9 + - - -
57J ASN* 3.6 14.0 + - - +
61J PHE* 4.1 18.4 - - + -
97J ILE* 4.0 31.2 - - + -
110J LYS* 3.4 38.4 - - + +
113J PHE* 4.0 20.9 - - + -
114J TYR* 4.0 19.1 - - + +
117J THR* 4.0 1.9 + - - -
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Residues in contact with MET 49 (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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178F GLN* 3.6 35.5 + - + +
179F SER* 3.8 26.9 - - - -
201F VAL* 3.9 17.3 - - + -
45J GLN* 2.9 42.1 + - + +
46J ASP* 3.9 12.1 - - + +
47J ILE 3.2 0.2 - - - -
48J LEU* 1.3 77.0 - - - +
50J GLU* 1.3 64.8 + - - +
51J ASN* 3.2 4.9 + - - +
54J ARG* 3.7 14.9 + - - +
113J PHE* 3.6 19.7 - - + -
117J THR* 3.6 18.2 - - + -
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Residues in contact with GLU 50 (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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144F ASN* 5.1 9.0 + - - +
46J ASP 3.1 14.0 + - - +
47J ILE 3.3 14.4 + - - +
48J LEU 4.1 1.0 - - - +
49J MET* 1.3 74.1 - - - +
51J ASN* 1.3 70.0 + - - +
52J ASN* 4.3 14.1 + - - +
53J LEU* 3.3 47.0 + - + +
54J ARG* 3.7 8.8 + - - +
57J ASN* 4.8 0.2 + - - -
93J THR* 4.9 8.7 + - - -
94J ARG* 3.9 24.8 + - - +
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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