Contacts of the helix formed by residues 110 - 126 (chain D) in PDB entry 2P1N
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 ILE 110 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25D GLU* 3.8 17.9 - - + +
26D SER* 3.7 26.2 - - - -
55D VAL* 4.1 16.8 - - + -
58D TYR* 4.6 3.1 - - + -
59D CYS* 4.0 29.8 - - - -
105D ALA* 3.1 17.9 + - - +
108D LEU* 3.7 17.0 - - + -
109D ASN* 1.3 75.1 - - - +
111D LYS* 1.3 64.8 + - - +
112D ASN* 4.5 8.1 - - - +
113D LEU* 3.1 24.0 + - + +
114D LEU* 2.9 23.7 + - - +
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Residues in contact with LYS 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D GLU 5.0 0.8 + - - -
27D GLN* 5.5 2.4 + - - +
109D ASN 3.8 4.8 + - - -
110D ILE* 1.3 71.6 - - - +
112D ASN* 1.4 59.3 + - - +
114D LEU* 3.1 10.8 + - + +
115D ASP* 2.8 65.4 + - - +
16E HIS* 5.4 5.4 - - + -
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Residues in contact with ASN 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D GLU* 4.6 16.4 - - - +
58D TYR* 2.6 33.2 + - - +
62D HIS* 3.9 22.9 - - + +
110D ILE* 4.5 5.4 - - - +
111D LYS* 1.4 79.8 + - - +
113D LEU* 1.3 55.8 + - - +
115D ASP* 3.2 9.7 + - - +
116D LEU* 2.9 27.9 + - - +
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Residues in contact with LEU 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D VAL* 3.7 34.8 - - + -
58D TYR* 3.2 43.9 + - + -
90D PHE* 4.4 8.1 - - + -
101D LEU* 4.2 16.2 - - + -
105D ALA* 3.3 26.7 - - + +
110D ILE* 3.1 20.6 + - + +
112D ASN* 1.3 76.0 - - - +
114D LEU* 1.3 55.5 + - - +
116D LEU* 3.5 4.1 + - + +
117D THR* 2.8 50.8 + - + +
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Residues in contact with LEU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ILE* 4.4 8.1 - - + +
105D ALA* 3.8 6.9 - - + +
106D ASN* 4.2 44.2 - - + +
109D ASN* 6.2 1.3 - - - -
110D ILE 2.9 12.4 + - - +
111D LYS* 3.3 16.6 - - + +
113D LEU* 1.3 72.7 - - - +
115D ASP* 1.3 57.3 + - - +
117D THR* 3.3 6.1 + - - +
118D CYS* 2.7 58.2 + - - +
13E VAL* 4.7 6.7 - - + -
16E HIS* 4.4 22.2 - - + +
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Residues in contact with ASP 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D LYS* 2.8 46.7 + - - +
112D ASN* 3.2 11.0 + - - +
114D LEU* 1.3 68.1 - - - +
116D LEU* 1.3 62.5 + - - +
118D CYS* 2.9 10.0 + - - -
119D GLN* 2.6 38.9 + - - +
16E HIS* 2.8 32.6 + - - -
20E PHE* 4.3 7.4 - - + -
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Residues in contact with LEU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D TYR* 4.2 14.4 - - + +
87D ASP* 3.3 44.6 - - + +
90D PHE* 4.3 8.1 - - + -
91D MET* 3.7 25.8 - - + -
112D ASN 2.9 18.2 + - - +
113D LEU* 4.0 5.8 - - + +
115D ASP* 1.3 73.7 - - - +
117D THR* 1.3 61.6 + - + +
119D GLN* 3.7 13.0 + - + +
120D THR* 2.7 38.8 + - - +
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Residues in contact with THR 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D MET* 4.2 9.9 - - - -
98D LEU* 4.3 5.5 - - + +
101D LEU* 3.6 38.8 - - + -
102D ILE* 3.5 38.0 - - - +
105D ALA* 4.5 1.0 - - - +
113D LEU* 2.8 34.5 + - + +
114D LEU* 3.3 9.9 + - - +
116D LEU* 1.3 74.2 - - - +
118D CYS* 1.3 64.1 + - - +
120D THR* 3.6 6.0 - - - -
121D VAL* 3.2 18.5 + - - +
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Residues in contact with CYS 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ILE* 4.0 10.1 - - - -
114D LEU* 2.7 39.3 + - - +
115D ASP 2.9 0.8 + - - -
117D THR* 1.3 69.4 + - - +
119D GLN* 1.3 65.9 + - - +
120D THR 3.0 2.3 + - - -
121D VAL* 3.1 4.2 + - - +
122D ALA* 2.9 22.2 + - - +
13E VAL* 4.4 5.6 - - - -
16E HIS* 3.3 38.8 - - + -
17E VAL* 3.8 28.4 - - + +
20E PHE* 3.8 9.4 - - + -
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Residues in contact with GLN 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D ASP* 2.6 40.9 + - - +
116D LEU* 3.8 12.6 + - + +
118D CYS* 1.3 70.4 - - - +
120D THR* 1.3 53.9 + - - +
122D ALA* 3.3 2.3 + - - +
123D ASP* 2.8 45.5 + - - +
20E PHE* 3.5 45.5 - - + -
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Residues in contact with THR 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D MET* 4.0 17.6 - - + +
98D LEU* 3.9 26.9 - - + -
116D LEU* 2.7 34.3 + - - +
117D THR* 3.6 7.9 - - - -
118D CYS 3.0 0.8 - - - -
119D GLN* 1.3 78.9 - - - +
121D VAL* 1.3 63.8 + - - +
123D ASP* 3.2 19.5 + - - +
124D MET* 3.3 15.8 + - + +
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Residues in contact with VAL 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D LEU* 4.2 19.5 - - + -
99D PHE* 4.8 8.7 - - + -
102D ILE* 3.7 19.5 - - + -
117D THR 3.2 13.0 + - - +
118D CYS 3.1 6.8 + - - +
120D THR* 1.3 72.9 - - - +
122D ALA* 1.3 58.2 + - - +
124D MET* 2.7 38.3 + - + +
125D ILE* 3.1 7.8 + - + +
137D PHE* 3.6 31.0 - - + -
9E PHE* 4.8 6.5 - - + -
17E VAL* 4.0 23.3 - - + -
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Residues in contact with ALA 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D CYS 2.9 11.4 + - - +
119D GLN 3.5 7.6 - - - +
121D VAL* 1.3 70.0 - - - +
123D ASP* 1.3 56.8 + - - +
124D MET 2.6 5.2 + - - -
125D ILE* 2.3 32.4 + - - +
126D LYS* 3.1 12.2 + - + +
17E VAL* 3.7 12.7 - - + +
20E PHE* 3.8 23.8 - - + +
21E ILE* 3.5 28.9 - - + -
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Residues in contact with ASP 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D GLN* 2.8 27.7 + - - +
120D THR* 3.4 14.3 - - - +
121D VAL 3.2 0.4 - - - -
122D ALA* 1.3 72.7 - - - +
124D MET* 1.3 58.8 + - - +
125D ILE 3.2 0.2 - - - -
126D LYS* 3.1 43.0 + - - +
128D LYS* 5.8 0.9 + - - -
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Residues in contact with MET 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D GLN* 3.9 23.3 - - - +
98D LEU* 4.0 26.9 - - - -
99D PHE* 4.2 13.5 - - + -
120D THR* 3.6 11.7 - - + +
121D VAL* 2.7 19.5 + - - +
122D ALA 2.7 0.6 - - - -
123D ASP* 1.3 82.4 - - - +
125D ILE* 1.3 60.3 + - - +
126D LYS 5.1 0.2 - - - -
128D LYS* 3.1 32.4 - - - +
133D ILE* 5.4 0.2 - - - +
136D THR* 4.8 12.5 + - + +
137D PHE* 3.8 30.1 - - + -
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Residues in contact with ILE 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D VAL* 3.5 24.0 - - + +
122D ALA* 2.3 26.9 + - - +
124D MET* 1.3 73.4 - - - +
126D LYS* 1.3 63.8 + - - +
127D GLY 3.4 0.2 + - - -
128D LYS* 3.1 23.0 + - - +
133D ILE* 3.6 23.8 - - + +
137D PHE* 3.7 29.8 - - + -
17E VAL* 4.2 13.2 - - + -
18E PHE* 5.1 2.9 - - + -
21E ILE* 4.6 9.2 - - + -
26E ASP* 5.4 2.5 - - + +
29E SER* 5.8 1.4 - - - -
30E VAL* 3.6 29.8 - - + -
37E TRP* 4.2 15.0 - - + -
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Residues in contact with LYS 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D ALA* 3.1 13.8 + - - +
123D ASP* 3.1 38.0 + - - +
124D MET 3.6 1.0 - - - +
125D ILE* 1.3 76.7 - - - +
127D GLY* 1.3 60.1 + - - +
128D LYS* 3.7 7.4 + - - +
20E PHE* 3.6 23.6 + - - +
21E ILE* 4.4 13.7 - - + -
22E GLN 5.8 0.4 - - - +
23E LEU* 5.8 2.7 - - + -
26E ASP* 3.6 27.8 - - - +
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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