Contacts of the helix formed by residues 78 - 86 (chain A) in PDB entry 4NE1
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 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A ARG* 3.6 38.6 + - - +
76A THR 3.7 2.1 + - - +
77A ILE* 1.3 76.6 - - - +
79A THR* 1.3 70.8 + - + +
80A GLU* 3.1 27.2 + - - +
81A ASP* 3.6 11.6 + - - +
82A VAL* 3.7 14.4 + - - +
31B SER* 3.9 9.9 - - - +
34B ALA* 3.8 5.8 - - - -
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Residues in contact with THR 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ASN* 1.3 80.3 + - + +
80A GLU* 1.3 77.6 + - - +
82A VAL* 3.5 4.7 + - - +
83A LYS* 3.2 29.7 + - - +
31B SER* 5.2 2.0 - - - +
33B ASP* 4.9 10.1 - - + -
34B ALA* 4.0 11.8 - - - +
37B LEU* 3.8 25.7 - - + +
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Residues in contact with GLU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ARG* 5.8 0.7 - - - +
78A ASN* 3.1 15.7 + - - +
79A THR* 1.3 93.0 + - - +
81A ASP* 1.3 69.8 + - - +
83A LYS* 4.3 15.5 + - - +
84A LEU* 3.1 28.0 + - - +
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Residues in contact with ASP 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LEU* 4.0 14.3 - - + +
68A PHE* 3.6 42.8 - - + +
69A ALA* 3.8 11.0 - - - +
71A HIS* 5.9 0.7 - - - -
72A ALA* 5.4 0.3 - - - +
74A ARG* 3.3 36.5 + - - -
77A ILE* 4.4 8.3 - - + +
78A ASN* 3.6 14.3 + - - +
79A THR 3.5 0.2 - - - -
80A GLU* 1.3 79.0 - - - +
82A VAL* 1.3 52.5 + - - +
84A LEU* 3.4 5.7 + - - +
85A LEU* 2.9 32.1 + - - +
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Residues in contact with VAL 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LEU* 4.4 8.5 - - + -
77A ILE* 4.8 8.7 - - + -
78A ASN 3.7 15.5 - - - +
79A THR 3.6 6.5 - - - +
80A GLU 3.3 0.2 - - - -
81A ASP* 1.3 73.4 - - - +
83A LYS* 1.3 61.7 + - + +
85A LEU* 2.9 26.2 + - - +
86A ALA* 3.2 5.7 + - - +
96A ILE* 6.1 1.1 - - + -
30B VAL* 5.9 0.7 - - + -
34B ALA* 3.8 24.5 - - + +
37B LEU* 3.7 26.5 - - + +
38B MET* 3.4 33.0 - - + -
41B LEU* 3.9 9.2 - - + +
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Residues in contact with LYS 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A THR* 3.2 20.0 + - - +
80A GLU* 4.6 17.7 + - - +
82A VAL* 1.3 79.7 - - + +
84A LEU* 1.3 59.6 + - - +
86A ALA* 3.4 24.9 + - - +
87A ARG* 3.8 1.0 + - - -
93A LEU* 4.1 17.2 - - + +
96A ILE* 4.4 9.2 - - + -
97A THR* 3.8 31.6 - - + +
100A SER* 3.3 35.0 + - - -
37B LEU* 3.8 21.5 - - + -
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Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A PHE* 4.6 26.4 - - + -
80A GLU 3.1 21.2 + - - +
81A ASP* 3.6 6.7 - - - +
82A VAL 3.1 0.2 - - - -
83A LYS* 1.3 74.1 - - - +
85A LEU* 1.3 60.0 + - - +
86A ALA 3.3 0.2 - - - -
87A ARG* 3.0 46.6 + - + +
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A PHE* 3.9 34.3 - - + +
64A ASP* 4.0 20.6 - - + +
65A LEU* 3.5 34.3 - - + -
68A PHE* 3.6 24.9 - - + -
81A ASP 2.9 10.6 + - - +
82A VAL* 2.9 13.9 + - - +
84A LEU* 1.3 74.7 - - - +
86A ALA* 1.3 54.3 + - - +
87A ARG* 3.1 34.1 + - - +
88A ARG* 4.3 5.9 - - - +
38B MET* 5.1 3.4 - - + -
41B LEU* 4.6 11.4 - - + -
81B PHE* 5.2 5.9 - - - -
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Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A VAL 3.2 8.5 + - - +
83A LYS* 3.4 15.9 + - - +
84A LEU 3.3 0.4 - - - -
85A LEU* 1.3 75.0 - - - +
87A ARG* 1.3 56.4 + - - +
88A ARG 3.2 6.9 + - - +
89A SER 4.1 1.4 - - - +
92A LEU* 3.8 25.3 - - + +
93A LEU* 3.9 20.7 - - + +
96A ILE* 5.2 10.5 - - + -
41B LEU* 3.8 27.3 - - + +
81B PHE* 5.5 1.3 - - - -
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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