Contacts of the strand formed by residues 140 - 147 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136D VAL* 3.7 8.6 - - - +
139D VAL* 1.3 76.0 - - - +
141D TRP* 1.3 66.8 + - - -
158D ILE 2.9 13.5 - - - -
160D LYS 3.4 10.8 - - - -
177D VAL* 2.9 31.2 + - - +
178D TRP* 3.2 13.2 - - - +
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Residues in contact with TRP 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D LEU* 3.5 57.8 - - + +
90D HIS* 3.6 29.2 - + - -
93D PHE* 3.7 19.3 - + + -
136D VAL* 3.7 10.1 - - - +
140D GLY* 1.3 77.7 - - - -
142D ALA* 1.3 60.9 + - - +
143D ILE* 4.0 10.5 - - + -
157D GLN* 3.5 3.8 - - - -
158D ILE* 2.7 44.3 + - + +
160D LYS 3.3 11.2 - - - -
161D HIS* 3.0 24.0 - + - -
174D ALA* 3.9 14.8 - - + -
175D LEU 3.3 9.0 - - - +
176D ASP* 3.3 46.0 - - + -
177D VAL* 3.9 2.8 - - - +
178D TRP* 3.8 2.2 - - - +
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Residues in contact with ALA 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D PHE* 3.1 26.1 - - + +
132D ALA* 4.1 7.0 - - + -
133D ALA* 3.5 44.0 - - + +
141D TRP* 1.3 71.8 - - - +
143D ILE* 1.3 60.5 + - - +
155D ILE* 5.3 0.2 - - + -
156D LEU 3.5 5.8 - - - -
157D GLN* 4.7 1.1 - - - +
175D LEU 3.0 28.9 + - - +
177D VAL* 4.9 0.2 - - - +
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Residues in contact with ILE 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D LEU* 4.6 7.0 - - + -
129D PHE* 3.8 4.0 - - - -
141D TRP* 4.0 14.3 - - + -
142D ALA* 1.3 76.9 - - - +
144D LEU* 1.3 60.0 + - - +
145D VAL* 3.4 24.7 - - + -
155D ILE* 3.1 10.6 - - - +
156D LEU* 2.9 52.9 + - + +
158D ILE* 3.8 24.7 - - + -
165D HIS* 3.9 16.2 - - + +
166D ALA 5.8 0.2 - - - +
171D VAL* 4.1 15.5 - - + -
173D LEU 3.3 6.1 - - - +
174D ALA* 4.0 23.1 - - + -
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Residues in contact with LEU 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ILE* 4.3 23.1 - - + -
115D ILE* 4.9 2.7 - - + -
119D PHE* 4.6 2.9 - - + -
125D PHE* 3.8 32.8 - - + -
129D PHE* 4.3 9.6 - - + -
143D ILE* 1.3 72.7 - - - +
145D VAL* 1.3 58.8 + - - +
153D LEU* 4.2 23.1 - - + -
154D LEU 3.4 19.7 - - - +
155D ILE* 4.1 4.0 - - + +
171D VAL* 3.6 1.4 - - - +
172D LEU* 2.7 44.5 + - + -
173D LEU* 2.9 31.0 + - + +
203D TRP* 5.2 0.2 - - + -
206D VAL* 4.7 2.7 - - + -
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Residues in contact with VAL 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D ILE* 3.4 32.5 - - + -
144D LEU* 1.3 78.8 - - - +
146D TYR* 1.3 63.8 + - - +
147D GLU* 4.4 2.9 - - + +
153D LEU* 3.3 10.2 - - - +
154D LEU* 2.8 51.3 + - + +
156D LEU* 4.6 14.6 - - + -
166D ALA* 4.9 2.0 - - + +
169D ALA* 3.7 23.3 - - + -
170D GLN 3.0 15.9 - - - +
171D VAL* 4.0 10.5 - - + -
172D LEU* 4.2 1.8 - - - -
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Residues in contact with TYR 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ILE* 4.3 9.2 - - + -
114D LEU* 5.4 2.2 - - + -
145D VAL* 1.3 73.0 - - - +
147D GLU* 1.3 60.1 + - - +
148D PRO* 3.0 37.3 + - + +
151D GLU* 3.1 52.5 + - + +
152D GLN* 3.8 7.6 - - - -
153D LEU* 4.0 11.0 - - + -
169D ALA* 3.5 2.3 - - - -
170D GLN* 2.8 25.4 + - + +
172D LEU* 4.1 10.5 - - + +
210D LEU* 4.7 2.2 - - + -
213D ALA* 3.6 45.4 + - + -
214D LEU* 3.8 29.5 + - + +
216D GLY* 6.0 0.2 - - - -
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Residues in contact with GLU 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A TYR* 2.5 33.0 + - - +
84A LEU* 3.9 24.9 - - + -
88A ILE* 3.9 13.7 - - + +
145D VAL* 3.8 3.0 + - + -
146D TYR* 1.3 72.7 - - - +
148D PRO* 1.3 61.5 - - + +
149D LEU* 3.0 23.9 + - - +
150D GLU* 3.0 22.9 + - - +
151D GLU* 2.7 37.7 + - - -
152D GLN* 2.7 20.5 + - + +
154D LEU* 3.9 16.4 - - + -
166D ALA* 5.4 0.4 - - + -
169D ALA* 4.6 6.5 - - + -
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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