Contacts of the helix formed by residues 96 - 116 (chain A) in PDB entry 4NJ4
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 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A LEU 4.1 0.4 + - - -
95A PHE* 1.3 75.8 - - - +
97A GLN* 1.3 61.0 + - - +
98A ASP* 3.6 7.8 + - - +
99A GLU* 2.9 36.9 + - - +
100A CYS* 2.9 27.8 + - - -
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Residues in contact with GLN 97 (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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96A SER* 1.3 73.8 - - - +
98A ASP* 1.3 57.1 + - - +
100A CYS* 3.3 4.7 + - - +
101A ALA* 2.9 28.3 + - - +
250A ARG* 3.5 28.4 + - - +
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Residues in contact with ASP 98 (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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96A SER* 3.2 7.9 + - - +
97A GLN* 1.3 75.8 - - - +
99A GLU* 1.3 59.9 + - + +
101A ALA* 3.3 9.7 + - - +
102A LYS* 2.9 28.6 + - - +
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Residues in contact with GLU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU 3.6 1.0 - - - +
95A PHE* 3.3 18.7 - - + -
96A SER* 2.9 40.2 + - - +
98A ASP* 1.3 79.4 - - + +
100A CYS* 1.3 57.6 + - - +
102A LYS* 3.3 6.2 + - - +
103A ILE* 2.9 37.4 + - + +
175A LYS* 2.5 38.6 + - - +
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Residues in contact with CYS 100 (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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95A PHE* 3.7 10.5 - - - -
96A SER 2.9 24.0 + - - +
97A GLN* 3.4 6.7 - - - +
98A ASP 3.2 0.2 - - - -
99A GLU* 1.3 77.1 - - - +
101A ALA* 1.3 51.1 + - - +
103A ILE* 3.3 2.1 + - - +
104A GLU* 2.7 45.6 + - - +
220A PHE* 4.0 15.2 - - - -
250A ARG* 3.6 23.6 - - - +
251A GLY* 3.4 38.4 - - - -
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Residues in contact with ALA 101 (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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97A GLN 2.9 16.9 + - - +
98A ASP* 3.3 10.5 + - - +
100A CYS* 1.3 76.1 - - - +
102A LYS* 1.3 63.1 + - - +
104A GLU* 3.3 13.1 + - - +
105A ALA* 3.0 23.4 + - - +
250A ARG* 3.6 6.3 - - - +
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Residues in contact with LYS 102 (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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98A ASP 2.9 14.2 + - - +
99A GLU* 3.3 8.9 + - - +
101A ALA* 1.3 77.6 - - - +
103A ILE* 1.3 64.0 + - - +
105A ALA* 3.3 14.0 + - + +
106A ARG* 3.4 35.7 + - - +
171A LEU* 4.4 27.4 - - + +
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Residues in contact with ILE 103 (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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95A PHE* 3.8 27.1 - - + -
99A GLU* 2.9 22.5 + - + +
100A CYS 3.7 3.6 - - - +
102A LYS* 1.3 77.9 - - + +
104A GLU* 1.3 56.9 + - - +
106A ARG* 3.0 10.2 + - - +
107A ILE* 2.9 32.6 + - + +
167A TRP* 4.0 17.0 - - + -
171A LEU* 4.1 26.7 - - + +
172A VAL* 3.9 11.4 - - + -
220A PHE* 3.5 44.6 - - + -
280A ILE* 4.2 2.5 - - + -
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Residues in contact with GLU 104 (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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100A CYS* 2.7 27.1 + - - +
101A ALA* 3.3 9.3 + - - +
103A ILE* 1.3 72.2 - - - +
105A ALA* 1.3 57.9 + - - +
107A ILE* 3.3 7.0 + - - +
108A ASP* 2.9 34.4 + - - -
220A PHE* 3.7 12.4 - - + +
221A PHE* 2.9 56.1 + - + -
250A ARG* 2.8 43.8 + - - -
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Residues in contact with ALA 105 (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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101A ALA 3.0 12.8 + - - +
102A LYS* 3.6 12.6 - - + +
103A ILE 3.2 0.2 - - - -
104A GLU* 1.3 75.2 - - - +
106A ARG* 1.3 60.4 + - + +
108A ASP* 3.4 10.4 + - - +
109A GLU* 2.9 24.9 + - - +
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Residues in contact with ARG 106 (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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102A LYS* 3.4 28.1 + - - +
103A ILE 3.0 8.7 + - - +
105A ALA* 1.3 77.2 - - + +
107A ILE* 1.3 62.0 + - - +
109A GLU* 2.6 43.7 + - - +
110A VAL* 2.9 31.9 + - - +
166A GLU* 6.3 0.4 - - - +
167A TRP* 3.4 61.8 - - + +
171A LEU* 4.5 6.7 - - + -
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Residues in contact with ILE 107 (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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103A ILE* 2.9 31.5 + - + +
104A GLU* 3.3 8.5 + - - +
106A ARG* 1.3 76.3 - - - +
108A ASP* 1.3 62.6 + - - +
110A VAL* 3.1 8.8 + - - +
111A VAL* 3.0 26.7 + - + +
167A TRP* 3.9 16.2 - - + -
192A ILE* 4.3 24.5 - - + -
194A ASP* 5.2 1.6 - - - +
220A PHE* 4.1 27.4 - - + -
221A PHE* 3.9 22.0 - - + -
276A ARG* 4.0 9.0 - - - +
278A ALA* 4.3 10.8 - - + -
280A ILE* 4.3 7.9 - - + -
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Residues in contact with ASP 108 (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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104A GLU 2.9 17.5 + - - +
105A ALA* 3.6 11.3 - - - +
107A ILE* 1.3 76.8 - - - +
109A GLU* 1.3 56.9 + - - +
111A VAL* 3.2 7.3 + - - +
112A SER* 2.9 30.1 + - - -
221A PHE* 3.7 6.9 - - - -
276A ARG* 2.8 40.8 + - - -
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Residues in contact with GLU 109 (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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105A ALA 2.9 15.1 + - - +
106A ARG* 2.6 49.6 + - - +
108A ASP* 1.3 75.7 - - - +
110A VAL* 1.3 58.5 + - - +
112A SER* 3.2 7.3 + - - -
113A ARG* 2.8 56.0 + - + +
167A TRP* 4.5 3.6 + - - -
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Residues in contact with VAL 110 (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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106A ARG 2.9 20.7 + - - +
107A ILE* 3.1 9.4 + - + +
109A GLU* 1.3 72.2 - - + +
111A VAL* 1.3 64.4 + - + +
113A ARG 3.2 0.9 + - - -
114A ALA* 2.9 21.1 + - - +
119A TYR* 3.5 31.1 - - + +
133A TYR* 4.0 21.8 - - + -
135A PHE* 3.8 24.5 - - + -
165A PRO* 5.0 4.0 - - + -
167A TRP* 4.0 25.6 - - + +
192A ILE* 4.3 9.6 - - + -
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Residues in contact with VAL 111 (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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107A ILE* 3.0 23.1 + - + +
108A ASP* 3.6 8.3 - - - +
110A VAL* 1.3 74.6 - - + +
112A SER* 1.3 58.7 + - - +
114A ALA* 3.2 3.5 + - - +
115A GLU* 2.9 50.9 + - + +
131A ASN* 5.6 2.7 - - - +
133A TYR* 3.7 34.5 - - + +
194A ASP* 3.7 22.7 - - - +
276A ARG* 4.2 9.4 - - - +
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Residues in contact with SER 112 (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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108A ASP 2.9 14.7 + - - -
109A GLU* 3.4 11.9 - - - -
111A VAL* 1.3 77.2 - - - +
113A ARG* 1.3 62.5 + - - +
115A GLU* 3.2 12.5 + - - +
116A LYS* 2.7 57.7 + - - +
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Residues in contact with ARG 113 (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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109A GLU* 2.8 46.7 + - + +
110A VAL 3.8 3.1 - - - +
112A SER* 1.3 74.8 - - - +
114A ALA* 1.3 62.8 + - - +
116A LYS* 3.1 15.6 + - + +
118A LEU* 3.1 63.9 + - + +
119A TYR* 3.7 40.9 + - + +
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Residues in contact with ALA 114 (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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110A VAL 2.9 12.8 + - - +
111A VAL 3.5 3.4 - - - +
113A ARG* 1.3 77.9 - - - +
115A GLU* 1.3 57.6 + - + +
117A GLY* 2.9 19.4 + - - -
118A LEU 4.8 0.9 - - - +
119A TYR* 3.7 19.0 - - + -
124A VAL* 3.9 14.3 - - + +
126A ARG* 3.3 16.9 + - - +
133A TYR* 3.5 33.2 - - + +
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Residues in contact with GLU 115 (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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111A VAL* 2.9 37.6 + - + +
112A SER* 3.2 11.1 + - - +
114A ALA* 1.3 78.0 - - + +
116A LYS* 1.3 59.3 + - + +
117A GLY* 3.2 1.0 + - - -
126A ARG* 4.7 9.4 - - - +
131A ASN* 5.8 1.6 + - - -
133A TYR* 6.0 0.2 - - - +
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Residues in contact with LYS 116 (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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112A SER* 2.7 44.2 + - - +
113A ARG* 3.5 11.6 - - + +
114A ALA 3.1 0.4 - - - -
115A GLU* 1.3 76.5 - - + +
117A GLY* 1.3 61.2 - - - +
118A LEU* 3.5 26.9 - - + +
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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