Contacts of the helix formed by residues 99 - 112 (chain A) in PDB entry 2R2J
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 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ILE* 3.6 9.4 - - - -
97A GLN* 2.7 34.0 + - - -
98A ARG* 1.3 76.7 - - - +
100A VAL* 1.3 64.1 + - - +
101A LYS* 3.7 7.3 - - - +
102A ALA* 3.2 14.6 + - - +
103A LEU* 3.0 24.4 + - - +
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Residues in contact with VAL 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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37A PRO 5.0 0.2 - - - +
38A ILE* 3.5 27.9 - - + +
41A GLU* 3.5 50.9 - - + +
42A ALA* 3.8 18.0 - - - +
45A VAL* 4.7 10.3 - - + -
99A SER* 1.3 71.8 - - - +
101A LYS* 1.3 58.6 + - - +
103A LEU* 3.3 4.4 + - - +
104A ALA* 2.9 28.9 + - + +
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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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97A GLN* 4.4 7.6 - - - +
99A SER* 3.7 11.0 - - - +
100A VAL* 1.3 74.8 - - - +
102A ALA* 1.3 84.2 + - + +
103A LEU 3.0 0.3 + - - -
104A ALA* 3.0 4.4 + - - +
105A ASP* 2.8 49.8 + - - +
108A ARG* 5.5 2.6 - - - +
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Residues in contact with ALA 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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94A TYR* 3.2 22.5 + - + +
97A GLN* 3.3 27.6 - - + +
99A SER* 3.2 13.2 + - - +
101A LYS* 1.3 86.6 - - + +
103A LEU* 1.3 56.7 + - - +
105A ASP* 3.7 5.4 - - - +
106A TYR* 2.9 29.6 + - - +
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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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21A LEU* 4.4 18.4 - - + -
35A LEU* 5.0 7.9 - - + -
38A ILE* 4.5 9.2 - - + -
39A PHE* 4.1 32.8 - - + +
42A ALA* 4.0 19.5 - - + -
58A PHE* 4.8 0.2 - - + -
81A LEU* 5.0 3.6 - - + -
94A TYR* 3.3 43.7 - - + -
97A GLN 5.0 0.7 - - - +
98A ARG* 5.8 0.9 - - - -
99A SER 3.0 15.7 + - - +
100A VAL* 3.5 8.3 - - - +
102A ALA* 1.3 78.7 - - - +
104A ALA* 1.3 57.5 + - - +
106A TYR* 3.1 5.7 + - + +
107A ILE* 3.0 34.4 + - + +
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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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42A ALA* 4.6 7.2 - - + -
45A VAL* 4.1 16.6 - - + -
46A ILE* 3.5 27.4 - - + +
100A VAL* 2.9 18.5 + - + +
101A LYS* 4.0 2.2 - - - +
103A LEU* 1.3 76.6 - - - +
105A ASP* 1.3 58.2 + - - +
107A ILE* 3.6 0.6 + - - +
108A ARG* 3.0 49.4 + - - +
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Residues in contact with ASP 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 LYS* 2.8 52.7 + - - +
102A ALA* 3.7 5.6 - - - +
104A ALA* 1.3 73.2 - - - +
106A TYR* 1.3 67.4 + - - +
108A ARG* 3.1 27.1 + - - +
109A GLN* 2.8 24.0 + - - +
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Residues in contact with TYR 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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21A LEU* 4.2 17.4 - - + +
83A LEU* 3.8 23.0 - - + +
92A ARG* 4.6 4.2 + - - +
93A GLU 4.3 4.8 - - - -
94A TYR* 3.5 57.5 + + + -
102A ALA 2.9 14.9 + - - +
103A LEU* 3.1 12.3 + - + +
105A ASP* 1.3 73.6 - - - +
107A ILE* 1.3 74.1 + - + +
109A GLN* 2.8 30.2 + - + +
110A GLN* 2.8 42.7 + - + +
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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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19A VAL* 5.3 8.9 - - + +
21A LEU* 3.3 29.6 - - + -
46A ILE* 3.8 32.8 - - + -
49A GLU* 5.9 1.1 - - - +
56A VAL* 4.0 20.2 - - + -
58A PHE* 3.3 35.0 - - + -
83A LEU* 5.3 2.0 - - + -
103A LEU* 3.0 18.9 + - + +
104A ALA 4.0 2.7 - - - +
106A TYR* 1.3 89.6 - - + +
108A ARG* 1.3 53.1 + - - +
110A GLN* 3.1 6.8 + - + +
111A LYS* 2.7 35.9 + - + +
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Residues in contact with ARG 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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45A VAL* 3.8 25.7 - - - +
46A ILE* 4.3 5.6 - - + -
48A GLU* 3.3 28.7 + - - +
49A GLU* 6.2 0.2 - - - -
101A LYS* 4.4 3.2 + - - +
104A ALA* 3.0 26.5 + - - +
105A ASP* 3.1 52.1 + - - +
107A ILE* 1.3 75.6 - - - +
109A GLN* 1.3 63.3 + - - +
111A LYS* 3.2 7.5 + - - +
112A SER* 3.0 23.3 + - - -
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Residues in contact with GLN 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 ASP 2.8 15.2 + - - +
106A TYR* 2.8 17.4 + - + +
108A ARG* 1.3 72.3 - - - +
110A GLN* 1.3 65.4 + - - +
112A SER* 2.7 42.0 + - - -
113A ASP* 5.0 3.1 - - - +
157A HIS* 3.3 31.7 + - - -
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Residues in contact with GLN 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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19A VAL* 5.3 6.1 - - + -
83A LEU* 3.5 31.1 - - + +
85A ARG* 2.9 46.6 + - - +
90A MSE 5.3 2.8 - - - +
106A TYR* 2.8 41.7 + - + +
107A ILE* 3.6 10.1 - - - +
109A GLN* 1.3 84.0 - - - +
111A LYS* 1.3 58.4 + - - +
112A SER 3.5 1.0 + - - +
154A ASN* 4.2 6.8 - - - +
157A HIS* 2.8 36.2 + - - -
158A ASP* 5.2 1.0 + - - -
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Residues in contact with LYS 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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18A ASP* 4.5 12.0 + - - +
19A VAL* 3.6 26.5 - - + -
49A GLU* 4.2 18.4 - - + +
55A GLN* 3.9 24.2 - - - +
56A VAL* 3.6 23.8 - - + -
85A ARG* 5.4 0.2 - - - +
107A ILE* 2.7 21.2 + - + +
108A ARG* 3.2 6.5 + - - +
110A GLN* 1.3 71.4 - - - +
112A SER* 1.3 66.8 + - - +
154A ASN* 5.7 0.2 - - - -
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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 ARG 3.0 10.8 + - - -
109A GLN* 2.7 38.2 + - - -
110A GLN 3.3 1.4 - - - +
111A LYS* 1.3 83.0 - - - +
113A ASP* 1.3 82.8 + - - +
114A PRO* 3.1 13.7 - - - +
154A ASN* 4.4 4.7 - - - +
157A HIS* 5.9 0.2 - - - -
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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