Contacts of the helix formed by residues 138 - 155 (chain G) in PDB entry 2X86
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 138 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G THR* 3.7 36.1 + - - +
84G TRP* 3.5 24.5 - - + -
118G ALA* 5.1 6.2 - - - +
136G PRO* 3.4 3.3 - - - +
137G LEU* 1.3 83.4 - - - +
139G VAL* 1.3 60.3 + - - +
140G PHE* 3.4 8.2 + - - +
141G GLY* 2.7 45.0 + - - -
142G TYR* 2.9 11.3 + - - +
268G LEU* 6.3 0.6 - - - +
271G ARG* 3.9 20.5 + - + +
401G ADP 5.6 0.6 + - - -
39H PHE* 3.5 8.6 - - - -
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Residues in contact with VAL 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G GLU 3.4 24.0 - - - +
84G TRP* 3.6 25.3 - - + -
86G GLY* 4.1 18.8 - - - -
89G MET* 3.8 14.7 - - + +
90G MET* 5.0 3.8 - - - -
138G ASN* 1.3 72.3 - - + +
140G PHE* 1.3 69.3 + - - +
142G TYR* 3.2 8.0 + - + -
143G SER* 2.9 22.5 + - - -
33H LEU* 4.3 9.4 - - + -
36H GLY* 3.8 25.8 - - - +
39H PHE* 3.9 11.8 - - + -
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Residues in contact with PHE 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G CYS 3.4 26.9 - - - -
79G SER* 3.9 5.6 - - - -
80G SER 3.7 20.6 - - - +
81G THR* 3.8 21.3 + - + -
83G GLU 4.9 0.4 + - - -
89G MET* 3.9 10.3 - - + -
93G ASN* 4.0 5.2 - - - -
116G SER* 3.9 12.8 - - - -
118G ALA* 4.1 4.9 - - + -
138G ASN* 3.2 8.6 - - - +
139G VAL* 1.3 81.7 - - - +
141G GLY* 1.3 65.9 + - - +
143G SER* 2.6 24.7 + - - -
144G LYS* 3.2 28.4 + - + +
400G NAP 3.2 28.0 - - - -
402G BMA 3.7 32.3 - - - -
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Residues in contact with GLY 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118G ALA* 4.4 14.6 - - - -
119G THR* 3.9 2.6 - - - +
136G PRO* 3.4 17.0 - - - +
138G ASN* 2.7 22.6 + - - -
140G PHE* 1.3 81.7 - - - +
142G TYR* 1.3 57.9 + - - +
144G LYS* 3.2 6.3 + - - +
145G PHE* 2.8 29.8 + - - +
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Residues in contact with TYR 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G MET* 4.1 29.4 - - + -
136G PRO* 3.6 10.9 - - + +
138G ASN 2.9 7.3 + - - +
139G VAL* 3.5 10.3 - - + +
140G PHE 3.2 0.4 - - - -
141G GLY* 1.3 76.1 - - - +
143G SER* 1.3 56.4 + - - +
145G PHE* 3.2 26.9 + + - +
146G LEU* 2.9 44.9 + - + +
33H LEU* 4.8 6.5 - - + -
39H PHE* 3.7 41.7 - + + -
42H LEU* 3.5 33.3 + - + +
43H VAL* 4.2 19.5 - - - -
47H ILE* 3.7 20.8 - - - +
50H TYR* 5.8 1.6 - + + -
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Residues in contact with SER 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G MET* 3.6 16.8 - - - +
90G MET* 3.9 21.5 - - - -
93G ASN* 3.2 34.3 + - - +
94G TYR* 4.1 12.2 + - - +
139G VAL 2.9 12.7 + - - -
140G PHE 2.6 20.2 + - - -
142G TYR* 1.3 77.5 - - - +
144G LYS* 1.3 61.2 + - - +
147G PHE* 3.5 20.1 + - - +
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Residues in contact with LYS 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76G GLY 5.1 1.2 + - - -
77G ALA* 3.6 12.8 - - - +
93G ASN* 4.6 8.2 - - + +
97G SER* 5.7 3.0 + - - -
114G ALA* 3.0 26.3 + - - +
115G SER* 4.1 10.7 - - - +
116G SER* 4.2 10.5 - - - +
119G THR* 3.9 13.9 - - + -
140G PHE* 3.7 32.3 - - + +
141G GLY* 3.2 7.7 + - - +
142G TYR 3.1 0.4 - - - -
143G SER* 1.3 82.5 + - - +
145G PHE* 1.3 66.7 + - - +
147G PHE* 3.1 7.6 + - + +
148G ASP* 3.0 24.9 + - - +
400G NAP 2.8 43.1 + - - -
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Residues in contact with PHE 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119G THR* 3.5 12.9 - - + +
131G ARG* 3.5 42.6 - - + -
134G GLU* 3.2 39.7 - - + -
136G PRO* 3.9 18.8 - - + -
141G GLY 2.8 16.8 + - - +
142G TYR* 3.5 29.6 - + - +
144G LYS* 1.3 77.0 - - - +
146G LEU* 1.3 72.6 + - + +
148G ASP* 3.0 7.8 + - - +
149G GLU* 3.0 44.8 + - + +
152G ARG* 4.9 0.4 - - - -
166G ARG* 5.6 0.4 - - - -
42H LEU 5.7 0.2 - - - -
43H VAL 4.5 4.7 - - - -
45H LEU 5.0 4.0 - - - -
46H ASN* 5.5 0.2 - - - -
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Residues in contact with LEU 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G MET* 3.6 14.8 - - + -
94G TYR* 3.5 30.7 + - + +
142G TYR* 2.9 42.7 + - + +
143G SER 4.5 0.2 - - - +
145G PHE* 1.3 87.7 - - + +
147G PHE* 1.3 59.3 + - - +
149G GLU* 3.3 12.7 + - + +
150G TYR* 2.9 22.9 + - - +
47H ILE* 4.0 22.4 - - + +
48H ALA 5.7 1.3 - - - +
49H ASP* 4.7 2.9 - - - +
50H TYR* 3.6 33.4 - - + +
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Residues in contact with PHE 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93G ASN 5.6 0.4 - - - +
94G TYR* 3.6 17.4 - + + -
97G SER* 3.6 34.1 - - - -
98G LYS* 3.5 33.9 - - + -
101G LEU* 4.0 17.0 - - + -
111G PHE* 4.0 8.7 - + - -
113G TYR* 3.7 40.4 - + - -
143G SER 3.5 13.7 + - - +
144G LYS* 3.1 11.0 + - + +
146G LEU* 1.3 77.1 - - - +
148G ASP* 1.3 59.9 + - - +
150G TYR* 2.9 10.3 + + + +
151G VAL* 2.8 46.9 + - + +
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Residues in contact with ASP 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113G TYR* 2.7 42.1 + - - -
115G SER* 2.6 28.6 + - - -
119G THR* 4.2 3.6 - - - +
144G LYS 3.0 14.8 + - - +
145G PHE* 3.4 7.6 - - - +
147G PHE* 1.3 75.6 - - - +
149G GLU* 1.3 58.3 + - - +
151G VAL* 3.2 2.3 + - - +
152G ARG* 2.8 40.9 + - - +
166G ARG* 2.8 26.7 + - - +
232G ILE* 3.8 13.7 - - + +
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Residues in contact with GLU 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131G ARG* 3.7 25.6 - - - +
145G PHE* 3.0 39.4 + - + +
146G LEU* 3.4 18.6 - - + +
147G PHE 3.1 0.2 - - - -
148G ASP* 1.3 76.1 - - - +
150G TYR* 1.3 63.0 + - - +
152G ARG* 2.9 40.9 + - - +
153G GLN* 3.2 32.4 + - - +
46H ASN* 4.5 7.6 - - - +
47H ILE 5.1 8.3 - - - +
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Residues in contact with TYR 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94G TYR* 3.7 19.3 - - + +
98G LYS* 3.6 33.7 + - + +
101G LEU* 4.0 22.2 - - + -
102G HIS* 2.6 37.4 + + - -
146G LEU 2.9 12.6 + - - +
147G PHE* 2.9 16.1 + + + +
149G GLU* 1.3 75.3 - - - +
151G VAL* 1.3 66.6 + - - +
153G GLN* 3.1 28.1 + - + +
154G ILE* 3.2 23.8 + - + +
48H ALA 4.1 12.1 - - - -
49H ASP* 4.3 10.3 - - + -
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Residues in contact with VAL 151 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G LEU* 4.3 9.0 - - + -
113G TYR* 3.4 29.2 - - + +
147G PHE* 2.8 44.3 + - + +
148G ASP 3.5 7.4 - - - +
150G TYR* 1.3 72.2 - - - +
152G ARG* 1.3 59.3 + - - +
154G ILE* 2.9 9.7 + - - +
155G LEU* 2.8 44.8 + - + +
162G ILE* 3.8 25.6 - - + +
231G GLY 5.8 0.7 - - - +
232G ILE* 4.4 8.1 - - + -
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Residues in contact with ARG 152 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129G GLU* 3.5 24.9 + - - +
130G SER* 3.8 2.0 - - - +
131G ARG* 3.9 10.4 - - - +
134G GLU* 2.5 44.9 + - - -
145G PHE* 4.6 0.4 - - - -
148G ASP* 2.8 23.3 + - - +
149G GLU* 2.9 33.2 + - - +
150G TYR 3.2 0.2 - - - -
151G VAL* 1.3 77.0 - - - +
153G GLN* 1.3 59.9 + - - +
155G LEU* 3.8 11.8 + - + +
156G PRO* 3.4 19.2 - - - +
166G ARG* 3.9 6.2 - - - +
232G ILE* 3.9 25.4 - - + +
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Residues in contact with GLN 153 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149G GLU* 3.2 23.7 + - - +
150G TYR* 3.1 23.6 + - + +
152G ARG* 1.3 77.4 - - - +
154G ILE* 1.3 65.1 + - + +
156G PRO* 3.7 8.1 - - - +
157G GLU* 5.3 2.3 + - - +
47H ILE 4.5 4.4 + - - -
48H ALA* 2.9 45.8 + - - +
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Residues in contact with ILE 154 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G LEU* 4.3 6.3 - - + -
102G HIS* 4.5 15.5 - - + -
105G LEU* 3.6 26.7 - - + -
150G TYR* 3.5 38.6 - - + +
151G VAL* 2.9 9.9 + - - +
153G GLN* 1.3 83.2 - - + +
155G LEU* 1.3 65.9 + - - +
156G PRO 3.4 0.2 - - - -
157G GLU* 3.0 18.5 + - + +
158G ALA* 3.2 10.6 + - + +
162G ILE* 3.9 17.7 - - + -
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Residues in contact with LEU 155 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G VAL* 2.8 31.4 + - + +
152G ARG* 4.1 14.6 - - + +
154G ILE* 1.3 76.6 - - - +
156G PRO* 1.3 70.8 - - + +
157G GLU 3.0 1.2 + - - -
158G ALA* 3.2 20.0 + - + +
162G ILE* 4.0 30.7 - - + +
230G SER* 4.1 21.8 - - - +
231G GLY* 4.2 19.3 - - - +
232G ILE* 5.0 3.4 - - + +
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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