Contacts of the strand formed by residues 169 - 174 (chain D) in PDB entry 1EAK
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 ILE 169 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D TRP* 4.3 3.6 - - + +
124D ILE* 4.1 21.1 - - + -
125D THR 2.8 8.8 + - - +
126D TYR* 3.2 6.0 - - + +
127D ARG 3.1 21.8 + - - -
148D PHE* 3.6 33.4 - - + -
159D PHE* 4.2 7.9 - - + -
167D ALA* 4.1 1.8 - - - -
168D ASP* 1.3 80.9 - - - +
170D MET* 1.3 60.8 + - - +
171D ILE* 3.6 17.0 + - + -
203D GLY* 3.2 27.1 - - - +
205D SER* 3.7 12.8 - - - +
405D PHE* 4.3 0.4 - - + -
408D ALA* 3.9 17.9 - - + -
409D MET* 4.2 5.6 - - - -
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Residues in contact with MET 170 (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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127D ARG* 3.8 11.4 - - - +
129D ILE* 3.4 35.4 - - + -
165D GLY 4.3 5.8 - - - +
166D GLU* 3.0 51.6 - - + +
167D ALA* 3.2 24.7 - - - +
169D ILE* 1.3 71.0 - - - +
171D ILE* 1.3 61.6 + - - +
172D ASN 4.0 0.2 + - - -
204D ASP* 2.8 35.4 + - - +
205D SER 3.1 23.7 + - - +
206D HIS* 4.4 4.1 - - - +
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Residues in contact with ILE 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D TYR* 3.8 27.4 - - + -
127D ARG 2.9 13.3 + - - +
128D ILE* 4.1 8.3 - - + -
129D ILE* 2.6 35.6 + - - +
130D GLY 3.5 1.0 + - - +
144D PHE* 3.3 45.1 - - + -
148D PHE* 3.8 2.9 - - + -
169D ILE* 3.9 11.7 - - + +
170D MET* 1.3 74.8 - - - +
172D ASN* 1.3 63.8 + - - +
173D PHE* 4.9 1.3 - - + -
205D SER* 3.6 4.5 - - - +
207D PHE* 4.0 7.9 - - + -
405D PHE* 3.5 38.1 - - + -
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Residues in contact with ASN 172 (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 ILE* 3.5 21.9 + - + +
130D GLY* 3.1 28.0 - - - +
131D TYR 4.6 0.2 - - - +
170D MET* 4.0 0.9 + - + +
171D ILE* 1.3 75.1 - - - +
173D PHE* 1.3 91.5 + - - +
205D SER 3.2 6.3 + - - -
206D HIS* 3.3 22.2 - - + +
207D PHE* 2.8 27.5 + - - -
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Residues in contact with PHE 173 (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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298B GLN* 4.9 0.5 - - - +
852B SO4 5.5 2.4 + - - -
130D GLY 4.0 5.2 - - - -
131D TYR* 3.7 32.8 - - - +
132D THR* 3.1 43.1 - - + -
140D VAL* 4.2 2.0 - - + -
144D PHE* 3.7 27.4 - + - -
171D ILE* 4.9 0.9 - - + -
172D ASN* 1.3 99.8 + - - +
174D GLY* 1.3 59.9 + - - +
178D HIS* 5.7 1.3 - - - -
207D PHE* 3.1 22.7 - - + +
209D ASP* 3.9 15.2 - - - +
213D TRP* 4.2 19.7 - + - -
397D LEU* 3.9 20.6 - - + -
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Residues in contact with GLY 174 (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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298B GLN* 3.6 11.0 - - - -
172D ASN 4.4 0.2 + - - -
173D PHE* 1.3 75.5 - - - +
175D ARG* 1.3 60.8 + - - -
178D HIS* 4.5 17.0 - - - -
184D PHE* 2.9 25.7 - - - -
206D HIS* 5.8 0.2 - - - +
207D PHE 2.9 7.3 + - - -
209D ASP* 3.1 20.2 + - - +
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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