Contacts of the strand formed by residues 161 - 168 (chain A) in PDB entry 2YD0
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 GLY 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A HIS* 1.3 75.0 - - - +
162A PHE* 1.3 60.1 + - - -
163A TYR* 3.6 1.4 + - - -
180A THR* 3.2 5.5 - - - -
181A GLN 2.9 37.0 + - - -
182A PHE* 3.6 13.1 - - - -
186A ALA* 3.6 19.7 - - - +
189A MET* 4.3 12.6 - - - -
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Residues in contact with PHE 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ILE* 3.8 20.4 - - + -
69A ALA* 3.8 23.6 - - + -
76A PHE* 3.8 31.8 - + + -
154A ASN 4.7 0.5 - - - +
155A LEU* 3.5 28.5 - - + -
156A SER* 2.9 22.2 + - - -
160A HIS 3.9 0.2 + - - -
161A GLY* 1.3 69.3 - - - -
163A TYR* 1.3 57.5 + - - +
178A ALA* 3.9 25.6 - - + -
179A SER 3.5 12.1 - - - -
180A THR* 3.7 12.3 - - + -
182A PHE* 4.2 1.0 - - - -
189A MET* 5.1 3.6 + - - +
190A ALA* 4.1 17.5 - - + +
249A PHE* 3.7 26.9 - + - -
251A ILE* 4.2 7.2 - - + -
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Residues in contact with TYR 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A LEU* 4.8 3.8 - - - -
156A SER* 3.4 9.0 - - - +
158A THR 3.5 23.1 - - - +
159A PHE* 3.4 30.0 + + - -
160A HIS 3.7 9.6 - - - +
161A GLY 3.8 10.5 - - - -
162A PHE* 1.3 75.6 - - - +
164A LYS* 1.3 73.2 + - - +
165A SER* 4.0 10.0 + - - -
178A ALA* 3.3 7.1 - - - -
179A SER* 2.8 52.8 + - - +
180A THR 3.9 19.9 + - - -
181A GLN* 3.9 3.3 - - + +
311A ILE* 4.0 5.2 - - + +
313A ASP* 2.8 32.9 + - + -
314A PHE* 3.4 23.4 - - - -
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Residues in contact with LYS 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A LEU* 3.9 30.5 - - + +
155A LEU* 4.5 15.1 - - + +
156A SER 3.0 15.6 + - - +
157A GLU* 2.8 33.9 + - - +
158A THR 4.6 3.3 - - - +
163A TYR* 1.3 83.6 - - - +
165A SER* 1.3 65.9 + - - +
166A THR* 4.0 20.5 - - + +
176A ILE* 3.9 22.9 - - + -
177A LEU 3.7 4.0 - - - -
313A ASP* 4.7 3.5 - - - +
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Residues in contact with SER 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A TYR* 4.0 11.0 + - - -
164A LYS* 1.3 75.8 - - - +
166A THR* 1.3 63.2 + - - +
176A ILE* 3.5 3.6 - - - +
177A LEU* 2.8 51.6 + - - +
179A SER* 5.4 1.3 - - - -
311A ILE* 4.4 3.4 - - - -
312A PRO* 3.6 14.6 - - - +
313A ASP* 2.5 40.6 + - - -
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Residues in contact with THR 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LYS* 4.0 28.5 - - + +
165A SER* 1.3 79.1 - - - +
167A TYR* 1.3 66.9 + - - +
174A LEU* 3.9 23.9 - - + +
175A ARG 3.1 11.7 - - - +
176A ILE* 4.5 10.5 - - + -
177A LEU* 4.6 0.7 - - - -
312A PRO* 3.7 5.6 - - - +
313A ASP* 2.9 11.1 + - - +
828A LYS* 2.8 29.5 + - - -
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Residues in contact with TYR 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A THR* 1.3 77.8 - - - +
168A ARG* 1.3 76.3 + - - +
169A THR* 4.6 6.1 - - + -
174A LEU* 3.5 7.4 - - - +
175A ARG* 2.7 68.5 + - + +
176A ILE 5.5 0.9 - - - -
177A LEU* 3.8 26.0 - - + -
253A ASP* 2.8 40.5 + - - -
254A PHE* 5.3 0.7 - + - -
272A VAL* 3.8 38.1 - - + -
273A PRO* 3.6 10.9 - - + +
274A ASP* 5.4 3.4 - - - -
312A PRO* 4.3 12.8 - - + -
329A GLU* 5.8 0.2 - - - +
828A LYS* 4.7 3.4 - - - +
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Residues in contact with ARG 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A TYR* 1.3 87.1 - - - +
169A THR* 1.3 67.6 + - - +
170A LYS 3.9 0.3 + - - -
172A GLY* 2.6 39.4 + - - -
173A GLU* 3.4 2.4 - - - +
174A LEU* 3.5 39.4 - - + +
274A ASP* 4.4 2.9 - - - +
793A LEU* 6.1 0.9 - - - +
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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