Contacts of the helix formed by residues 97 - 118 (chain A) in PDB entry 1N54
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 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A GLU* 5.2 3.8 - - + +
61A LEU* 3.9 26.4 - - + +
65A LYS* 4.7 6.1 + - - +
93A LEU* 2.7 14.2 + - + +
94A ASN* 3.1 6.0 + - - +
96A ARG* 1.3 82.9 - - + +
98A TYR* 1.3 66.8 + - - +
99A ASN* 3.2 18.9 - - - +
100A PHE* 2.8 51.0 + - + +
101A GLY 3.6 2.4 + - - -
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Residues in contact with TYR 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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94A ASN* 3.4 13.3 + - - +
97A ASN* 1.3 71.5 - - - +
99A ASN* 1.3 72.2 + - - +
100A PHE 2.7 12.5 + - - -
101A GLY* 3.0 10.4 + - - -
102A GLY 3.3 7.8 + - - -
264A LEU* 3.1 46.0 - - + -
265A GLN 3.9 9.0 + - - -
266A HIS* 3.6 35.0 + + - -
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Residues in contact with ASN 99 (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 LYS* 4.5 6.1 - - - +
97A ASN* 3.2 13.1 - - - +
98A TYR* 1.3 93.4 - - - +
100A PHE* 1.3 55.9 + - - +
102A GLY* 3.9 5.2 - - - +
103A GLU* 2.6 40.2 + - - +
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Residues in contact with PHE 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 3.5 33.9 - - + -
65A LYS* 4.1 13.7 - - + +
68A ILE* 4.0 17.9 - - + -
69A LEU* 4.1 22.2 - - + -
72A LEU* 4.0 22.0 - - + -
90A VAL* 4.9 7.6 - - + -
93A LEU* 3.3 39.7 - - + +
97A ASN* 2.8 30.0 + - + +
98A TYR 2.7 5.3 + - - -
99A ASN* 1.3 71.0 - - - +
101A GLY* 1.3 69.0 + - - +
102A GLY 3.0 1.3 - - - -
103A GLU* 3.0 9.0 + - - +
104A PHE* 2.9 29.4 + + + +
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Residues in contact with GLY 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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90A VAL* 5.5 2.9 - - - -
94A ASN* 3.1 24.2 + - - +
97A ASN 3.6 0.4 + - - -
98A TYR 3.0 4.4 + - - -
100A PHE* 1.3 85.4 - - - +
102A GLY* 1.3 56.0 + - - +
104A PHE* 3.5 9.6 - - - +
105A VAL* 3.0 38.9 + - - +
139A VAL* 5.0 4.3 - - - -
266A HIS* 4.0 6.7 - - - -
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Residues in contact with GLY 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 TYR 3.3 9.4 + - - -
99A ASN* 4.3 4.0 - - - -
100A PHE 3.0 1.2 - - - -
101A GLY* 1.3 78.7 - - - +
103A GLU* 1.3 58.1 + - - +
105A VAL* 4.5 2.2 - - - +
106A GLU* 2.9 30.2 + - - +
266A HIS* 3.4 23.0 - - - -
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Residues in contact with GLU 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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65A LYS* 2.8 35.5 + - + +
69A LEU* 3.8 23.4 - - + +
99A ASN* 2.6 25.8 + - - +
100A PHE* 3.0 6.9 + - - +
102A GLY* 1.3 76.0 - - - +
104A PHE* 1.3 61.3 - - - +
106A GLU* 3.7 11.6 - - + +
107A ALA* 3.3 19.9 + - - +
110A ARG* 5.2 0.9 + - - -
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Residues in contact with PHE 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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69A LEU* 3.8 16.8 - - + -
72A LEU* 4.0 16.2 - - + -
73A CYS* 3.5 37.7 - - - -
90A VAL* 3.2 42.8 - - + -
100A PHE* 2.9 20.5 + + + +
101A GLY* 3.5 8.3 - - - +
103A GLU* 1.3 75.9 - - - +
105A VAL* 1.3 68.7 + - + +
106A GLU 3.1 1.1 - - - -
107A ALA* 3.0 5.5 + - - +
108A MET* 2.8 43.4 + - + +
130A PHE* 3.8 25.1 - + - -
134A LEU* 4.4 8.1 - - + -
139A VAL* 5.6 0.4 - - + -
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Residues in contact with VAL 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 GLY 3.0 18.7 + - - +
102A GLY* 4.6 4.3 - - - +
104A PHE* 1.3 85.2 - - + +
106A GLU* 1.3 61.9 + - - +
107A ALA 3.4 0.2 + - - -
108A MET* 3.8 7.6 - - - +
109A ILE* 3.3 27.1 + - + +
131A LEU* 5.1 2.2 - - + -
134A LEU* 4.8 3.4 - - + -
139A VAL* 4.4 12.3 - - + -
140A ILE* 4.4 22.9 - - + -
266A HIS* 5.2 11.2 - - + -
267A ASN 5.5 3.1 - - - +
268A LEU* 3.5 31.9 - - + -
269A PRO* 6.0 2.0 - - + -
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Residues in contact with GLU 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 GLY 2.9 24.5 + - - +
103A GLU* 3.7 13.5 - - + +
104A PHE 3.1 0.4 - - - -
105A VAL* 1.3 79.9 - - - +
107A ALA* 1.3 62.0 + - - +
109A ILE* 4.8 2.2 - - - +
110A ARG* 3.2 33.5 + - - +
269A PRO* 4.7 17.0 - - - +
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Residues in contact with ALA 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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69A LEU* 4.8 9.9 - - + -
73A CYS* 3.8 19.1 - - - -
103A GLU 3.3 11.5 + - - +
104A PHE* 3.0 10.3 + - - +
106A GLU* 1.3 78.2 - - - +
108A MET* 1.3 68.2 + - - +
110A ARG* 2.9 31.6 + - - +
111A GLN* 2.9 22.2 + - - +
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Residues in contact with MET 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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73A CYS* 4.2 9.2 - - - -
76A ALA* 3.8 17.9 - - + -
104A PHE* 2.8 49.5 + - + +
105A VAL* 3.8 7.4 - - - +
107A ALA* 1.3 70.6 - - - +
109A ILE* 1.3 66.3 + - + +
111A GLN* 2.9 12.1 + - - +
112A LEU* 2.8 21.3 + - - +
127A LEU* 4.1 22.5 - - + +
130A PHE* 3.5 36.1 - - + -
131A LEU* 3.8 35.7 - - + -
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Residues in contact with ILE 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 VAL* 3.3 18.5 + - + +
106A GLU* 4.8 2.7 - - - +
107A ALA 3.4 0.4 - - - -
108A MET* 1.3 74.7 - - + +
110A ARG* 1.3 53.0 + - - +
112A LEU* 3.0 10.8 + - + +
113A LYS* 2.6 42.6 + - + +
131A LEU* 3.4 31.9 - - + -
148A MET* 4.2 12.8 - - + -
268A LEU* 4.1 22.0 - - + -
269A PRO* 5.7 8.1 - - + -
271A PHE* 4.2 26.9 - - + -
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Residues in contact with ARG 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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69A LEU* 5.7 3.8 - - - +
103A GLU 5.2 1.0 + - - -
106A GLU* 3.2 34.2 + - - +
107A ALA* 2.9 37.9 + - - +
109A ILE* 1.3 78.4 - - - +
111A GLN* 1.3 62.6 + - - +
113A LYS* 3.2 13.3 + - + +
114A GLU* 3.1 27.2 + - + +
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Residues in contact with GLN 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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73A CYS* 4.3 20.7 - - + +
77A ARG* 3.5 38.7 + - - +
107A ALA 2.9 10.0 + - - +
108A MET* 2.9 15.6 + - - +
110A ARG* 1.3 72.4 - - - +
112A LEU* 1.3 58.3 + - - +
114A GLU* 2.8 33.7 + - - +
115A SER* 2.9 23.1 + - - +
123A GLU* 5.3 2.0 + - - -
127A LEU* 4.0 22.0 - - + -
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A MET 2.8 9.9 + - - +
109A ILE* 3.2 15.3 - - + +
111A GLN* 1.3 75.2 - - - +
113A LYS* 1.3 62.5 + - + +
114A GLU 3.3 0.3 + - - -
115A SER* 3.9 1.8 - - - -
116A LEU* 3.2 44.7 + - + +
124A ALA* 3.7 30.7 - - + +
127A LEU* 3.3 32.2 - - + +
128A VAL* 4.0 23.1 - - + -
131A LEU* 4.4 16.4 - - + -
148A MET* 5.3 10.1 - - + -
152A PHE* 5.3 4.0 - - + -
168A TRP* 5.4 0.7 - - + -
271A PHE* 5.2 8.5 - - + -
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Residues in contact with LYS 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 ILE* 2.6 25.1 + - + +
110A ARG* 3.3 17.3 - - + +
111A GLN 3.1 0.4 - - - -
112A LEU* 1.3 75.1 - - - +
114A GLU* 1.3 58.5 + - + +
116A LEU* 4.5 7.4 - - - +
117A LYS* 4.0 16.5 + - - +
271A PHE* 4.4 26.9 - - + -
272A THR 5.5 6.4 + - - +
274A PRO* 5.4 13.4 - - + +
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Residues in contact with GLU 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 ARG* 3.1 15.2 + - + +
111A GLN* 2.8 18.3 + - - +
113A LYS* 1.3 78.1 - - - +
115A SER* 1.3 65.6 + - - +
116A LEU 3.4 0.2 - - - -
117A LYS* 3.0 44.8 + - + +
118A ALA* 3.3 9.5 + - - +
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Residues in contact with SER 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 GLN* 2.9 23.6 + - - +
112A LEU* 3.7 11.0 - - - -
114A GLU* 1.3 77.9 - - - +
116A LEU* 1.3 61.9 + - - +
118A ALA* 3.2 6.5 + - - +
119A ASN 3.0 4.9 + - - -
120A ASN* 2.9 39.7 + - - +
123A GLU* 4.2 12.8 + - - +
124A ALA* 4.2 20.1 - - - -
127A LEU* 4.1 7.1 - - - +
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Residues in contact with LEU 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 LEU* 3.2 22.4 + - + +
113A LYS* 4.8 3.4 - - - +
115A SER* 1.3 79.3 - - - +
117A LYS* 1.3 58.7 + - - +
119A ASN* 3.0 16.7 + - - +
120A ASN 4.7 0.7 - - - +
121A TYR* 3.3 36.1 + - + +
124A ALA* 3.6 27.4 - - + -
152A PHE* 6.2 1.1 - - + -
168A TRP* 3.7 18.6 - - + -
169A TYR* 3.9 12.3 - - + +
271A PHE* 4.1 15.3 - - + -
274A PRO* 3.5 40.4 - - + -
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Residues in contact with LYS 117 (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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113A LYS 4.0 8.4 + - - +
114A GLU* 3.0 59.0 + - + +
116A LEU* 1.3 79.3 - - - +
118A ALA* 1.3 61.5 + - - +
119A ASN* 3.1 15.7 + - - +
274A PRO* 5.8 4.6 - - + +
279A ASP 4.9 2.1 - - - +
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Residues in contact with ALA 118 (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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114A GLU 3.8 8.3 - - - +
115A SER* 3.2 8.6 + - - +
117A LYS* 1.3 83.7 - - + +
119A ASN* 1.3 71.4 + - - +
120A ASN* 3.2 25.2 + - - +
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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