Contacts of the helix formed by residues 108 - 128 (chain A) in PDB entry 2XFN
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 ASN 108 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A VAL* 3.8 1.6 - - + +
107A TRP* 1.3 74.9 - - - +
109A PRO* 1.4 61.0 - - - +
110A ILE* 2.9 23.9 + - - +
111A THR* 3.2 27.1 + - + +
112A TYR* 2.7 35.9 + - - +
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Residues in contact with PRO 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A TRP 3.3 9.4 - - - +
108A ASN* 1.4 89.0 - - - +
110A ILE* 1.3 60.1 + - + +
112A TYR* 3.4 9.1 + - + +
113A LEU* 3.0 33.6 + - + +
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Residues in contact with ILE 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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108A ASN* 2.9 14.7 + - - +
109A PRO* 1.3 74.0 - - + +
111A THR* 1.3 67.1 + - - +
113A LEU* 3.2 10.3 + - + +
114A ASP* 3.1 20.1 + - - +
158A THR* 4.4 12.1 - - + -
489A VAL* 3.7 24.0 - - + +
492A LEU* 3.7 29.4 - - + -
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Residues in contact with THR 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A VAL* 3.5 13.0 - - + -
108A ASN* 3.2 29.1 + - + +
110A ILE* 1.3 74.8 - - - +
112A TYR* 1.3 61.4 + - - +
114A ASP* 3.2 0.9 + - - +
115A HIS* 2.9 59.9 + - + +
158A THR* 4.0 21.3 - - + +
160A SER* 3.8 18.8 - - - +
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Residues in contact with TYR 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A VAL* 3.4 34.9 - - + +
107A TRP 5.1 0.4 - - - +
108A ASN 2.7 21.5 + - - +
109A PRO* 3.6 10.5 - - + +
110A ILE 3.2 0.2 - - - -
111A THR* 1.3 73.5 - - - +
113A LEU* 1.3 69.7 + - + +
115A HIS* 3.4 2.1 + - + -
116A ASN* 2.9 38.6 + - + +
482A LEU* 5.4 1.6 - - - +
483A GLU* 3.9 25.5 + - - +
486A LEU* 3.7 30.4 - - + +
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Residues in contact with LEU 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 PRO* 3.0 21.6 + - + +
110A ILE* 3.5 12.1 - - + +
112A TYR* 1.3 81.1 - - + +
114A ASP* 1.3 59.2 + - - +
116A ASN* 3.9 3.4 - - - +
117A ASN* 2.9 31.5 + - - +
486A LEU* 3.9 36.3 - - + -
487A PRO* 3.4 32.5 - - + +
488A SER 4.6 1.3 - - - +
489A VAL* 4.3 10.1 - - + -
492A LEU* 3.8 35.9 - - + -
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Residues in contact with ASP 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 ILE 3.1 12.2 + - - +
111A THR 3.2 6.7 + - - +
113A LEU* 1.3 79.5 - - - +
115A HIS* 1.3 58.3 + - - +
117A ASN* 3.4 5.7 + - - +
118A PHE* 2.9 28.8 + - - +
155A LEU 3.6 10.6 - - - +
156A CYS* 3.7 1.7 - - - -
157A TRP* 2.9 32.5 + - - +
158A THR* 2.7 43.8 + - + +
161A ALA* 3.1 13.0 - - - +
489A VAL* 3.9 10.9 + - + +
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Residues in contact with HIS 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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90A HIS* 6.4 1.8 - + - -
104A PRO 5.6 0.2 + - - -
106A VAL* 3.6 28.0 - - + +
111A THR* 2.9 40.1 + - + +
112A TYR* 3.9 4.5 - - + +
114A ASP* 1.3 73.9 - - - +
116A ASN* 1.3 65.7 + - - +
118A PHE* 3.1 11.1 + - - +
119A TRP* 3.1 32.1 + - + +
158A THR* 4.3 0.4 - - - -
160A SER* 2.9 32.2 + - - -
161A ALA* 3.3 32.7 + - + -
164A LEU* 4.0 25.3 - - + +
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Residues in contact with ASN 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 TYR* 2.9 40.5 + - + +
113A LEU* 3.9 4.6 - - - +
115A HIS* 1.3 77.8 - - - +
117A ASN* 1.3 61.8 + - - +
119A TRP* 3.6 5.0 + - - +
120A ARG* 3.1 39.6 + - - +
482A LEU 4.3 2.3 - - - +
483A GLU* 3.0 55.6 + - - +
486A LEU* 4.4 6.2 - - + +
487A PRO 5.8 0.2 - - - +
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Residues in contact with ASN 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 LEU 2.9 20.1 + - - +
114A ASP* 3.8 6.2 - - - +
116A ASN* 1.3 74.7 + - - +
118A PHE* 1.3 60.9 + - - +
120A ARG* 3.0 37.1 - - - +
121A THR* 2.7 54.8 + - - -
155A LEU* 4.5 17.5 - - - +
488A SER* 3.4 28.0 - - - -
490A PRO* 5.8 0.5 - - - +
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Residues in contact with PHE 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 ASP 2.9 17.8 + - - +
115A HIS* 3.1 6.9 + - - +
117A ASN* 1.3 79.4 + - - +
119A TRP* 1.3 108.6 + + - +
121A THR* 3.7 4.2 - - - -
122A MET* 3.0 60.3 + - + +
148A MET* 5.4 0.2 - - + -
152A LEU* 3.3 26.5 - - + -
155A LEU* 4.3 17.7 - - + +
156A CYS* 3.9 25.1 - - - -
161A ALA* 5.0 5.6 - - + -
165A ALA* 3.3 25.1 - - + -
168A PHE* 4.9 3.4 - + - -
169A VAL* 6.1 0.7 - - + -
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Residues in contact with TRP 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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103A PHE* 3.2 49.7 - + + +
115A HIS* 3.1 37.0 + - + +
116A ASN* 4.2 4.5 - - - +
118A PHE* 1.3 103.1 - + - +
120A ARG* 1.3 64.3 + - - +
122A MET* 3.2 6.2 + - - +
123A ASP* 3.1 27.8 + - - +
164A LEU* 3.9 29.3 - - + +
165A ALA 5.2 0.2 - - - -
168A PHE* 3.5 55.9 - + + -
195A THR* 3.8 24.6 - - + +
1501A XCG 4.2 5.4 - + - -
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Residues in contact with ARG 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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116A ASN* 3.1 30.1 + - - +
117A ASN* 3.0 36.5 - - - +
119A TRP* 1.3 77.2 - - - +
121A THR* 1.3 57.0 + - - +
123A ASP* 3.2 7.1 + - - +
124A ASP* 2.8 50.0 + - - +
127A ARG* 4.9 0.8 + - - +
483A GLU 2.9 29.6 + - - +
484A ARG* 3.3 23.1 + - - +
485A HIS 4.2 0.2 - - - -
486A LEU 2.8 30.3 + - - +
487A PRO* 4.1 0.8 - - - +
488A SER 3.9 7.1 - - - +
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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 ASN* 2.7 44.8 + - - -
118A PHE 3.7 2.9 - - - -
120A ARG* 1.3 73.3 + - - +
122A MET* 1.3 60.2 + - - +
124A ASP* 4.1 11.5 + - + +
125A MET* 2.9 45.5 + - + +
155A LEU* 3.9 34.3 - - + -
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Residues in contact with MET 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 PHE* 3.0 56.6 + - + +
119A TRP* 3.2 7.8 + - - +
121A THR* 1.3 76.4 - - - +
123A ASP* 1.3 58.1 + - - +
125A MET* 3.6 0.4 + - - -
126A GLY* 3.0 23.6 + - - -
148A MET* 3.9 13.7 - - + -
151A LEU* 4.7 7.0 - - - -
155A LEU* 5.0 3.1 - - - +
168A PHE* 4.3 7.2 - - + -
185A PHE* 3.4 38.8 - - + -
186A LEU* 3.6 31.8 - - + +
189A VAL* 4.9 7.8 - - + +
195A THR* 3.8 15.5 - - + -
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Residues in contact with ASP 123 (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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119A TRP 3.1 13.4 + - - +
120A ARG* 3.8 7.7 - - - +
122A MET* 1.3 74.6 - - - +
124A ASP* 1.3 66.7 + - - +
126A GLY* 3.2 3.3 + - - +
127A ARG* 3.1 41.4 + - - +
189A VAL* 4.4 2.3 - - - +
190A LYS* 5.9 0.3 - - - -
194A GLY* 3.4 10.6 - - - -
195A THR* 2.7 52.1 + - - +
196A THR* 4.8 0.9 + - - -
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Residues in contact with ASP 124 (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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120A ARG* 2.8 43.8 + - - +
121A THR* 3.2 12.2 + - + +
123A ASP* 1.3 77.2 - - - +
125A MET* 1.3 64.9 + - + +
127A ARG* 3.2 45.7 + - - +
128A GLU* 3.7 11.0 + - - +
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Residues in contact with MET 125 (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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121A THR* 2.9 39.4 + - + +
122A MET* 3.9 3.6 - - - +
124A ASP* 1.3 77.5 - - + +
126A GLY* 1.3 64.2 + - - +
128A GLU* 3.0 22.5 + - - +
129A ILE* 3.6 2.6 - - - +
143A TRP* 3.4 59.9 - - + +
146A MET* 6.3 0.2 - - - -
151A LEU* 4.1 28.9 - - + -
155A LEU* 4.7 2.7 - - - -
186A LEU* 3.5 31.0 - - + -
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Residues in contact with GLY 126 (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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122A MET 3.0 15.9 + - - -
123A ASP* 3.2 6.0 + - - -
125A MET* 1.3 76.3 - - - +
127A ARG* 1.3 54.7 + - - +
129A ILE* 3.0 29.3 + - - +
186A LEU* 4.4 4.2 - - - +
190A LYS* 3.0 41.6 + - - +
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Residues in contact with ARG 127 (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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120A ARG* 4.9 0.6 + - - +
123A ASP* 3.1 32.2 + - - +
124A ASP* 3.2 45.9 + - - +
125A MET 3.2 0.6 - - - -
126A GLY* 1.3 76.3 - - - +
128A GLU* 1.3 65.4 + - - +
129A ILE 3.3 1.5 + - - -
190A LYS* 4.0 13.5 + - + +
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Residues in contact with GLU 128 (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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124A ASP 3.9 10.7 - - - +
125A MET* 3.0 15.5 + - - +
127A ARG* 1.3 82.8 - - - +
129A ILE* 1.3 57.1 + - - +
130A PRO* 3.5 9.6 - - - +
137A ALA* 3.5 1.3 - - - +
138A PRO* 3.5 43.3 - - + +
143A TRP* 4.0 21.8 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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