Contacts of the helix formed by residues 89 - 106 (chain C) 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 SER 89 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86C ALA 4.0 4.9 + - - +
87C ARG 3.4 4.1 - - - +
88C ARG* 1.3 80.3 - - - +
90C ASN* 1.3 63.3 + - - +
91C SER* 4.6 9.0 + - - -
92C LEU* 3.3 32.3 + - - +
93C LEU* 3.4 18.5 + - - +
80D ASP* 5.3 10.6 + - - +
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Residues in contact with ASN 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ARG 5.1 1.7 - - - +
89C SER* 1.3 72.8 - - - +
91C SER* 1.3 58.1 + - - +
93C LEU* 3.3 22.9 - - + +
94C LYS* 3.2 25.8 + - - +
63G LYS* 3.7 33.5 - - - +
24H LYS* 5.9 0.4 - - - +
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Residues in contact with SER 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C SER* 4.6 8.0 + - - -
90C ASN* 1.3 76.6 - - - +
92C LEU* 1.3 61.2 + - - +
94C LYS* 3.5 13.7 - - - +
95C TYR* 3.1 30.0 + - - +
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Residues in contact with LEU 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C LEU 5.6 0.2 - - - +
86C ALA* 3.8 33.9 - - + +
89C SER* 3.3 26.2 + - - +
90C ASN 3.3 0.6 - - - -
91C SER* 1.3 78.0 + - - +
93C LEU* 1.3 57.6 + - - +
95C TYR* 4.8 2.9 - - + -
96C ILE* 2.9 66.5 + - + +
41D LEU* 3.9 11.4 - - + -
44D VAL* 4.2 20.2 - - + -
80D ASP 5.1 5.2 - - - +
81D PHE* 3.9 27.8 - - + -
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Residues in contact with LEU 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ALA* 4.2 7.8 + - - +
87C ARG 6.1 0.2 - - - +
89C SER 3.4 9.2 + - - +
90C ASN* 3.3 26.2 - - + +
92C LEU* 1.3 76.9 - - - +
94C LYS* 1.3 62.0 + - - +
96C ILE* 5.2 1.1 - - - -
97C THR* 2.9 52.8 + - + +
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Residues in contact with LYS 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C ASN* 3.2 10.5 + - - +
91C SER* 3.5 16.6 - - - +
92C LEU 3.3 0.2 - - - -
93C LEU* 1.3 78.8 - - + +
95C TYR* 1.3 61.5 + - - +
97C THR* 3.2 11.8 + - - -
98C ASP* 3.1 29.1 - - - +
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Residues in contact with TYR 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C SER 3.1 15.3 + - - +
92C LEU* 4.1 4.5 - - + +
94C LYS* 1.3 79.2 - - + +
96C ILE* 1.3 63.8 + - + +
98C ASP* 3.2 9.5 - - + +
99C LYS* 3.1 66.1 + - + +
40D GLU* 4.7 2.9 - - - -
43D LYS* 6.0 2.3 - - - -
44D VAL* 4.2 27.8 - - + -
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Residues in contact with ILE 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C VAL* 5.7 2.9 - - + +
83C LYS* 4.4 23.6 - - + -
86C ALA* 4.9 11.4 - - + -
92C LEU* 2.9 41.7 + - + +
93C LEU* 4.5 0.9 - - - +
95C TYR* 1.3 81.2 - - + +
97C THR* 1.3 56.2 + - + +
99C LYS* 3.3 4.1 + - + +
100C SER* 2.7 32.6 + - - -
37D LEU* 4.5 11.5 - - + +
40D GLU* 3.7 41.1 - - + +
41D LEU* 4.3 7.4 - - + +
44D VAL* 4.2 15.0 - - + -
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Residues in contact with THR 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C LYS* 3.6 31.2 - - + +
93C LEU* 2.9 43.5 + - + +
94C LYS* 3.2 8.0 + - - -
96C ILE* 1.3 73.4 - - + +
98C ASP* 1.3 68.2 + - - +
100C SER* 2.8 23.0 + - - -
101C GLU* 3.0 21.3 + - - +
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Residues in contact with ASP 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C LYS* 3.1 24.0 + - - +
95C TYR* 3.2 13.6 - - - +
97C THR* 1.3 80.6 + - - +
99C LYS* 1.3 65.3 + - + +
101C GLU* 3.3 7.5 + - - +
102C GLU* 3.1 26.1 + - - +
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Residues in contact with LYS 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C TYR* 3.1 56.0 + - + +
96C ILE* 3.3 11.9 + - + +
98C ASP* 1.3 83.8 - - + +
100C SER* 1.3 56.8 + - - +
102C GLU* 3.0 33.7 + - - +
103C ILE* 3.0 35.6 + - - +
37D LEU* 4.4 0.7 - - + -
40D GLU* 3.0 40.8 - - + +
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Residues in contact with SER 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C LYS* 4.0 18.1 + - - -
96C ILE 2.7 18.2 + - - -
97C THR* 2.8 19.7 + - - -
99C LYS* 1.3 71.4 - - - +
101C GLU* 1.3 63.3 + - - +
103C ILE* 4.1 1.6 - - - +
104C ALA* 3.2 26.9 + - - +
37D LEU* 3.9 29.6 - - - +
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Residues in contact with GLU 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C THR* 3.0 22.5 + - - +
98C ASP* 3.8 6.7 - - - +
100C SER* 1.3 78.1 + - - +
102C GLU* 1.3 61.4 + - - +
104C ALA* 3.8 7.3 + - + +
105C GLN* 3.4 20.1 + - - +
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Residues in contact with GLU 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C ASP 3.1 16.3 + - - +
99C LYS* 3.0 36.8 + - - +
100C SER 3.3 0.2 - - - -
101C GLU* 1.3 75.6 - - - +
103C ILE* 1.3 75.7 + - - +
105C GLN* 3.2 30.2 - - - +
106C ALA* 3.5 6.6 + - - +
40D GLU* 4.9 2.2 - - - +
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Residues in contact with ILE 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C LYS 3.0 20.4 + - - +
100C SER* 4.7 2.7 - - - +
102C GLU* 1.3 86.6 - - - +
104C ALA* 1.3 60.3 - - - +
106C ALA* 3.2 31.5 + - + +
33D ASP* 4.7 19.8 - - + +
36D GLN* 3.2 50.3 - - + +
37D LEU* 4.1 10.5 - - + -
40D GLU* 3.2 37.9 - - + +
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Residues in contact with ALA 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C SER 3.2 21.4 + - - +
101C GLU* 3.8 9.2 - - + +
102C GLU 3.3 0.4 - - - -
103C ILE* 1.3 76.1 - - - +
105C GLN* 1.3 60.0 + - - +
106C ALA 3.7 4.3 + - - +
33D ASP* 5.0 9.8 + - - +
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Residues in contact with GLN 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C GLU 3.4 12.9 + - - +
102C GLU* 3.2 21.3 + - - +
104C ALA* 1.3 77.4 - - - +
106C ALA* 1.3 58.7 + - - +
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Residues in contact with ALA 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C GLU* 3.5 8.2 + - - +
103C ILE* 3.2 27.9 + - + +
104C ALA 4.0 4.5 - - - +
105C GLN* 1.3 81.6 - - - +
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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