Contacts of the helix formed by residues 94 - 109 (chain A) in PDB entry 2P1Q
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 ASP 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A LYS* 5.7 0.5 + - - -
93A ILE* 1.3 77.4 - - - +
95A GLN* 1.3 59.7 + - - +
96A ALA* 4.2 8.1 - - - +
97A THR* 2.8 37.7 + - - -
98A LEU* 2.9 24.6 + - - +
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Residues in contact with GLN 95 (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 ASP* 1.3 74.3 - - - +
96A ALA* 1.3 64.2 + - - +
98A LEU* 3.2 9.3 + - - +
99A PHE* 3.0 65.2 + - + -
124A MET* 3.8 18.3 - - + +
136A THR* 2.5 34.9 + - - +
137A PHE* 3.9 2.4 - - - -
138A ASN* 4.2 9.5 + - - -
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Residues in contact with ALA 96 (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 LYS* 6.2 0.9 - - - +
94A ASP* 3.4 9.0 + - - +
95A GLN* 1.3 78.8 - - - +
97A THR* 1.4 58.5 + - - +
99A PHE* 3.1 8.9 + - - +
100A GLU* 2.9 32.0 + - - +
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Residues in contact with THR 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 LYS* 3.2 36.0 + - - +
51A ILE* 4.5 8.0 - - + +
54A LYS* 4.7 10.5 - - + -
93A ILE* 3.9 29.2 - - + -
94A ASP* 2.8 32.0 + - - -
96A ALA* 1.4 71.5 - - - +
98A LEU* 1.3 62.2 + - - +
100A GLU* 3.3 8.2 + - - +
101A LEU* 2.9 22.6 + - + +
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Residues in contact with LEU 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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91A MET* 4.2 26.2 - - - +
93A ILE* 3.7 18.8 - - + +
94A ASP 2.9 13.9 + - - +
95A GLN* 3.3 10.8 - - - +
97A THR* 1.3 78.8 - - - +
99A PHE* 1.3 65.8 + - + +
101A LEU* 3.1 4.0 + - - +
102A ILE* 3.0 50.4 + - + +
117A THR* 4.6 5.2 - - + +
120A THR* 4.4 17.7 - - + -
121A VAL* 4.0 11.7 - - + -
124A MET* 3.9 29.2 - - + -
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Residues in contact with PHE 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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95A GLN* 3.0 52.3 + - + -
96A ALA* 3.6 10.5 - - - +
98A LEU* 1.3 92.6 - - + +
100A GLU* 1.3 66.0 + - - +
102A ILE* 3.9 7.6 - - + +
103A LEU* 3.3 30.5 + - + +
121A VAL* 4.7 4.9 - - + -
124A MET* 4.7 4.7 - - + -
137A PHE* 4.3 30.5 - + - -
9B PHE* 3.7 32.8 - + + -
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Residues in contact with GLU 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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48A THR* 3.3 34.8 + - - +
50A LYS* 5.1 5.2 + - - -
51A ILE* 3.4 31.8 - - + +
96A ALA* 2.9 17.1 + - - +
97A THR* 3.8 2.2 - - - +
99A PHE* 1.3 77.3 - - - +
101A LEU* 1.3 56.5 + - - +
103A LEU* 3.3 10.8 + - + +
104A ALA* 3.0 27.9 + - - +
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Residues in contact with LEU 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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51A ILE* 4.0 10.7 - - + +
54A LYS* 4.0 22.2 - - + -
55A VAL* 3.8 28.7 - - + +
90A PHE* 4.1 10.8 - - + -
91A MET* 3.5 31.9 - - + -
93A ILE* 3.8 12.1 - - + -
97A THR* 2.9 15.3 + - + +
98A LEU* 3.1 9.4 + - - +
100A GLU* 1.3 75.8 - - - +
102A ILE* 1.3 59.9 - - - +
104A ALA* 3.3 1.2 + - - +
105A ALA* 2.9 29.2 + - - +
113A LEU* 4.1 11.2 - - + -
117A THR* 3.8 13.7 - - + -
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Residues in contact with ILE 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 LEU* 3.0 30.5 + - + +
99A PHE* 3.9 12.8 - - - +
101A LEU* 1.3 67.9 - - - +
103A LEU* 1.3 66.9 + - - +
105A ALA* 3.3 2.2 + - - +
106A ASN* 2.9 25.9 + - - +
114A LEU* 3.9 4.6 - - + +
117A THR* 3.5 34.1 - - - +
118A CYS* 3.9 16.6 - - - -
121A VAL* 3.5 30.3 - - + -
9B PHE* 4.2 13.9 - - + -
13B VAL* 3.8 26.9 - - + -
17B VAL* 5.6 0.9 - - + -
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Residues in contact with LEU 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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46A ASN 6.0 1.1 - - - +
99A PHE* 3.3 20.8 + - + +
100A GLU* 3.7 8.3 - - + +
101A LEU 3.3 0.6 - - - -
102A ILE* 1.3 79.1 - - - +
104A ALA* 1.3 56.8 + - - +
106A ASN* 3.5 4.9 + - - +
107A TYR* 2.8 31.6 + - - +
9B PHE* 3.8 18.6 - - + -
10B PRO* 3.4 36.6 - - + -
13B VAL* 4.9 3.4 - - + -
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Residues in contact with ALA 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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46A ASN 5.4 3.1 + - - +
47A VAL* 4.3 19.7 - - + -
51A ILE* 3.5 32.1 - - + -
55A VAL* 4.1 12.6 - - + -
100A GLU 3.0 8.1 + - - +
101A LEU 3.6 3.4 - - - +
102A ILE 3.2 0.2 - - - -
103A LEU* 1.3 75.1 - - - +
105A ALA* 1.3 56.6 + - - +
107A TYR* 4.3 5.4 - - - -
108A LEU* 2.7 42.9 + - + +
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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 LEU 2.9 17.0 + - - +
102A ILE* 3.7 6.3 - - - +
104A ALA* 1.3 75.4 - - - +
106A ASN* 1.3 53.4 + - - +
109A ASN* 2.8 27.7 + - - -
110A ILE* 3.0 17.8 + - - +
113A LEU* 3.7 34.9 - - + +
114A LEU* 3.9 25.0 - - + +
117A THR* 4.5 0.9 - - - +
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Residues in contact with ASN 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 ILE 2.9 16.1 + - - +
103A LEU* 3.6 5.5 + - - +
105A ALA* 1.3 73.8 - - - +
107A TYR* 1.3 65.8 - - - +
109A ASN* 3.2 15.9 + - - +
114A LEU* 4.1 20.3 - - + +
10B PRO* 4.1 10.7 - - - +
12B GLU* 2.9 37.6 + - - +
13B VAL* 3.3 30.6 + - + +
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Residues in contact with TYR 107 (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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28A THR* 2.8 35.0 + - + +
32A MET* 4.7 6.9 - - + +
43A PRO 4.5 0.5 + - - -
44A LEU* 3.7 13.4 - - + +
45A PRO* 3.3 30.4 - - + +
46A ASN* 3.3 41.1 - - + +
47A VAL* 3.1 36.6 - - + -
103A LEU 2.8 22.4 + - - +
104A ALA* 3.7 2.5 - - - +
106A ASN* 1.3 75.4 - - - +
108A LEU* 1.3 67.1 + - + +
109A ASN* 4.8 0.2 - - - +
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Residues in contact with LEU 108 (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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26A SER* 2.5 32.9 + - - +
28A THR* 3.2 14.3 + - - -
29A ILE* 4.1 11.7 - - + -
44A LEU* 3.9 22.9 - - + -
47A VAL* 4.2 10.3 - - + -
52A LEU* 4.5 11.0 - - + -
55A VAL* 4.0 21.5 - - + -
104A ALA 2.7 22.5 + - - +
107A TYR* 1.3 95.0 - - + +
109A ASN* 1.3 70.5 + - - +
110A ILE* 3.7 25.6 - - + -
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Residues in contact with ASN 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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25A GLU 3.9 0.9 - - - +
27A GLN* 3.1 63.4 + - + +
28A THR* 3.7 9.6 - - - +
105A ALA 2.8 10.8 + - - -
106A ASN* 3.2 11.6 + - - +
107A TYR 3.3 0.2 - - - -
108A LEU* 1.3 79.2 - - - +
110A ILE* 1.3 57.2 + - - +
111A LYS* 3.8 7.6 + - - +
114A LEU* 5.5 7.0 - - - +
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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