Contacts of the strand formed by residues 172 - 177 (chain D) in PDB entry 5MEN
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 SER 172 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135D LEU* 4.1 8.5 - - - -
136D PHE 3.2 13.9 - - - -
137D THR* 4.0 9.6 - - - -
139D PHE* 3.7 8.6 - - - -
157D ASP 4.2 0.3 - - - +
158D LYS* 3.2 3.1 - - - -
159D CYS 2.9 32.3 + - - +
161D LEU* 4.3 8.5 - - - +
170D SER* 4.0 5.0 + - - -
171D ASN* 1.3 82.5 + - - +
173D ALA* 1.3 59.4 + - - +
139E THR* 6.4 0.7 - - - -
190E ARG* 2.5 31.8 + - - -
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Residues in contact with ALA 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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135D LEU* 3.5 3.8 - - - +
136D PHE* 2.9 29.5 + - + +
139D PHE* 4.1 2.2 - - + -
145D VAL* 4.3 11.7 - - + -
156D THR* 3.6 27.8 - - - +
158D LYS* 4.1 10.1 - - - +
172D SER* 1.3 74.1 - - - +
174D VAL* 1.3 71.4 + - - +
188D PHE* 4.0 17.9 - - + -
190E ARG* 4.3 2.0 - - - +
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Residues in contact with VAL 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D VAL* 4.1 21.8 - - + -
134D CYS 3.1 12.6 - - - +
135D LEU* 4.0 12.6 - - + -
154D TYR 4.2 0.3 - - - +
155D ILE* 3.5 1.0 - - - +
156D THR* 3.0 43.1 + - + +
173D ALA* 1.3 81.5 - - - +
175D ALA* 1.3 61.7 + - - +
176D TRP* 4.2 11.0 - - + -
188D PHE* 3.8 3.8 - - - -
141E VAL* 4.3 13.5 - - + -
143E LEU* 5.3 0.9 - - + -
188E SER* 4.4 12.6 - - - +
190E ARG* 3.8 27.6 - - - -
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Residues in contact with ALA 175 (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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133D VAL* 3.9 0.9 - - - +
134D CYS* 2.9 34.2 + - + +
153D VAL* 5.6 0.7 - - + -
154D TYR 3.2 6.1 - - - -
155D ILE* 3.4 24.5 - - + -
174D VAL* 1.3 74.9 - - - +
176D TRP* 1.3 63.3 + - - +
182D PHE* 4.5 2.0 - - + -
187D ALA* 3.8 23.3 - - + -
188D PHE* 3.6 16.8 - - + -
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Residues in contact with TRP 176 (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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132D SER 4.1 9.9 - - - +
133D VAL* 3.7 17.0 - - + +
153D VAL* 3.6 0.9 - - - +
154D TYR* 2.7 85.5 + + + +
156D THR* 4.2 12.3 - - + -
174D VAL* 4.2 12.3 - - + -
175D ALA* 1.3 76.2 - - - +
177D SER* 1.3 64.6 + - - +
178D ASN* 4.8 1.3 - - + -
182D PHE* 3.8 10.5 - - - -
143E LEU* 3.6 40.1 - - + +
145E THR* 4.4 9.4 + - - +
174E LEU* 4.1 16.6 - - + -
176E GLU* 5.2 2.0 - - - -
186E ALA* 3.4 36.1 - - + -
187E LEU* 4.8 1.1 - - - -
188E SER* 5.3 0.9 - - - -
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Residues in contact with SER 177 (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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132D SER 5.2 2.8 + - - +
152D ASP* 2.3 35.0 + - - -
153D VAL* 3.2 11.1 - - - +
154D TYR* 4.6 0.9 - - - +
176D TRP* 1.3 83.5 - - - +
178D ASN* 1.3 62.0 + - - +
179D LYS* 3.6 12.0 + - - +
182D PHE* 3.2 45.3 - - - -
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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
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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