Contacts of the strand formed by residues 176 - 180 (chain D) in PDB entry 1EFP
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 ALA 176 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D GLU 3.5 2.4 + - - -
116D LEU* 3.4 14.2 - - + +
117D ILE 3.1 22.0 + - - -
141D TRP* 3.7 10.5 - - - -
142D ALA 3.7 16.6 - - - +
172D VAL* 3.9 17.7 - - + -
173D SER 3.5 16.6 - - - +
174D LEU* 2.5 11.4 + - + +
175D PRO* 1.3 74.4 - - - +
177D VAL* 1.3 64.1 + - - +
178D VAL* 5.1 2.7 - - + -
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Residues in contact with VAL 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D ILE* 3.5 16.8 - - + +
119D ALA* 5.2 1.3 - - + -
132D GLY* 3.4 32.3 - - - +
135D LEU* 4.0 20.2 - - + -
136D ALA* 3.8 34.5 - - + +
139D LEU* 4.2 0.4 - - + -
141D TRP* 3.8 15.9 - - + -
142D ALA 3.3 4.6 + - - -
143D GLN* 3.2 6.0 - - + +
144D ALA 3.0 23.4 + - - +
176D ALA* 1.3 76.7 - - - +
178D VAL* 1.3 70.9 - - - +
179D THR* 4.9 1.0 - - + +
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Residues in contact with VAL 178 (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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116D LEU* 4.0 23.1 - - + -
117D ILE 2.7 11.2 + - - +
118D ILE* 3.4 17.7 - - + -
119D ALA 2.8 29.9 + - - -
144D ALA* 3.3 22.9 - - + +
147D ALA* 3.8 22.4 - - + -
150D VAL* 4.4 22.0 - - + -
157D ALA* 6.3 2.2 - - + -
159D VAL* 5.1 1.6 - - + -
172D VAL* 5.9 2.0 - - + -
176D ALA* 5.0 4.3 - - + -
177D VAL* 1.3 80.5 - - - +
179D THR* 1.3 67.5 + - - +
180D ALA* 5.5 0.4 - - - -
184D LEU* 5.6 1.6 - - + -
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Residues in contact with THR 179 (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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118D ILE* 5.3 0.2 - - - -
119D ALA* 2.8 7.0 - - + +
120D GLY 3.4 21.1 - - - +
121D LYS* 4.2 6.1 - - - +
129D ASN* 5.9 1.1 + - - +
132D GLY* 3.9 27.4 - - - +
133D GLN* 4.5 9.6 - - - +
144D ALA 3.0 4.0 + - - -
145D THR* 3.0 32.6 - - + -
146D PHE* 3.0 7.8 + - - -
147D ALA* 3.0 29.5 + - - +
177D VAL* 4.9 2.0 - - + +
178D VAL* 1.3 81.7 - - - +
180D ALA* 1.3 60.3 + - - +
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Residues in contact with ALA 180 (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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38D PHE* 3.4 9.6 - - - +
41D ILE* 3.7 22.0 - - + -
42D ALA* 4.3 11.4 - - - +
118D ILE* 4.9 2.9 - - + -
119D ALA 2.7 13.4 + - - +
120D GLY* 3.8 1.3 - - - -
121D LYS* 2.9 26.7 + - - +
146D PHE* 4.8 0.4 - - - -
147D ALA 4.2 0.4 - - - -
179D THR* 1.3 74.2 - - - +
181D ASP* 1.3 59.3 + - - +
184D LEU* 3.6 27.4 - - + -
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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
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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