Contacts of the strand formed by residues 156 - 161 (chain F) in PDB entry 1YPH
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 GLN 156 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D ILE* 3.9 19.9 - - + +
19D GLY* 4.1 4.9 - - - +
20D GLU* 3.3 24.8 + - - +
21D GLU* 3.5 25.6 + - - +
22D ALA* 4.6 1.1 - - - -
139D THR* 3.2 8.5 - - - +
140D GLY 3.0 37.5 + - - +
142D GLY 5.1 1.6 - - - +
144D THR* 4.2 18.4 - - + +
152F PRO* 3.9 23.4 + - + +
154F ARG* 3.1 21.9 + - - +
155F LEU* 1.3 76.9 - - - +
157F GLN* 1.3 62.7 + - - +
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Residues in contact with GLN 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B PRO* 4.7 1.6 - - - +
9B VAL 2.6 30.2 + - - +
10B LEU* 4.1 6.2 - - - +
16D ILE* 3.9 4.5 - - - -
19D GLY* 3.1 4.5 - - - -
20D GLU* 2.9 64.6 + - - +
21D GLU 4.4 1.4 + - - -
22D ALA* 3.4 19.0 - - + +
23D VAL 4.5 1.4 + - - +
26D SER* 4.7 1.0 + - - -
27D TRP* 2.9 33.8 + - - +
137D VAL* 4.3 5.4 - - + -
138D THR 3.3 7.6 - - - +
139D THR* 3.7 15.9 - - + -
156F GLN* 1.3 76.2 - - - +
158F ALA* 1.3 61.6 + - - +
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Residues in contact with ALA 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ILE* 3.7 22.4 - - + -
19D GLY* 4.0 7.9 - - - -
20D GLU* 4.2 6.7 - - - -
137D VAL* 3.3 6.5 - - - +
138D THR* 2.9 36.7 + - + +
157F GLN* 1.3 77.2 - - - +
159F SER* 1.3 62.5 + - - +
160F LEU* 3.6 2.4 - - - +
188F VAL* 4.0 26.2 - - + -
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Residues in contact with SER 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LEU* 4.4 11.4 - - - +
12B GLY* 3.8 40.8 + - - +
20D GLU* 4.7 4.7 + - - -
135D THR* 3.9 15.2 - - - +
136D CYS 3.2 10.3 - - - -
137D VAL* 3.9 13.1 - - - +
158F ALA* 1.3 72.7 - - - +
160F LEU* 1.3 64.6 + - - +
186F SER* 4.8 1.2 + - - -
188F VAL* 3.8 14.6 - - - +
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Residues in contact with LEU 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D THR* 4.2 5.6 - - - +
136D CYS* 2.8 41.9 + - - +
138D THR* 3.8 15.0 - - + +
158F ALA 3.6 14.6 - - - +
159F SER* 1.3 77.0 - - - +
161F PRO* 1.3 71.8 - - + +
183F ALA* 3.9 12.1 - - + +
184F GLY* 3.9 19.7 - - - +
186F SER* 4.0 2.7 - - - +
188F VAL* 3.8 19.5 - - + +
189F SER* 6.0 0.9 - - - -
190F SER 6.0 2.7 - - - +
199F LEU* 3.8 20.0 - - + -
228F TYR* 3.7 23.3 - - - +
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Residues in contact with PRO 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D GLY* 4.4 13.0 - - - +
134D THR 3.3 10.5 - - - +
135D THR* 4.5 4.7 - - - +
160F LEU* 1.3 86.0 - - + +
162F LEU* 1.3 68.9 + - - +
163F LEU* 4.1 7.5 - - + +
183F ALA* 3.2 4.4 - - - -
184F GLY 2.9 42.5 + - - +
186F SER* 3.3 26.9 - - - +
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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