Contacts of the helix formed by residues 93 - 114 (chain A) in PDB entry 2N23
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 93 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A MET* 3.6 7.2 - - - +
91A PHE* 4.1 0.9 - - - +
92A ASN* 1.3 85.4 + - - +
94A ARG* 1.3 62.0 + - - +
95A THR* 3.0 19.3 + - - +
96A VAL* 2.8 45.8 + - + +
97A MET* 3.0 28.6 + - - +
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Residues in contact with ARG 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A THR* 4.3 8.3 + - - -
52A PRO 4.7 1.8 + - - -
53A ALA* 4.3 12.0 + - - +
55A SER 2.7 29.3 + - - -
56A GLU* 3.0 27.9 + - - +
57A LYS 3.7 12.1 + - - -
58A MET* 4.2 15.5 - - + +
93A ASN* 1.3 71.6 - - - +
95A THR* 1.3 61.0 + - - +
97A MET* 3.2 20.4 + - - +
98A ASP* 2.8 31.9 + - - +
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Residues in contact with THR 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ASN* 3.0 16.2 + - - +
94A ARG* 1.3 75.2 - - - +
96A VAL* 1.3 63.8 + - + +
98A ASP* 3.9 3.8 - - - +
99A ASN* 2.8 47.1 + - - +
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Residues in contact with VAL 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER 4.7 3.8 - - - +
5A GLY* 3.8 21.5 - - - -
6A ALA 4.6 4.5 - - - +
91A PHE* 3.1 42.6 - - + -
93A ASN* 2.8 36.5 + - + +
95A THR* 1.3 74.1 - - + +
97A MET* 1.3 54.1 + - - +
99A ASN* 3.1 5.3 + - - +
100A ILE* 2.7 45.3 + - + +
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Residues in contact with MET 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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50A ALA* 3.6 19.5 - - + -
51A THR* 3.3 16.8 - - - +
58A MET* 3.2 40.4 - - + -
59A MET 3.2 25.6 - - - +
60A LEU* 3.6 18.3 - - + +
91A PHE* 4.3 5.8 - - + -
93A ASN 3.0 18.6 + - - +
94A ARG* 3.3 26.9 - - - +
96A VAL* 1.3 76.6 - - - +
98A ASP* 1.3 52.9 + - - +
101A LYS* 2.6 50.8 + - - +
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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
----------------------------------------------------------
94A ARG 2.8 19.1 + - - +
95A THR* 3.9 4.9 - - - +
97A MET* 1.3 73.9 - - - +
99A ASN* 1.3 59.3 + - - +
101A LYS* 3.3 26.6 + - - +
102A MET* 2.9 60.8 + - - +
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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
----------------------------------------------------------
1A PRO* 4.8 7.8 - - - +
2A SER* 3.6 33.4 + - - -
4A SER 5.4 0.7 - - - +
95A THR* 2.8 44.3 + - - +
96A VAL* 3.6 5.6 - - - +
98A ASP* 1.3 76.9 + - - +
100A ILE* 1.3 55.5 + - + +
102A MET* 3.3 18.7 + - - +
103A THR* 2.6 42.7 + - - -
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Residues in contact with ILE 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A HIS* 3.9 6.5 - - - +
4A SER* 3.5 40.6 - - - +
16A ILE* 3.5 24.7 - - + -
18A ILE* 4.2 2.7 - - + -
60A LEU* 3.8 13.9 - - + -
91A PHE* 3.8 12.3 - - + -
96A VAL* 2.7 39.8 + - + +
97A MET 3.9 2.2 - - - +
99A ASN* 1.3 68.8 - - + +
101A LYS* 1.3 67.5 + - - +
103A THR* 4.2 0.7 - - - -
104A LEU* 2.8 55.7 + - + +
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Residues in contact with LYS 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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48A LEU* 3.6 8.0 - - + +
50A ALA* 3.3 34.3 - - + +
51A THR 5.2 4.0 + - - -
60A LEU* 3.4 14.5 - - + +
97A MET* 2.6 29.9 + - - +
98A ASP* 3.3 37.7 + - - +
100A ILE* 1.3 73.1 - - - +
102A MET* 1.3 59.5 + - + +
105A GLN* 2.9 34.2 + - - +
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Residues in contact with MET 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 44.6 + - - +
99A ASN* 3.6 22.4 - - - +
101A LYS* 1.3 71.4 - - + +
103A THR* 1.3 60.7 + - - +
105A GLN* 4.2 5.6 - - - +
106A GLN* 2.8 45.3 + - + +
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Residues in contact with THR 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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2A SER* 2.9 24.7 + - - +
3A HIS* 3.7 33.8 - - + +
18A ILE* 3.8 23.1 - - + -
99A ASN 2.6 28.1 + - - -
100A ILE* 4.2 1.3 - - - -
102A MET* 1.3 73.9 - - - +
104A LEU* 1.3 67.5 + - - +
106A GLN* 4.2 2.1 - - - +
107A ILE* 3.0 34.7 + - + +
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Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 3.2 36.3 - - + -
27A LEU* 3.8 10.3 - - + -
42A LEU* 4.7 11.9 - - + -
48A LEU* 3.8 13.7 - - + -
60A LEU* 4.5 10.3 - - + -
61A ARG 4.6 5.6 - - - +
62A LEU* 3.6 27.4 - - + -
100A ILE* 2.8 44.3 + - + +
103A THR* 1.3 76.4 - - - +
105A GLN* 1.3 66.8 + - - +
106A GLN 3.3 0.2 + - - -
107A ILE* 3.9 0.7 - - - +
108A ILE* 2.9 37.2 + - + +
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Residues in contact with GLN 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LYS* 4.9 10.5 + - - +
48A LEU* 3.4 28.4 - - + +
101A LYS 2.9 21.7 + - - +
102A MET* 3.6 6.3 - - - +
104A LEU* 1.3 77.5 - - - +
106A GLN* 1.3 70.8 + - - +
108A ILE* 3.5 2.3 - - - +
109A SER* 2.7 65.5 + - - -
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Residues in contact with GLN 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 MET* 2.8 32.8 + - + +
103A THR* 4.2 2.7 - - - +
105A GLN* 1.3 89.1 + - + +
107A ILE* 1.3 55.9 + - - +
109A SER* 3.1 8.5 + - - -
110A ARG* 2.7 58.5 + - - +
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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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18A ILE* 3.5 27.1 - - + -
20A GLU* 3.4 29.6 - - - +
25A ALA* 3.5 22.4 - - + -
42A LEU* 3.7 9.2 - - + -
103A THR* 3.0 24.7 + - + +
106A GLN* 1.3 74.0 - - - +
108A ILE* 1.3 63.9 + - - +
110A ARG* 3.0 43.8 + - - +
111A TYR* 3.1 34.0 - - + +
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Residues in contact with ILE 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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42A LEU* 3.8 24.2 - - + +
45A ILE* 3.5 33.7 - - + +
46A ASP 4.1 6.5 - - - +
47A LYS* 3.9 2.7 - - + +
48A LEU* 3.8 30.3 - - + -
62A LEU* 4.4 1.1 - - + -
104A LEU* 2.9 25.9 + - + +
105A GLN 3.5 4.7 - - - +
107A ILE* 1.3 75.6 - - - +
109A SER* 1.3 59.2 + - - +
111A TYR* 3.0 28.4 + - - +
112A LYS* 3.2 44.2 + - + +
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Residues in contact with SER 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 GLN* 2.7 40.1 + - - -
106A GLN* 3.5 9.9 - - - -
108A ILE* 1.3 72.9 - - - +
110A ARG* 1.3 55.6 - - - +
111A TYR 3.1 2.0 - - - -
112A LYS* 3.4 16.0 - - - +
113A ASP* 2.7 37.3 + - - +
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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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20A GLU* 2.8 33.3 + - - -
106A GLN* 2.7 41.9 + - + +
107A ILE* 3.0 34.1 + - + +
109A SER* 1.3 73.4 - - - +
111A TYR* 1.3 63.8 + - + +
112A LYS 3.3 0.2 - - - -
113A ASP* 5.0 2.0 - - - -
114A ALA* 2.9 28.3 + - - +
115A ASP* 4.0 9.2 + - - +
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Residues in contact with TYR 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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24A PRO* 3.2 18.3 - - + +
25A ALA* 2.7 27.7 + - - +
42A LEU* 3.8 29.8 - - + -
43A SER* 3.9 18.6 - - - +
65A LYS* 6.1 2.2 - - - +
107A ILE* 3.1 40.5 - - + +
108A ILE* 3.0 9.3 + - - +
110A ARG* 1.3 83.3 - - + +
112A LYS* 1.3 63.0 - - + +
114A ALA* 4.1 9.6 - - - +
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Residues in contact with LYS 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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45A ILE 3.3 19.4 + - - -
46A ASP* 2.9 35.8 + - - +
65A LYS* 4.6 7.5 - - - +
108A ILE* 3.2 32.7 + - + +
109A SER* 3.0 16.8 + - - +
111A TYR* 1.3 82.8 - - - +
113A ASP* 1.3 62.2 + - - +
114A ALA* 3.3 3.0 - - - +
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Residues in contact with ASP 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A SER* 2.7 17.5 + - - +
110A ARG* 5.0 1.8 - - - -
112A LYS* 1.3 72.6 - - - +
114A ALA* 1.3 69.8 + - - +
115A ASP* 3.2 29.2 + - - +
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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 ARG 2.9 22.3 + - - +
111A TYR* 4.2 12.6 - - - +
112A LYS 4.3 2.9 - - - +
113A ASP* 1.3 80.8 - - - +
115A ASP* 1.3 58.6 + - - +
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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
------------------------------------------------------------
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