Contacts of the helix formed by residues 138 - 154 (chain M) in PDB entry 2DFS
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 HIS 138 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100M TYR* 3.2 30.8 - + - -
107M LEU* 3.7 15.7 - - - +
118M ILE* 3.1 51.4 - - + +
119M TYR* 4.1 14.1 - + - -
123M ILE* 4.9 2.9 - - + -
127M TYR* 3.4 31.3 - + + +
136M ASP 3.4 1.8 + - - -
137M PRO* 1.3 77.7 - - - +
139M ILE* 1.3 64.2 + - - +
140M PHE* 3.5 26.5 - + - +
141M ALA* 3.2 14.2 + - - +
142M VAL* 3.4 10.0 + - - +
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Residues in contact with ILE 139 (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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100M TYR* 3.5 30.7 - - + +
107M LEU* 3.8 9.1 - - + +
119M TYR* 4.1 9.9 - - + -
138M HIS* 1.3 72.8 - - - +
140M PHE* 1.3 64.8 + - + +
142M VAL* 3.4 6.8 + - + +
143M ALA* 3.1 25.6 + - - +
159M ILE* 5.4 4.3 - - + -
161M VAL* 5.7 1.6 - - + -
172M SER* 3.6 37.7 - - - +
175M TYR* 4.1 21.1 - - + -
176M ALA* 4.3 14.4 - - + +
659M VAL* 3.8 29.8 - - + -
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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
----------------------------------------------------------
118M ILE 3.6 18.4 - - - -
119M TYR* 3.7 30.1 - + + -
123M ILE* 4.1 7.6 - - + -
124M ILE* 3.6 35.7 - - + -
127M TYR* 3.8 28.3 - + + -
138M HIS* 3.5 16.4 - - - +
139M ILE* 1.3 77.0 - - + +
141M ALA* 1.4 58.5 + - - +
143M ALA* 3.2 4.7 + - + +
144M GLU* 2.9 29.5 + - - +
175M TYR* 3.7 37.2 - + + -
178M ARG* 5.7 0.4 - - + -
179M TYR* 3.6 27.6 - + + -
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Residues in contact with ALA 141 (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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102M TYR* 3.8 22.2 - - + +
127M TYR* 4.0 24.6 - - + -
132M MET* 4.4 18.5 - - + +
135M MET* 5.6 1.3 - - + -
138M HIS 3.2 18.7 + - - +
140M PHE* 1.4 75.6 - - - +
142M VAL* 1.3 62.0 + - + +
144M GLU* 3.5 6.1 + - - +
145M GLU* 3.2 24.8 + - - +
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Residues in contact with VAL 142 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102M TYR* 5.2 2.5 - - + -
107M LEU* 3.9 30.5 - - + +
132M MET* 5.0 13.0 - - + -
138M HIS 3.4 12.0 + - - +
139M ILE* 3.6 11.0 - - + +
140M PHE 3.4 0.4 - - - -
141M ALA* 1.3 76.5 - - + +
143M ALA* 1.4 59.3 + - - +
145M GLU* 3.6 7.0 + - + +
146M ALA* 3.2 21.8 + - - +
159M ILE* 4.3 17.9 - - + -
657M HIS* 3.9 28.1 + - + +
658M TYR 5.0 3.6 - - - +
659M VAL* 4.4 8.5 - - + -
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Residues in contact with ALA 143 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139M ILE 3.1 13.2 + - - +
140M PHE* 3.2 9.4 + - - +
142M VAL* 1.4 74.2 - - - +
144M GLU* 1.3 63.4 + - - +
146M ALA* 3.3 2.3 + - - +
147M TYR* 3.1 18.7 + - - +
159M ILE* 4.4 3.7 - - - +
176M ALA* 4.3 9.0 - - + +
179M TYR* 3.5 28.7 - - + -
180M PHE* 3.2 33.7 - - + -
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Residues in contact with GLU 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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127M TYR* 3.7 12.8 - - + +
128M SER* 3.6 3.3 + - - -
129M GLY* 3.0 32.6 + - - -
130M GLN 3.8 4.3 - - - +
140M PHE 2.9 12.7 + - - +
141M ALA* 3.7 9.0 - - - +
143M ALA* 1.3 73.3 - - - +
145M GLU* 1.3 56.3 + - - +
147M TYR* 3.3 14.4 + - - +
148M LYS* 2.9 55.3 + - - +
179M TYR* 2.6 39.9 + - - +
183M VAL* 4.9 2.3 - - - +
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Residues in contact with GLU 145 (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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132M MET* 3.5 41.4 + - - +
141M ALA 3.2 14.0 + - - +
142M VAL* 3.8 5.8 - - - +
143M ALA 3.3 0.2 - - - -
144M GLU* 1.3 80.1 - - - +
146M ALA* 1.3 55.3 + - - +
148M LYS* 2.7 40.2 + - - +
149M GLN* 3.0 70.2 + - - +
657M HIS* 4.5 6.5 - - - +
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Residues in contact with ALA 146 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142M VAL 3.2 12.3 + - - +
143M ALA 3.3 9.4 + - - +
145M GLU* 1.3 75.3 - - - +
147M TYR* 1.3 61.2 + - - +
149M GLN 3.7 0.2 + - - -
150M MET* 3.2 24.3 + - - +
157M GLN* 3.4 10.6 - - + +
159M ILE* 4.3 4.7 - - + -
180M PHE* 4.0 15.7 - - + -
433M ILE* 3.9 8.7 - - + +
657M HIS* 3.6 33.3 - - + +
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Residues in contact with TYR 147 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143M ALA 3.1 13.2 + - - +
144M GLU* 3.3 18.8 + - - +
146M ALA* 1.3 74.0 - - - +
148M LYS* 1.3 62.4 + - - +
150M MET* 3.4 40.0 - - + +
151M ALA* 3.8 7.3 + - - +
179M TYR* 5.7 0.7 - - + -
180M PHE* 4.1 17.0 - + + -
183M VAL* 3.8 30.6 + - + -
184M SER* 3.3 19.9 - - - -
228M PHE* 3.9 19.7 - + - -
232M TYR* 3.1 33.5 + - + +
433M ILE* 3.9 5.5 - - + +
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Residues in contact with LYS 148 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129M GLY* 5.3 4.7 - - - +
130M GLN 2.7 30.1 + - - +
131M ASN* 4.0 11.8 - - - +
132M MET 4.3 0.2 - - - +
144M GLU* 2.9 37.0 + - - +
145M GLU* 2.7 41.2 + - - +
147M TYR* 1.3 74.9 - - - +
149M GLN* 1.3 60.6 + - + +
150M MET 3.4 0.2 + - - -
151M ALA* 3.6 4.3 + - - +
152M ARG* 3.1 32.7 + - + +
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Residues in contact with GLN 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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145M GLU* 3.0 48.6 + - - +
146M ALA 4.9 0.2 - - - -
148M LYS* 1.3 72.6 - - + +
150M MET* 1.3 64.7 + - - +
152M ARG* 3.9 23.3 - - - +
153M ASP* 2.9 37.3 + - - +
157M GLN* 3.1 19.6 + - - +
655M THR* 4.9 9.9 - - + +
657M HIS* 3.5 21.0 + - - -
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Residues in contact with MET 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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146M ALA 3.2 8.6 + - - +
147M TYR* 3.4 41.5 - - + +
148M LYS 3.2 0.2 - - - -
149M GLN* 1.3 77.4 - - - +
151M ALA* 1.4 56.9 + - + +
154M GLU* 3.0 24.3 + - - -
155M ARG 3.1 30.0 + - - +
157M GLN* 3.2 5.1 - - + +
228M PHE* 4.0 12.8 - - + -
232M TYR* 3.4 42.7 + - + +
431M SER* 4.1 8.7 - - - -
432M PHE 4.1 8.1 - - - +
433M ILE* 3.6 28.7 - - + -
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Residues in contact with ALA 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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147M TYR 3.8 6.0 + - - +
148M LYS* 3.6 5.4 + - - +
150M MET* 1.4 77.6 - - - +
152M ARG* 1.3 65.5 + - - +
153M ASP 3.4 0.8 + - - -
154M GLU* 4.0 11.9 + - - +
232M TYR* 4.2 26.2 - - + -
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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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148M LYS* 3.1 23.0 + - + +
149M GLN* 4.0 22.6 - - - +
151M ALA* 1.3 78.6 - - - +
153M ASP* 1.4 93.9 + - - +
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Residues in contact with ASP 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 GLN* 2.9 23.2 + - - +
152M ARG* 1.4 126.9 + - - +
154M GLU* 1.4 64.7 + - - +
155M ARG* 3.8 23.2 - - + +
157M GLN* 5.6 0.7 - - - -
655M THR* 5.9 0.9 - - - -
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Residues in contact with GLU 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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150M MET 3.0 10.3 + - - +
151M ALA* 4.0 8.4 + - - +
152M ARG 3.8 1.6 - - - -
153M ASP* 1.4 77.6 - - - +
155M ARG* 1.3 58.3 + - - +
156M ASN* 5.5 1.2 + - - -
232M TYR* 2.7 31.1 + - - -
430M HIS* 2.8 31.9 + - - -
431M SER* 4.6 5.3 + - - -
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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