Contacts of the helix formed by residues 138 - 155 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81M THR* 3.7 34.6 + - - +
84M TRP* 3.5 24.5 - - + -
118M ALA* 5.0 5.5 - - - +
136M PRO* 3.4 3.2 - - - +
137M LEU* 1.3 81.2 - - - +
139M VAL* 1.3 59.5 + - + +
140M PHE* 3.4 8.4 + - - +
141M GLY* 2.7 45.6 + - - -
142M TYR* 2.9 11.6 + - - +
268M LEU* 6.2 1.2 - - - +
271M ARG* 3.9 20.5 + - + +
401M ADP 5.4 1.6 + - - -
39N PHE* 3.5 8.0 - - - -
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Residues in contact with VAL 139 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83M GLU 3.4 23.1 - - - +
84M TRP* 3.6 25.2 - - + -
86M GLY* 4.1 18.4 - - - -
89M MET* 3.8 15.6 - - + +
90M MET* 5.0 3.8 - - - -
138M ASN* 1.3 71.3 - - - +
140M PHE* 1.3 68.9 + - - +
142M TYR* 3.2 8.2 + - + +
143M SER* 2.9 22.9 + - - -
33N LEU* 4.3 11.0 - - + -
36N GLY* 3.8 25.1 - - - +
39N PHE* 4.0 12.0 - - + -
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Residues in contact with PHE 140 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78M CYS 3.4 26.0 - - - -
79M SER* 3.9 4.7 - - - -
80M SER 3.7 22.7 - - - +
81M THR* 3.8 23.3 + - + -
83M GLU 4.9 0.6 + - - +
89M MET* 3.9 10.5 - - + -
93M ASN* 4.0 5.6 - - - -
116M SER* 3.9 22.9 - - - -
118M ALA* 4.1 6.3 - - + -
138M ASN* 3.2 8.8 + - - +
139M VAL* 1.3 82.7 - - - +
141M GLY* 1.3 66.0 + - - +
143M SER* 2.6 25.1 + - - -
144M LYS* 3.2 28.4 + - + +
400M NAP 3.1 28.3 - - - -
402M BMA 3.7 18.4 - - - -
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Residues in contact with GLY 141 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118M ALA* 4.4 13.9 - - - -
119M THR* 3.8 2.3 - - - +
136M PRO* 3.4 16.8 - - - +
138M ASN* 2.7 22.2 + - - -
140M PHE* 1.3 82.3 - - - +
142M TYR* 1.3 57.8 + - - +
144M LYS* 3.2 6.2 + - - +
145M PHE* 2.8 29.8 + - - +
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Residues in contact with TYR 142 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90M MET* 4.1 29.4 - - + -
136M PRO* 3.6 8.8 - - + +
138M ASN 2.9 7.2 + - - +
139M VAL* 3.5 8.5 - - + +
140M PHE 3.2 0.2 - - - -
141M GLY* 1.3 77.0 - - - +
143M SER* 1.3 57.5 + - - +
145M PHE* 3.2 25.0 + + - +
146M LEU* 2.9 52.9 + - + +
33N LEU* 4.7 6.7 - - + -
39N PHE* 3.7 44.4 - + + -
42N LEU* 3.3 37.3 + - + +
43N VAL* 4.1 22.0 - - - -
47N ILE* 3.7 7.3 - - - +
50N TYR* 5.8 1.3 - + - -
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Residues in contact with SER 143 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89M MET* 3.6 15.7 - - - +
90M MET* 3.9 22.2 - - - -
93M ASN* 3.2 33.1 + - - +
94M TYR* 4.1 12.0 + - - +
139M VAL 2.9 13.5 + - - -
140M PHE 2.6 20.0 + - - -
142M TYR* 1.3 76.2 - - - +
144M LYS* 1.3 61.5 + - - +
146M LEU 4.0 0.2 + - - -
147M PHE* 3.5 19.9 + - - +
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Residues in contact with LYS 144 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74M HIS 5.9 0.2 + - - -
76M GLY 5.0 1.4 + - - -
77M ALA* 3.6 13.8 - - - +
93M ASN* 4.6 7.8 - - + +
113M TYR* 5.9 0.2 - - - -
114M ALA* 3.0 26.5 + - - +
115M SER* 4.1 12.1 - - - +
116M SER* 4.2 10.3 - - - +
119M THR* 3.9 14.4 - - + -
140M PHE* 3.2 31.4 + - + +
141M GLY* 3.2 7.5 + - - +
142M TYR 3.1 0.2 - - - -
143M SER* 1.3 82.9 + - - +
145M PHE* 1.3 65.3 + - - +
147M PHE* 3.1 7.6 + - + +
148M ASP* 3.0 25.4 + - - -
400M NAP 2.9 40.5 + - - -
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Residues in contact with PHE 145 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119M THR* 3.5 13.1 - - + +
131M ARG* 3.5 42.6 - - + -
134M GLU* 3.2 41.5 - - + -
136M PRO* 3.9 16.6 - - + -
141M GLY 2.8 17.0 + - - +
142M TYR* 3.5 29.2 - + - +
144M LYS* 1.3 77.4 - - - +
146M LEU* 1.3 73.0 + - + +
148M ASP* 3.0 8.5 + - - +
149M GLU* 3.0 45.4 + - + +
152M ARG* 4.9 0.2 - - - -
166M ARG* 5.6 0.4 - - - -
42N LEU 5.5 0.4 - - - -
43N VAL 4.3 5.6 - - - -
45N LEU 4.9 4.3 - - - -
46N ASN* 5.5 0.2 - - - -
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Residues in contact with LEU 146 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90M MET* 3.7 14.8 - - + -
94M TYR* 3.5 30.2 + - + +
142M TYR* 2.9 43.0 + - + +
143M SER 4.5 0.7 - - - +
145M PHE* 1.3 89.8 - - + +
147M PHE* 1.3 57.7 + - - +
149M GLU* 3.3 10.7 + - + +
150M TYR* 2.9 22.5 + - - +
47N ILE* 4.0 25.6 - - + +
48N ALA 5.8 0.9 - - - +
49N ASP* 4.8 2.0 - - - +
50N TYR* 3.6 32.3 - - + +
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Residues in contact with PHE 147 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93M ASN 6.0 0.2 - - - -
94M TYR* 3.6 18.1 - + + -
97M SER* 3.6 35.4 - - - -
98M LYS* 3.5 34.5 - - + -
101M LEU* 4.0 16.2 - - + -
111M PHE* 4.0 7.9 - + - -
113M TYR* 3.7 39.3 - + - -
143M SER 3.5 12.4 + - - +
144M LYS* 3.1 11.0 + - + +
146M LEU* 1.3 77.1 - - - +
148M ASP* 1.3 59.9 - - - +
150M TYR* 2.9 10.2 + + + +
151M VAL* 2.8 47.2 + - + +
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Residues in contact with ASP 148 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113M TYR* 2.7 42.1 + - - -
115M SER* 2.6 28.6 + - - -
119M THR* 4.2 3.8 - - - +
144M LYS 3.0 15.1 + - - +
145M PHE* 3.0 8.0 + - - +
147M PHE* 1.3 75.0 - - - +
149M GLU* 1.3 58.8 + - - +
151M VAL* 3.2 2.9 + - - +
152M ARG* 2.8 39.9 + - - +
166M ARG* 2.8 24.9 + - - +
232M ILE* 3.8 14.4 - - + +
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Residues in contact with GLU 149 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131M ARG* 3.7 24.7 - - - +
145M PHE* 3.0 38.6 + - + +
146M LEU* 3.4 17.7 - - + +
148M ASP* 1.3 76.4 - - - +
150M TYR* 1.3 63.5 + - - +
152M ARG* 2.9 40.6 + - - +
153M GLN* 3.2 31.5 + - - +
46N ASN* 4.3 10.4 - - - +
47N ILE 5.2 8.0 + - - +
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Residues in contact with TYR 150 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94M TYR* 3.7 18.6 - - + +
98M LYS* 3.6 32.5 + - + +
101M LEU* 4.0 22.4 - - + -
102M HIS* 2.6 37.2 + + - -
146M LEU 2.9 13.4 + - - +
147M PHE* 2.9 15.2 + + + +
149M GLU* 1.3 74.4 - - - +
151M VAL* 1.3 67.7 + - - +
153M GLN* 3.1 26.2 + - + +
154M ILE* 3.2 27.0 + - + +
48N ALA 3.9 12.6 - - - -
49N ASP* 4.2 12.1 - - + -
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Residues in contact with VAL 151 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101M LEU* 4.3 8.5 - - + -
113M TYR* 3.5 28.0 - - + +
147M PHE* 2.8 45.2 + - + +
148M ASP 3.5 7.2 - - - +
150M TYR* 1.3 72.2 - - - +
152M ARG* 1.3 58.7 + - - +
154M ILE* 2.9 10.0 + - - +
155M LEU* 2.8 44.8 + - + +
162M ILE* 3.7 26.0 - - + -
231M GLY 5.8 1.1 - - - +
232M ILE* 4.4 8.3 - - + -
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Residues in contact with ARG 152 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129M GLU* 3.5 25.1 + - - +
130M SER* 3.8 1.8 - - - +
131M ARG* 3.9 10.0 - - - +
134M GLU* 2.5 43.9 + - - -
145M PHE* 4.6 0.4 - - - -
148M ASP* 2.8 23.5 + - - +
149M GLU* 2.9 33.6 + - - +
150M TYR 3.2 0.4 - - - -
151M VAL* 1.3 76.5 - - - +
153M GLN* 1.3 60.6 + - - +
155M LEU* 4.1 11.9 - - + +
156M PRO* 3.4 19.6 - - - +
166M ARG* 4.0 6.4 - - - +
232M ILE* 3.9 27.0 - - + +
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Residues in contact with GLN 153 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149M GLU* 3.2 22.6 + - - +
150M TYR* 3.1 23.7 + - + +
152M ARG* 1.3 77.0 - - + +
154M ILE* 1.3 64.5 + - + +
156M PRO* 3.7 8.3 - - - +
157M GLU* 5.3 2.6 + - - +
47N ILE 4.2 4.9 + - - -
48N ALA* 2.9 48.1 + - - +
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Residues in contact with ILE 154 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101M LEU* 4.3 6.1 - - + -
102M HIS* 4.5 15.5 - - + -
105M LEU* 3.5 28.7 - - + -
150M TYR* 3.5 38.6 - - + +
151M VAL* 2.9 10.2 + - - +
153M GLN* 1.3 81.6 - - + +
155M LEU* 1.3 65.8 + - - +
156M PRO 3.4 0.2 - - - -
157M GLU* 3.0 19.2 + - + +
158M ALA* 3.2 9.8 + - + +
162M ILE* 3.9 16.6 - - + -
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Residues in contact with LEU 155 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151M VAL* 2.8 32.0 + - + +
152M ARG* 4.1 14.4 - - + +
154M ILE* 1.3 76.2 - - - +
156M PRO* 1.4 69.8 - - + +
157M GLU 3.0 1.2 + - - -
158M ALA* 3.2 20.8 + - + +
162M ILE* 4.0 31.0 - - + +
230M SER* 4.1 21.3 - - - -
231M GLY* 4.2 18.8 - - - -
232M ILE* 5.1 2.9 - - + +
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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
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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