Contacts of the strand formed by residues 140 - 147 (chain M) in PDB entry 1P7G
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 GLY 140 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136M VAL* 3.8 4.6 - - - +
139M VAL* 1.3 77.8 - - - +
141M TRP* 1.3 69.2 + - - -
158M ILE 3.0 13.5 - - - -
160M LYS 3.3 14.4 - - - -
177M VAL* 3.0 31.7 + - - -
178M TRP* 3.6 7.9 - - - -
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Residues in contact with TRP 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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89M LEU* 3.4 45.0 - - + +
90M HIS* 3.3 37.7 - + - -
93M PHE* 3.7 25.6 - + + -
136M VAL* 3.5 13.6 - - - +
140M GLY* 1.3 75.8 - - - -
142M ALA* 1.3 61.9 + - - +
143M ILE* 4.0 9.6 - - + -
157M GLN* 3.7 1.0 - - - -
158M ILE* 2.7 42.5 + - + +
160M LYS 3.2 16.6 - - - -
161M HIS* 3.1 23.0 - + - -
174M ALA* 3.9 9.6 - - + -
175M LEU 3.3 15.0 - - - -
176M ASP* 3.4 45.1 - - + -
177M VAL* 4.0 2.2 - - - -
178M TRP* 3.9 2.6 - - - +
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Residues in contact with ALA 142 (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 PHE* 3.6 23.9 - - + +
132M ALA* 4.4 5.8 - - + -
133M ALA* 3.6 40.2 - - + +
141M TRP* 1.3 73.4 - - - +
143M ILE* 1.3 64.8 + - - +
156M LEU 3.6 5.8 - - - -
157M GLN* 4.9 1.1 - - - +
175M LEU* 3.0 31.4 + - + +
177M VAL* 4.8 0.2 - - - +
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Residues in contact with ILE 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 LEU* 4.3 10.1 - - + -
129M PHE* 3.6 6.8 - - - -
141M TRP* 4.0 16.4 - - + -
142M ALA* 1.3 81.3 - - - +
144M LEU* 1.3 59.0 + - - +
145M VAL* 3.5 24.7 - - + -
154M LEU 3.6 0.3 - - - +
155M ILE* 3.1 9.1 - - - +
156M LEU* 3.0 50.0 + - + +
158M ILE* 3.8 14.1 - - + -
165M HIS* 3.6 29.2 - - + +
166M ALA 5.8 0.4 - - - +
171M VAL* 4.2 10.8 - - + -
173M LEU 3.3 12.1 - - - +
174M ALA* 4.1 12.3 - - + -
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Residues in contact with LEU 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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111M ILE* 4.0 24.0 - - + -
115M ILE* 5.3 0.9 - - + -
119M PHE* 4.6 1.8 - - + -
125M PHE* 3.9 30.1 - - + -
129M PHE* 3.6 10.2 - - + -
143M ILE* 1.3 72.3 - - - +
145M VAL* 1.3 54.0 + - - +
153M LEU* 4.1 29.8 - - + -
154M LEU 3.4 12.1 - - - +
155M ILE* 4.3 6.3 - - + +
171M VAL* 3.6 1.7 - - - -
172M LEU* 2.6 52.6 + - + -
173M LEU* 2.8 30.4 + - + +
203M TRP* 5.6 0.4 - - + -
206M VAL* 4.6 2.5 - - + -
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Residues in contact with VAL 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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143M ILE* 3.5 33.2 - - + -
144M LEU* 1.3 78.9 - - - +
146M TYR* 1.3 63.4 + - - +
147M GLU* 4.4 2.9 - - + +
153M LEU* 3.4 8.8 - - - +
154M LEU* 2.8 52.0 + - + +
156M LEU* 4.3 15.3 - - + -
166M ALA* 5.0 1.6 - - + +
169M ALA* 3.9 22.9 - - + -
170M GLN 3.0 12.6 - - - +
171M VAL* 4.1 13.0 - - + -
172M LEU* 4.2 4.0 - - - -
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Residues in contact with TYR 146 (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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114M LEU* 4.5 7.4 - - + -
118M PHE* 5.7 0.2 - + - -
145M VAL* 1.3 75.2 - - - +
147M GLU* 1.3 67.5 + - - +
148M PRO* 3.1 21.9 - - + +
151M GLU* 3.0 39.7 + - + +
152M GLN* 3.7 22.2 - - - -
153M LEU* 4.3 4.9 - - + -
169M ALA* 3.5 0.5 - - - -
170M GLN* 2.7 32.7 + - + +
172M LEU* 4.1 8.7 - - + +
210M LEU* 3.9 16.2 - - + -
213M ALA* 3.7 44.4 - - + -
214M LEU* 3.9 29.5 + - + +
218P ILE* 5.3 2.0 - - + -
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Residues in contact with GLU 147 (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 VAL* 3.9 3.7 - - + -
146M TYR* 1.3 71.6 - - - +
148M PRO* 1.3 66.0 - - + +
149M LEU* 3.0 27.2 + - - +
150M GLU 3.0 22.0 + - - -
151M GLU* 2.9 30.0 + - - -
152M GLN* 2.8 18.7 + - + +
154M LEU* 3.9 15.7 - - + -
166M ALA* 5.3 0.2 - - + -
167M ALA 5.1 0.5 - - - +
169M ALA* 4.3 9.0 - - + -
18P TYR* 2.6 34.5 + - - +
84P LEU* 3.7 24.7 - - + -
88P ILE* 4.0 13.1 - - + +
220P LEU* 5.2 0.7 - - - +
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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
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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