Contacts of the strand formed by residues 161 - 166 (chain B) in PDB entry 4YZS
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 161 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156B PRO* 3.3 3.5 - - - +
157B SER* 2.6 43.5 + - - +
159B ASP* 3.8 5.7 - - + +
160B GLY* 1.3 80.9 - - - +
162B LEU* 1.3 61.3 + - - +
163B PHE* 3.9 17.9 - - + -
174B THR* 5.9 2.2 - - + -
177B PHE 4.4 4.3 - - - +
178B THR* 4.0 11.0 - - + +
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Residues in contact with LEU 162 (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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154B ILE* 3.6 23.6 - - + -
155B ILE 3.5 3.4 - - - -
156B PRO* 4.0 17.9 - - + -
160B GLY 3.8 6.7 - - - +
161B ALA* 1.3 83.5 - - - +
163B PHE* 1.3 68.7 + - - +
174B THR* 4.4 2.3 - - - +
175B VAL* 3.2 37.2 + - + +
177B PHE* 3.3 33.1 + - + +
178B THR 3.7 16.8 - - - +
179B VAL* 4.0 12.6 - - + +
182B LEU* 4.9 9.2 - - + -
245B VAL* 6.4 0.2 - - + -
259B PHE* 4.4 15.5 - - + -
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Residues in contact with PHE 163 (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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154B ILE* 3.2 6.1 - - - -
155B ILE* 2.5 53.1 + - + +
157B SER* 3.4 30.1 - - - -
161B ALA* 3.9 17.3 - - + -
162B LEU* 1.3 76.4 - - - +
164B GLN* 1.3 61.2 + - - +
165B TRP 3.7 1.2 + - - -
172B MET* 4.1 22.9 - - + -
173B GLU 3.6 5.8 - - - +
174B THR* 3.4 34.3 - - + -
175B VAL* 4.5 1.1 - - - +
397B LEU* 3.5 27.8 - - + -
399B SER* 5.4 7.4 - - - -
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Residues in contact with GLN 164 (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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152B LYS 2.9 33.4 + - - +
153B MET 3.4 7.4 - - - +
154B ILE* 4.5 13.2 - - + +
163B PHE* 1.3 71.2 - - - +
165B TRP* 1.3 64.8 + - - +
166B ASP* 3.6 8.6 + - + +
171B SER 3.7 0.2 - - - +
172B MET* 3.5 3.2 - - - -
173B GLU* 2.7 58.7 + - + +
174B THR 5.6 0.2 - - - -
175B VAL* 4.5 16.4 - - + +
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Residues in contact with TRP 165 (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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152B LYS* 3.0 20.1 - - - +
153B MET* 2.8 46.6 + - + +
155B ILE* 3.7 12.6 - - + -
163B PHE 3.7 2.0 + - - -
164B GLN* 1.3 69.6 - - - +
166B ASP* 1.3 72.0 + - - +
167B ARG* 3.3 27.2 + - + +
170B GLU* 4.8 8.7 - - - +
171B SER 3.4 18.8 - - - -
172B MET* 3.5 24.5 - - + -
395B LEU* 3.9 17.9 - - + -
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Residues in contact with ASP 166 (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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152B LYS* 3.6 16.4 - - + +
164B GLN* 3.6 10.0 + - + +
165B TRP* 1.3 74.6 + - - +
167B ARG* 1.3 57.7 + - - +
168B ASP* 2.8 37.4 + - - +
169B ARG* 3.8 31.0 + - + +
170B GLU 3.1 20.6 + - - -
171B SER* 3.0 30.4 + - - +
173B GLU* 4.9 6.4 - - - +
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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