Contacts of the strand formed by residues 172 - 177 (chain B) in PDB entry 1MS4
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 THR 172 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B PHE* 3.5 19.9 - - + -
164B PRO 2.4 30.3 + - - +
165B ALA* 2.9 18.1 + - - +
167B MET* 3.5 42.8 - - + -
170B MET* 4.0 1.1 + - + -
171B HIS* 1.3 74.9 - - - +
173B ASN* 1.3 61.2 + - - +
196B VAL* 4.6 4.3 - - + -
197B THR 3.7 3.8 - - - -
198B ASN* 4.2 1.1 - - - +
199B LYS* 3.5 14.7 - - - -
204B PHE* 5.6 2.2 - - + -
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Residues in contact with ASN 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B TRP 5.1 1.2 + - - -
123B HIS* 3.1 26.8 + - - +
124B GLY 4.4 0.4 - - - -
125B ASP* 3.2 28.3 + - - -
126B ALA* 3.4 20.5 + - - +
129B TRP* 4.1 2.6 - - - -
163B PHE* 3.6 10.5 - - - -
172B THR* 1.3 75.1 - - - +
174B GLN* 1.3 75.3 + - - +
197B THR* 2.7 26.0 + - - +
198B ASN 4.0 14.1 - - - +
199B LYS* 2.9 32.2 + - + -
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Residues in contact with GLN 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B TYR* 2.8 28.9 + - - -
120B TRP* 3.4 27.4 + - + +
123B HIS* 3.0 29.3 - - - +
125B ASP 3.1 12.6 - - - +
126B ALA* 4.1 2.4 - - + -
129B TRP* 3.7 33.4 - - + +
163B PHE* 3.5 9.4 - - - -
173B ASN* 1.3 90.6 - - - +
175B PHE* 1.3 63.9 + - - +
196B VAL* 3.4 6.2 - - - +
197B THR* 2.9 34.2 + - - +
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Residues in contact with PHE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LEU* 4.9 0.9 - - + -
120B TRP* 4.0 2.0 - - - -
129B TRP* 3.1 35.9 + + - -
131B ILE* 3.5 48.0 - - + +
159B LEU* 5.1 2.5 - - + -
163B PHE* 3.4 44.6 - + + -
174B GLN* 1.3 77.7 - - - +
176B LEU* 1.3 68.0 + - - +
194B VAL* 3.9 22.2 - - + -
195B GLN 3.1 15.5 - - - +
196B VAL* 4.0 9.6 - - + -
208B PHE* 3.7 44.6 - + - -
219B PHE* 4.2 4.0 - + - -
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Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B VAL* 4.1 9.6 - - + +
96B ASP* 3.4 27.8 - - + +
111B GLY* 3.5 33.9 - - - +
113B TYR* 3.7 19.3 - - + +
120B TRP* 3.6 38.8 - - + +
129B TRP* 4.3 1.1 - - - +
131B ILE* 4.4 4.7 - - - -
175B PHE* 1.3 84.2 - - - +
177B GLY* 1.3 68.9 + - - +
194B VAL* 3.4 7.9 - - - +
195B GLN* 2.9 35.6 + - + +
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Residues in contact with GLY 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B VAL 6.0 0.2 + - - -
96B ASP* 4.2 9.8 + - - +
98B THR* 3.4 16.4 - - - -
109B LEU* 3.9 27.1 + - - +
110B VAL* 5.9 1.0 - - - +
131B ILE* 4.8 0.6 - - - +
176B LEU* 1.3 83.4 - - - +
178B GLY* 1.3 60.9 + - - -
179B ALA 3.1 5.9 + - - -
192B TYR* 5.5 0.2 - - - -
193B PRO 4.0 7.4 - - - -
194B VAL* 4.2 1.3 - - - -
195B GLN* 3.2 16.2 + - - -
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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