Contacts of the strand formed by residues 162 - 168 (chain A) in PDB entry 1Y8Q
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 HIS 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A VAL* 3.4 10.6 - - - +
159A PHE* 2.9 34.4 + - + +
161A TYR* 1.3 83.4 - - + +
163A GLY* 1.3 59.5 + - - +
239A ASP* 3.1 37.7 + - - +
242A LEU* 3.6 27.0 - - + +
246A LEU* 6.0 0.2 - - + -
291A PHE* 5.8 4.5 - - + -
294A TYR* 3.7 31.4 + + + -
295A CYS* 4.9 0.6 - - + +
302A VAL* 3.5 4.7 - - - +
331A PHE 3.3 8.5 - - - +
332A ASP* 3.3 30.9 + - - -
334A MET* 5.4 1.1 - - + -
335A LYS* 4.9 4.6 + - - -
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Residues in contact with GLY 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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157A ASP 3.3 12.6 - - - -
158A VAL* 4.1 1.8 - - - -
159A PHE* 5.4 2.0 - - - -
162A HIS* 1.3 79.0 - - - +
164A TYR* 1.3 64.6 + - - +
239A ASP* 4.9 0.9 - - - +
306A VAL* 3.7 20.0 - - - -
330A PHE* 3.7 3.6 - - - +
331A PHE* 2.9 29.6 + - - +
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Residues in contact with TYR 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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139A ILE* 4.1 10.0 - - - +
155A THR* 3.4 29.2 + - + +
156A GLY* 3.1 23.6 - - - -
157A ASP* 3.0 46.3 + - + +
159A PHE* 4.5 6.3 - + - -
163A GLY* 1.3 76.8 - - - +
165A THR* 1.3 86.2 + - - +
166A PHE* 4.1 10.3 - - + -
243A LEU* 3.6 45.0 - - + +
247A LEU* 5.1 3.3 - - + +
306A VAL* 3.8 5.4 - - - +
328A PHE* 4.2 6.3 - + - -
329A PHE* 3.0 13.5 - - - +
330A PHE* 3.8 16.4 - - + -
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Residues in contact with THR 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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155A THR 3.3 8.7 - - - -
164A TYR* 1.3 86.8 - - - +
166A PHE* 1.3 63.6 + - - +
306A VAL* 3.7 17.5 - - + +
309A ILE* 4.9 2.8 - - + +
310A LEU* 3.6 42.3 - - + +
313A GLU* 5.5 4.6 - - - +
327A ASN 4.5 0.4 + - - -
328A PHE* 3.4 3.8 - - - -
329A PHE* 2.8 61.2 + - + +
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Residues in contact with PHE 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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153A PHE* 4.0 8.5 - + - -
154A PHE* 3.3 8.5 - - - +
155A THR* 2.8 49.7 + - + +
164A TYR* 4.1 2.0 - - + -
165A THR* 1.3 77.6 - - - +
167A ALA* 1.3 84.0 + - - +
168A ASN* 3.8 9.4 - - + -
214A CYS 4.0 9.6 - - - -
216A VAL* 3.4 44.9 - - + -
219A ALA* 3.6 23.6 - - + -
310A LEU* 4.8 1.0 - - - +
327A ASN* 3.3 27.1 - - - -
328A PHE* 3.6 30.5 - + + -
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Residues in contact with ALA 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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153A PHE 3.3 4.9 - - - -
154A PHE* 3.8 26.0 - - + -
166A PHE* 1.3 92.1 - - - +
168A ASN* 1.3 61.2 + - - +
169A LEU* 4.3 5.4 - - + -
213A PHE* 3.5 27.6 - - + +
313A GLU* 5.7 4.7 - - + +
324A PRO* 6.3 0.4 - - + -
325A HIS 4.6 5.4 - - - +
327A ASN* 2.9 17.7 + - - +
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Residues in contact with ASN 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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143A ASP* 2.9 38.4 + - - +
147A HIS* 4.8 16.6 - - - +
151A ILE 4.4 2.3 - - - +
152A LYS* 4.1 1.4 - - - -
153A PHE* 2.9 28.9 + - + +
166A PHE* 3.8 9.4 - - + -
167A ALA* 1.3 75.1 - - - +
169A LEU* 1.3 60.9 + - - +
170A GLY* 3.1 18.0 + - - -
213A PHE* 3.9 7.6 - - - +
214A CYS 3.1 23.7 + - - +
215A PRO* 3.3 9.1 - - - +
216A VAL 3.9 0.2 - - - +
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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