Contacts of the strand formed by residues 175 - 178 (chain B) in PDB entry 3STJ
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 PHE 175 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B LEU* 3.7 2.1 - - - -
163B GLY 3.2 8.4 + - - -
164B ARG* 2.9 43.8 + - + +
167B LEU* 3.6 19.1 - - + -
169B LEU* 4.0 18.8 - - + -
170B GLU* 4.1 23.3 - - + -
172B LEU 5.2 0.9 - - - -
173B GLU* 3.6 33.0 - - + -
174B ASN* 1.3 77.7 - - - +
176B ILE* 1.3 59.9 + - - +
203B THR* 4.1 16.4 - - + -
204B ALA* 5.0 1.8 - - + -
217B PHE* 3.7 29.4 - - + -
218B ALA 3.5 19.5 - - - -
219B ILE* 3.9 24.2 - - + -
220B PRO* 4.4 0.2 - - - -
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Residues in contact with ILE 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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135B LEU* 3.7 14.4 - - + -
159B VAL* 4.0 25.8 - - + -
161B ALA 3.8 4.0 - - - +
162B LEU* 3.9 15.9 - - + -
163B GLY 5.9 0.2 - - - +
174B ASN 5.0 0.2 - - - +
175B PHE* 1.3 71.8 - - - +
177B GLN* 1.3 71.8 + - - +
178B THR* 5.2 0.9 - - - +
191B LEU* 4.0 20.0 - - + -
199B ILE 3.2 30.1 - - - +
200B GLY* 4.5 3.1 - - - -
216B GLY 3.6 0.3 - - - +
217B PHE* 3.2 6.2 - - - -
218B ALA* 2.9 40.2 + - + +
220B PRO* 3.6 26.0 - - + -
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Residues in contact with GLN 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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150A LEU* 3.9 4.7 - - - +
153A THR* 3.2 37.2 + - - +
159B VAL* 3.6 4.0 - - - -
160B SER* 2.7 32.8 + - - -
161B ALA* 2.9 26.3 + - + +
164B ARG* 2.9 32.6 + - + -
175B PHE 3.9 0.2 + - - -
176B ILE* 1.3 76.4 - - - +
178B THR* 1.3 59.2 + - - +
214B GLY 5.2 0.6 + - - -
215B ILE* 3.9 24.2 - - + +
216B GLY 3.2 12.1 - - - +
217B PHE* 3.5 24.3 - - + -
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Residues in contact with THR 178 (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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141B ALA* 4.2 7.3 - - - +
158B ILE 2.9 22.2 + - - -
159B VAL* 4.9 1.6 - - - -
160B SER* 3.8 5.6 - - - -
176B ILE* 5.2 2.5 - - - +
177B GLN* 1.3 75.9 - - - +
179B ASP* 1.3 59.9 + - - +
180B ALA* 3.3 18.0 + - + +
182B ILE* 3.5 31.2 - - + -
191B LEU* 3.9 26.9 - - + -
202B ASN* 4.7 1.1 - - - +
214B GLY 3.3 4.4 - - - +
215B ILE* 4.0 0.3 - - - -
216B GLY* 2.9 36.2 + - - +
217B PHE* 5.5 0.7 - - - -
218B ALA* 5.5 0.4 - - + -
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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