Contacts of the helix formed by residues 109 - 122 (chain A) in PDB entry 2OLM
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 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A ASP* 3.1 21.4 + - + +
107A PHE 4.5 0.2 - - - -
108A ARG* 1.3 78.1 - - - +
110A PRO* 1.3 63.8 - - - +
111A GLN* 3.1 20.6 + - - +
112A LYS* 3.2 28.6 + - + +
113A VAL* 3.0 32.0 + - - +
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Residues in contact with PRO 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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55A SER* 4.6 10.7 + - - +
107A PHE 5.7 0.2 - - - +
108A ARG 3.4 11.2 - - - +
109A ASP* 1.3 88.0 - - - +
111A GLN* 1.3 55.6 + - - +
113A VAL* 3.9 7.2 - - + +
114A LYS* 3.0 29.8 + - - +
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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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109A ASP* 3.1 13.7 + - - +
110A PRO* 1.3 77.3 - - - +
112A LYS* 1.3 67.2 + - + +
114A LYS* 3.5 7.6 + - - +
115A GLU* 3.2 22.3 + - - +
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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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105A PRO* 3.7 20.5 - - + +
106A ASP* 4.3 4.7 - - + +
109A ASP* 3.2 33.0 + - + +
110A PRO 3.3 0.4 - - - -
111A GLN* 1.3 78.8 - - + +
113A VAL* 1.3 65.5 + - - +
115A GLU* 3.3 9.5 + - + +
116A PHE* 3.0 24.3 + - - +
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Residues in contact with VAL 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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52A CYS* 5.2 7.6 - - - -
55A SER* 3.5 28.5 - - - +
105A PRO* 4.2 7.4 - - + -
106A ASP 3.9 1.6 - - - +
107A PHE* 3.6 54.7 - - + +
109A ASP 3.0 22.1 + - - +
110A PRO* 3.9 5.4 - - + +
111A GLN 3.3 0.2 - - - -
112A LYS* 1.3 74.3 - - - +
114A LYS* 1.3 65.1 + - - +
116A PHE* 3.1 3.2 + - + +
117A LEU* 2.9 32.5 + - + +
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Residues in contact with LYS 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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55A SER* 4.9 7.1 - - - +
58A GLY* 3.3 30.1 - - - +
59A LEU* 4.2 8.0 - - + +
110A PRO 3.0 19.9 + - - +
111A GLN* 3.6 7.2 - - - +
113A VAL* 1.3 76.7 - - - +
115A GLU* 1.3 56.8 + - - +
117A LEU* 3.2 10.2 + - - +
118A GLN* 2.6 63.1 + - + +
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Residues in contact with GLU 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 3.2 11.2 + - - +
112A LYS* 3.7 13.7 - - + +
113A VAL 3.3 0.2 - - - -
114A LYS* 1.3 79.2 - - - +
116A PHE* 1.3 56.6 + - - +
118A GLN* 3.4 16.1 + - - +
119A GLU* 3.0 34.8 + - + +
123A LYS* 5.5 0.5 + - - -
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Residues in contact with PHE 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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31A ASP 3.8 21.8 - - - -
94A LEU* 5.1 2.9 - - + -
97A PHE* 4.4 8.7 - + - -
103A ALA 3.6 13.5 - - - -
104A ILE* 4.3 11.9 - - + -
105A PRO* 3.5 31.4 - - + -
107A PHE* 4.1 8.5 - + - -
112A LYS 3.0 13.9 + - - +
113A VAL 3.4 7.6 - - - +
115A GLU* 1.3 74.6 - - - +
117A LEU* 1.3 72.5 + - + +
119A GLU* 3.1 8.7 + - - +
120A LYS* 2.9 51.9 + - + +
126A TRP* 3.5 31.6 - + - -
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Residues in contact with LEU 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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31A ASP* 3.8 36.8 - - + +
52A CYS* 4.5 2.2 - - - +
55A SER* 3.5 44.4 - - - +
56A LEU* 3.8 13.2 - - + +
59A LEU* 4.1 16.5 - - + +
107A PHE* 5.9 0.4 - - + -
113A VAL* 2.9 28.9 + - + +
114A LYS* 3.7 4.9 - - - +
116A PHE* 1.3 84.4 - - + +
118A GLN* 1.3 57.8 + - - +
120A LYS* 4.2 3.8 - - - -
121A TYR* 2.9 43.9 + - + +
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Residues in contact with GLN 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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59A LEU* 3.6 16.7 - - + +
60A ASN 5.7 0.7 + - - -
114A LYS* 2.6 50.4 + - - +
115A GLU* 3.5 16.9 - - - +
117A LEU* 1.3 77.2 - - - +
119A GLU* 1.3 57.2 + - - +
122A GLU* 2.9 35.7 + - + +
123A LYS* 2.8 47.1 + - - +
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Residues in contact with GLU 119 (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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103A ALA* 5.5 0.7 - - - +
115A GLU* 3.0 18.8 + - - +
116A PHE* 3.1 10.1 + - - +
118A GLN* 1.3 75.5 - - - +
120A LYS* 1.3 58.1 + - - +
123A LYS* 3.7 29.3 + - + +
124A LYS 2.9 8.7 + - - -
125A ARG* 2.8 69.4 + - + -
126A TRP* 4.0 15.6 - - + -
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Residues in contact with LYS 120 (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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30A PHE* 3.1 40.4 + - - -
31A ASP* 2.7 31.1 + - - +
93A TRP* 3.5 25.4 - - + +
94A LEU* 3.7 29.2 - - + +
116A PHE* 2.9 30.6 + - + +
117A LEU* 3.7 5.2 - - + +
119A GLU* 1.3 78.4 - - - +
121A TYR* 1.3 86.0 + - + +
124A LYS* 3.7 4.0 - - - -
126A TRP* 3.9 9.8 - - + -
1006A UNX 2.7 23.5 - - - -
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Residues in contact with TYR 121 (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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30A PHE* 3.3 19.9 - - - -
31A ASP* 2.6 31.9 + - - -
41A ASN* 4.9 0.9 + - - -
44A VAL* 4.0 19.0 - - + +
46A SER* 4.9 0.3 + - - -
56A LEU* 4.0 14.1 - - + -
59A LEU* 4.5 3.1 - - + -
63A HIS* 3.6 30.7 - + + +
93A TRP* 3.6 57.8 - + + -
117A LEU* 2.9 35.4 + - + +
120A LYS* 1.3 90.4 - - + +
122A GLU* 1.3 68.7 + - + +
124A LYS* 3.8 10.7 - - - -
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Residues in contact with GLU 122 (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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59A LEU* 3.8 16.3 - - + +
60A ASN 3.4 34.0 + - - +
61A PRO* 4.7 2.6 - - + +
63A HIS* 6.1 0.9 - - - +
117A LEU 4.9 0.2 - - - +
118A GLN* 2.9 40.7 + - + +
121A TYR* 1.3 84.7 - - + +
123A LYS* 1.3 68.7 + - + +
124A LYS* 3.3 9.9 + - - +
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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