Contacts of the helix formed by residues 106 - 118 (chain A) in PDB entry 2HXO
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 TRP 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A VAL* 4.2 10.8 - - + -
28A LEU* 3.3 70.1 - - + +
29A ASP* 2.6 26.4 + - - -
32A GLY* 5.5 1.1 - - - -
33A GLU* 5.3 7.0 - - + +
63A LEU 4.9 0.2 - - - -
66A ALA* 3.9 22.9 - - + -
67A THR* 3.7 23.8 - - - -
70A VAL* 4.2 3.4 - - + -
104A HIS* 3.4 30.4 - + + +
105A PRO* 1.3 81.9 - - + +
107A LEU* 1.3 90.6 + - + +
108A ALA 3.3 0.2 - - - -
109A THR* 3.2 18.1 + - - +
110A GLN* 3.3 23.8 + - + +
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Residues in contact with LEU 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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67A THR* 3.6 39.9 - - + +
70A VAL* 3.8 14.1 - - + -
71A VAL* 4.2 10.3 - - + -
97A LEU* 5.6 1.3 - - + -
100A ALA* 3.6 33.0 - - + -
101A THR* 3.7 19.7 - - + +
104A HIS* 2.9 22.0 + - + +
106A TRP* 1.3 98.7 - - + +
108A ALA* 1.3 62.9 + - - +
110A GLN* 3.1 3.1 + - - +
111A LEU* 3.0 33.0 + - + +
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Residues in contact with ALA 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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101A THR* 4.5 9.9 - - + +
104A HIS 4.4 0.4 + - - -
105A PRO 3.6 5.1 + - - +
106A TRP 3.3 0.8 - - - -
107A LEU* 1.3 79.3 - - - +
109A THR* 1.3 63.0 + - - +
111A LEU* 3.4 12.4 + - - +
112A ALA* 3.4 19.9 + - - +
161A GLY* 4.4 16.8 - - - +
164A ALA* 3.9 28.5 - - + -
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Residues in contact with THR 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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33A GLU* 4.6 6.5 - - - +
105A PRO 4.6 3.7 + - - -
106A TRP* 3.2 11.9 + - - -
108A ALA* 1.3 77.5 - - - +
110A GLN* 1.3 74.5 + - - +
112A ALA* 3.3 7.9 + - + +
113A THR* 3.2 29.8 + - + +
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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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28A LEU* 6.1 0.4 - - + +
33A GLU* 2.8 35.0 + - - +
63A LEU* 3.5 35.3 - - + +
67A THR* 3.2 27.9 + - + +
106A TRP* 3.3 26.9 + - + +
107A LEU 3.1 8.8 + - - +
109A THR* 1.3 83.6 - - - +
111A LEU* 1.3 53.1 + - - +
113A THR* 2.7 28.6 + - - +
114A GLN* 2.8 29.6 + - - +
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Residues in contact with LEU 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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67A THR* 3.8 21.5 - - + -
71A VAL* 4.3 7.0 - - + -
97A LEU* 5.0 14.4 - - + -
101A THR* 4.3 15.7 - - + -
107A LEU* 3.0 33.1 + - + +
108A ALA* 3.7 9.2 - - - +
109A THR 3.2 0.2 - - - -
110A GLN* 1.3 74.4 - - - +
112A ALA* 1.3 64.0 + - - +
114A GLN* 3.2 3.6 + - - +
115A LEU* 3.0 36.8 + - + +
123A VAL* 4.2 21.5 - - + -
127A ILE* 5.9 3.1 - - + -
157A LEU* 4.9 23.8 - - + -
160A ALA* 6.5 0.2 - - + -
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Residues in contact with ALA 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 ALA 3.4 9.1 + - - +
109A THR* 3.3 12.2 + - + +
111A LEU* 1.3 77.6 - - - +
113A THR* 1.3 58.2 + - + +
115A LEU 3.4 0.9 + - - -
116A SER* 2.7 36.3 + - - -
157A LEU* 5.6 1.3 - - - +
162B GLN* 3.3 29.2 + - - +
165B ALA* 5.0 9.6 - - + -
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Residues in contact with THR 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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109A THR* 3.2 19.5 + - + +
110A GLN* 2.7 41.8 + - - +
112A ALA* 1.3 75.0 - - + +
114A GLN* 1.3 60.4 + - - +
116A SER* 4.4 3.4 - - - +
117A ARG* 2.9 59.0 + - - +
118A THR* 3.2 9.1 + - - -
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Residues in contact with GLN 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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64A GLY* 3.8 28.1 + - - -
67A THR* 4.4 10.1 + - - -
110A GLN* 2.8 23.3 + - - +
111A LEU* 3.4 11.2 - - + +
113A THR* 1.3 79.2 + - - +
115A LEU* 1.3 63.3 + - + +
118A THR* 3.1 56.1 + - - +
121A GLY* 3.3 14.8 - - - -
122A THR 4.2 1.2 + - - -
123A VAL* 3.0 34.5 - - + +
124A ALA* 4.7 4.8 - - + +
182B PHE* 5.1 0.3 - - - -
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Residues in contact with LEU 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 LEU* 3.0 20.9 + - + +
113A THR 3.3 0.2 - - - -
114A GLN* 1.3 82.4 - - + +
116A SER* 1.3 60.3 + - - +
123A VAL* 5.0 2.2 - - + -
124A ALA* 3.5 35.2 - - + -
128A PHE* 5.7 3.1 - - + -
153A MSE 4.4 21.5 - - + -
154A HIS* 6.0 2.2 - - + +
157A LEU* 3.4 35.2 - - + -
162B GLN* 3.8 13.6 + - + +
166B ASN* 4.2 1.4 + - - +
179B ARG* 3.9 6.9 + - - -
182B PHE* 3.5 20.9 - - - -
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Residues in contact with SER 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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112A ALA 2.7 21.5 + - - -
113A THR* 4.2 1.8 - - - -
115A LEU* 1.3 80.5 - - - +
117A ARG* 1.3 72.7 + - - +
162B GLN* 3.6 4.3 + - - -
165B ALA* 3.4 26.1 - - - +
166B ASN* 2.8 28.4 + - - +
179B ARG* 5.2 0.3 + - - -
182B PHE* 3.2 22.2 - - - -
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Residues in contact with ARG 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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60A ALA* 6.0 4.2 - - - +
113A THR* 2.9 44.7 + - - +
116A SER* 1.3 89.9 - - - +
118A THR* 1.3 62.8 + - - +
119A PRO* 3.0 16.0 - - - +
165B ALA 5.7 2.7 - - - +
182B PHE* 3.9 4.0 - - - -
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Residues in contact with THR 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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64A GLY* 6.4 0.2 - - - -
113A THR* 3.2 14.3 + - - -
114A GLN* 3.1 50.2 + - - +
116A SER 3.8 0.4 - - - -
117A ARG* 1.3 81.8 + - - +
119A PRO* 1.3 58.1 - - - +
120A TRP* 3.2 2.7 - - + +
121A GLY* 2.9 28.6 + - - +
124A ALA* 5.9 1.4 - - - +
182B PHE* 4.0 3.3 - - - -
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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