Contacts of the helix formed by residues 109 - 122 (chain A) in PDB entry 2X9D
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 GLN 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A LEU* 6.4 0.9 - - + -
105A PRO* 5.0 8.5 - - + -
106A ASP* 2.9 13.9 + - + +
107A GLU 2.8 3.8 + - - -
108A LYS* 1.3 76.0 - - + +
110A TYR* 1.3 61.6 + - - +
111A ASP 3.2 2.9 - - - -
112A THR* 3.0 26.8 + - + +
113A VAL* 3.1 14.7 + - - +
1209A ITC 4.4 16.4 - - - +
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Residues in contact with TYR 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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105A PRO* 3.5 29.9 + - + -
106A ASP 3.4 9.7 + - - -
107A GLU* 2.7 47.8 + - + +
108A LYS 3.6 0.2 - - - -
109A GLN* 1.3 70.8 - - - +
111A ASP* 1.3 60.0 + - - +
113A VAL* 3.3 6.6 + - - +
114A GLU* 2.8 34.5 + - - +
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Residues in contact with ASP 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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107A GLU 4.5 0.6 + - - -
108A LYS 5.3 1.9 + - - +
109A GLN 3.2 0.4 - - - -
110A TYR* 1.3 85.5 - - - +
112A THR* 1.3 53.1 + - - +
114A GLU* 3.4 11.7 - - + +
115A THR* 2.8 37.3 + - - +
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Residues in contact with THR 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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67A SER* 3.6 36.9 + - - +
68A LEU* 4.4 14.3 - - + +
108A LYS 5.1 1.2 + - - -
109A GLN* 3.0 21.2 + - + +
111A ASP* 1.3 76.6 - - - +
113A VAL* 1.3 60.1 + - - +
115A THR* 3.3 5.4 + - - -
116A GLN* 2.9 43.9 + - - +
1209A ITC 3.9 9.9 - - - +
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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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105A PRO* 3.9 16.2 - - + -
109A GLN 3.1 12.0 + - - +
110A TYR* 3.9 6.5 - - - +
112A THR* 1.3 75.4 - - - +
114A GLU* 1.3 61.8 + - - +
116A GLN* 3.5 12.1 + - + +
117A LEU* 3.1 40.9 + - + +
134A ILE* 6.0 0.7 - - + -
1209A ITC 3.5 67.3 - - + +
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Residues in contact with GLU 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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110A TYR 2.8 18.2 + - - +
111A ASP* 3.4 14.8 - - + +
113A VAL* 1.3 77.4 - - - +
115A THR* 1.3 57.8 + - - +
117A LEU* 3.3 15.5 + - - +
118A ARG* 3.0 39.4 + - - +
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Residues in contact with THR 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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68A LEU* 3.7 24.4 - - + +
69A PRO* 4.8 11.7 - - + -
111A ASP 2.8 25.3 + - - -
112A THR* 3.3 4.4 + - - -
114A GLU* 1.3 69.2 - - - +
116A GLN* 1.3 57.5 + - - +
118A ARG* 2.8 34.4 + - - +
119A PHE* 2.8 34.7 + - + +
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Residues in contact with GLN 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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67A SER 2.7 29.6 + - - +
68A LEU* 4.9 1.3 - - + -
69A PRO* 5.6 1.1 - - - -
78A PHE* 3.8 18.8 - - + -
82A ASN* 3.7 1.2 - - - +
112A THR* 2.9 28.6 + - - +
113A VAL* 3.5 15.8 - - + +
115A THR* 1.3 78.1 - - - +
117A LEU* 1.3 62.2 + - + +
119A PHE* 3.4 7.1 + - - +
120A MET* 3.2 27.4 + - - +
134A ILE* 4.0 18.0 - - + +
1209A ITC 2.6 63.0 + - - +
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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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113A VAL* 3.1 37.3 + - + +
114A GLU* 3.6 15.0 - - - +
115A THR 3.3 0.2 - - - -
116A GLN* 1.3 72.8 - - + +
118A ARG* 1.3 65.9 + - - +
120A MET* 3.4 8.3 + - - +
121A THR* 3.1 27.9 + - - +
127A LEU* 4.2 21.4 - - + +
130A GLY* 4.9 1.4 - - - -
131A LEU* 3.8 44.4 - - + +
134A ILE* 4.5 15.7 - - + -
1209A ITC 5.5 0.2 - - + -
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Residues in contact with ARG 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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114A GLU* 3.0 24.4 + - + +
115A THR* 2.8 43.7 + - - +
117A LEU* 1.3 73.2 - - - +
119A PHE* 1.3 60.0 - - - +
121A THR* 2.6 28.1 + - - +
122A GLU* 2.9 44.0 + - + +
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Residues in contact with PHE 119 (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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69A PRO* 3.7 32.3 - - + -
70A ALA 5.3 2.2 - - - -
72A GLY 6.3 0.2 - - - -
73A GLU 3.4 25.1 - - - -
74A SER 4.3 1.6 - - - -
75A TRP* 3.8 24.7 - - + -
78A PHE* 3.8 33.0 - + + -
115A THR* 2.8 24.0 + - + +
116A GLN* 3.5 5.4 - - - +
118A ARG* 1.3 73.3 - - - +
120A MET* 1.3 65.6 + - - +
122A GLU* 3.3 25.3 + - - +
123A ASN* 2.9 38.6 + - - -
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Residues in contact with MET 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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75A TRP* 4.1 20.9 - - + -
78A PHE* 5.1 1.3 - - + -
79A LEU* 3.9 35.2 - - + -
116A GLN 3.2 15.8 + - - +
117A LEU* 3.5 8.5 - - - +
118A ARG 3.2 0.6 - - - -
119A PHE* 1.3 80.9 - - + +
121A THR* 1.3 65.3 + - - +
123A ASN* 2.9 13.1 + - - -
125A PHE* 3.2 54.2 + - + -
130A GLY* 4.2 19.7 - - - +
133A ALA* 4.1 13.2 - - + -
134A ILE* 3.8 15.9 - - + -
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Residues in contact with THR 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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117A LEU 3.1 17.4 + - - +
118A ARG* 2.6 24.9 + - - +
120A MET* 1.3 74.8 - - + +
122A GLU* 1.3 62.5 + - - +
123A ASN 3.4 0.9 + - - -
124A GLY* 3.5 9.0 + - - -
125A PHE* 3.1 23.6 - - - +
126A SER 4.3 1.3 - - - +
127A LEU* 4.0 32.3 - - + +
130A GLY* 5.9 0.4 - - - -
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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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118A ARG* 2.9 44.6 + - + +
119A PHE* 3.4 29.7 + - - +
120A MET 3.1 0.4 - - - -
121A THR* 1.3 78.5 + - - +
123A ASN* 1.3 61.5 + - - +
124A GLY 3.5 1.1 + - - -
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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