Contacts of the helix formed by residues 108 - 127 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B VAL* 4.1 1.3 - - - +
107B TRP* 1.3 77.2 - - - +
109B PRO* 1.3 63.0 - - - +
110B ILE* 2.9 34.2 + - - +
111B THR* 3.3 23.2 + - - +
112B TYR* 2.8 33.8 + - - +
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Residues in contact with PRO 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B TRP 3.3 5.6 - - - +
108B ASN* 1.3 93.9 - - - +
110B ILE* 1.3 73.9 + - + +
112B TYR* 3.5 7.5 + - + +
113B LEU* 3.1 29.3 + - + +
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Residues in contact with ILE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ASN* 2.9 11.6 + - - +
109B PRO* 1.3 83.8 - - + +
111B THR* 1.3 67.0 + - - +
113B LEU* 3.2 9.3 + - + +
114B ASP* 3.0 22.0 + - - +
157B TRP* 6.1 0.2 - - + -
158B THR* 4.0 14.8 - - + -
489B VAL* 3.7 24.3 - - + +
492B LEU* 4.1 25.8 - - + -
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Residues in contact with THR 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B VAL* 3.6 13.7 - - + -
108B ASN* 3.3 24.0 + - - +
110B ILE* 1.3 79.5 - - - +
112B TYR* 1.3 57.0 + - - -
114B ASP* 3.2 0.7 + - - +
115B HIS* 2.8 49.2 + - + +
158B THR* 4.0 18.7 - - - +
160B SER* 3.3 35.6 - - - +
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Residues in contact with TYR 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B VAL* 3.2 37.8 - - + +
107B TRP 5.0 1.6 - - - +
108B ASN 2.8 22.5 + - - +
109B PRO* 3.5 9.4 - - + +
110B ILE 3.2 0.2 - - - -
111B THR* 1.3 73.7 - - - +
113B LEU* 1.3 62.0 + - + +
115B HIS* 3.9 1.0 - - - +
116B ASN* 2.9 36.8 + - + +
482B LEU* 5.7 4.3 - - - +
483B GLU* 5.4 7.7 - - + +
486B LEU* 3.7 30.3 - - + +
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Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B PRO* 3.1 16.9 + - + +
110B ILE* 3.6 11.4 - - + +
112B TYR* 1.3 78.2 - - + +
114B ASP* 1.3 58.7 + - - +
116B ASN* 3.8 3.9 - - - +
117B ASN* 2.9 32.6 + - - +
486B LEU* 3.8 37.9 - - + -
487B PRO* 3.4 33.1 - - + +
488B SER 4.6 1.8 - - - +
489B VAL* 4.5 10.1 - - + +
492B LEU* 3.7 37.2 - - + -
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Residues in contact with ASP 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ILE 3.0 16.3 + - - +
111B THR 3.6 3.6 - - - +
113B LEU* 1.3 78.2 - - - +
115B HIS* 1.3 62.6 + - - +
117B ASN* 3.4 5.7 + - - +
118B PHE* 3.0 23.2 + - - +
155B LEU 3.6 10.6 - - - +
156B CYS* 3.7 2.5 - - - -
157B TRP* 2.8 31.5 + - - +
158B THR* 2.7 40.0 + - + +
161B ALA* 3.1 13.2 - - - +
489B VAL* 3.9 12.9 + - + +
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Residues in contact with HIS 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B HIS* 6.1 3.6 - + - -
106B VAL* 3.5 28.5 - - + +
111B THR* 2.8 42.2 + - + +
112B TYR 4.0 2.5 - - - +
114B ASP* 1.3 68.8 - - - +
116B ASN* 1.3 67.7 + - - +
118B PHE* 3.1 12.0 + - - +
119B TRP* 3.1 30.1 + - + +
160B SER* 2.7 37.7 + - - -
161B ALA* 3.3 23.1 + - + -
164B LEU* 3.9 28.1 - - + +
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Residues in contact with ASN 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B TYR* 2.9 33.2 + - + +
113B LEU* 3.8 5.1 - - - +
115B HIS* 1.3 76.7 - - - +
117B ASN* 1.3 63.6 + - - +
119B TRP* 3.6 6.0 + - - +
120B ARG* 3.1 34.1 + - - +
482B LEU 4.3 2.9 - - - +
483B GLU* 3.0 55.6 + - - +
486B LEU* 4.3 8.2 - - + +
487B PRO 5.7 0.2 - - - +
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Residues in contact with ASN 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LEU 2.9 19.5 + - - +
114B ASP* 3.8 6.8 - - - +
116B ASN* 1.3 74.4 + - - +
118B PHE* 1.3 61.4 + - - +
120B ARG* 2.9 38.2 - - - +
121B THR* 2.7 55.2 + - - -
155B LEU* 4.6 18.0 - - - +
488B SER* 3.5 30.0 - - - -
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Residues in contact with PHE 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ASP 3.0 14.8 + - - +
115B HIS* 3.1 9.5 + - - +
117B ASN* 1.3 79.2 + - - +
119B TRP* 1.3 114.1 + + - +
121B THR* 3.2 4.3 + - - -
122B MET* 3.0 62.6 + - + +
148B MET* 5.4 0.2 - - + -
152B LEU* 3.4 30.5 - - + -
155B LEU* 4.7 15.7 - - + +
156B CYS* 4.2 17.3 - - - -
161B ALA* 5.0 4.7 - - + -
165B ALA* 3.3 31.2 - - + -
168B PHE* 4.4 4.0 - + - -
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Residues in contact with TRP 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B PHE* 3.0 57.4 - + + +
115B HIS* 3.1 35.1 + - + +
116B ASN* 4.1 5.2 - - - +
118B PHE* 1.3 102.7 - + - +
120B ARG* 1.3 63.2 + - - +
122B MET* 3.3 6.2 + - - +
123B ASP* 3.2 25.9 + - - +
164B LEU* 3.9 27.8 - - + +
168B PHE* 3.5 50.9 - + + -
195B THR* 3.7 22.8 - - + +
1501B XCG 3.8 8.7 - + - -
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Residues in contact with ARG 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ASN* 3.1 26.0 + - - +
117B ASN* 2.9 37.0 - - - +
119B TRP* 1.3 78.1 - - - +
121B THR* 1.3 57.8 + - - +
123B ASP* 3.2 7.6 + - - +
124B ASP* 2.8 50.1 + - - +
483B GLU 3.0 27.1 + - - +
484B ARG* 3.3 23.4 + - - +
485B HIS 4.1 0.4 - - - -
486B LEU 2.7 30.5 + - - +
487B PRO* 4.1 0.8 - - - +
488B SER 3.9 6.9 - - - +
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Residues in contact with THR 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ASN* 2.7 47.6 + - - -
118B PHE 3.7 3.1 - - - -
120B ARG* 1.3 70.9 + - - +
122B MET* 1.3 67.2 + - - +
124B ASP* 3.6 11.0 + - + +
125B MET* 2.8 47.5 + - + +
155B LEU* 3.8 27.5 - - + +
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Residues in contact with MET 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B PHE* 3.0 53.3 + - + +
119B TRP* 3.5 7.4 - - - +
121B THR* 1.3 77.1 - - - +
123B ASP* 1.3 58.9 + - - +
125B MET* 3.5 3.3 + - - +
126B GLY* 3.0 23.2 + - - -
148B MET* 4.1 11.4 - - + -
151B LEU* 5.1 4.7 - - - -
155B LEU* 5.5 3.4 - - + -
168B PHE* 3.6 17.7 - - + -
185B PHE* 3.3 37.0 - - + -
186B LEU* 3.6 29.0 - - + +
189B VAL* 4.9 7.1 - - + +
195B THR* 3.8 13.5 - - + -
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Residues in contact with ASP 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B TRP 3.2 8.9 + - - +
120B ARG* 3.2 8.4 + - - +
122B MET* 1.3 75.8 - - - +
124B ASP* 1.3 63.6 + - - +
126B GLY* 3.2 2.8 + - - -
127B ARG* 3.2 43.6 + - - +
189B VAL* 4.4 2.1 - - - +
190B LYS* 5.9 0.3 - - - -
194B GLY* 3.5 11.3 - - - -
195B THR* 2.7 50.2 + - - +
196B THR* 4.7 0.9 + - - -
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Residues in contact with ASP 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ARG* 2.8 43.4 + - - +
121B THR* 3.2 12.3 + - + +
123B ASP* 1.3 72.4 - - - +
125B MET* 1.3 66.2 + - + +
127B ARG* 2.7 49.3 + - - +
128B GLU* 4.0 7.8 + - - +
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Residues in contact with MET 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B THR* 2.8 39.4 + - + +
122B MET* 3.9 4.3 - - - +
124B ASP* 1.3 76.3 - - + +
126B GLY* 1.4 64.1 + - - +
128B GLU* 3.1 12.2 + - - +
129B ILE* 3.5 12.6 - - - +
143B TRP* 3.3 63.3 - - + +
151B LEU* 4.0 29.6 - - + -
155B LEU* 4.7 2.2 - - - -
186B LEU* 3.5 31.9 - - + -
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Residues in contact with GLY 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B MET 3.0 15.1 + - - -
123B ASP* 3.2 5.3 + - - -
125B MET* 1.4 77.7 - - - +
127B ARG* 1.3 56.6 + - - +
128B GLU 3.0 0.2 - - - -
129B ILE* 3.0 30.1 + - - +
186B LEU* 4.5 3.7 - - - +
190B LYS* 3.0 39.9 + - - +
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Residues in contact with ARG 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ARG 5.3 0.2 + - - -
123B ASP* 3.2 29.5 + - - +
124B ASP* 2.7 45.0 + - - +
125B MET 3.2 1.4 - - - -
126B GLY* 1.3 76.5 - - - +
128B GLU* 1.3 65.6 + - + +
129B ILE 3.3 1.2 + - - -
190B LYS* 4.4 8.3 + - - +
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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
------------------------------------------------------------
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