Contacts of the strand formed by residues 187 - 191 (chain A) in PDB entry 2YZ5
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 187 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A HIS 3.0 10.5 + - - -
151A ALA* 3.0 13.6 - - + -
152A ILE 3.0 23.2 + - - -
181A VAL* 4.4 1.8 - - - +
185A GLY 3.9 12.8 - - - -
186A LEU* 1.3 80.2 - - - +
188A LEU* 1.3 66.5 + - - +
218A GLY* 3.3 32.1 - - - +
219A LEU 4.0 1.8 - - - -
220A VAL* 3.9 18.4 - - + -
251A TYR* 3.5 37.9 - + + -
253A PHE* 3.6 25.8 - + + -
258A PRO* 3.4 24.0 - - + -
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Residues in contact with LEU 188 (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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151A ALA* 4.5 3.1 - - - -
152A ILE* 4.0 20.2 - - + +
155A LEU* 4.3 26.2 - - + -
178A LEU* 4.4 13.0 - - + -
181A VAL* 4.6 11.9 - - + -
187A PHE* 1.3 77.8 - - - +
189A ASP* 1.3 61.9 + - - +
190A VAL* 3.2 5.5 + - + +
204A PRO* 4.6 16.6 - - + -
208A LEU 5.5 0.4 - - - +
209A LEU* 4.9 0.2 - - + -
212A ALA* 3.7 29.4 - - + -
217A ILE* 3.7 16.8 - - + -
218A GLY 3.0 8.1 + - - -
219A LEU* 3.7 18.1 - - + -
220A VAL* 2.9 26.6 + - - +
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Residues in contact with ASP 189 (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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5A HIS* 3.2 29.6 + - - +
102A TYR* 4.7 8.4 + - - +
104A ILE* 4.2 10.1 - - + +
151A ALA* 4.6 1.2 - - - +
152A ILE 2.9 24.1 + - - +
153A GLY* 3.4 9.2 - - - -
154A HIS* 3.0 20.3 + - - -
155A LEU 4.8 0.7 + - - -
188A LEU* 1.3 69.7 - - - +
190A VAL* 1.3 61.7 + - - +
191A ASN* 2.9 31.5 + - - +
203A TYR 3.2 12.1 - - - +
204A PRO* 3.7 7.8 - - - +
220A VAL* 3.6 8.7 - - - +
221A LEU 5.2 0.2 - - - -
222A GLY* 4.6 1.9 - - - -
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Residues in contact with VAL 190 (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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188A LEU 3.9 3.6 - - - +
189A ASP* 1.3 69.8 - - - +
191A ASN* 1.3 58.6 + - - +
202A VAL* 4.8 10.1 - - + -
203A TYR 3.1 9.2 - - - +
204A PRO* 4.6 1.3 - - + -
209A LEU* 4.3 10.8 - - + -
219A LEU* 3.6 47.1 - - + -
220A VAL 2.9 12.9 + - - +
221A LEU* 3.4 25.5 - - + +
222A GLY 3.1 24.0 + - - +
238A VAL* 3.7 17.3 - - + -
242A LEU* 4.2 11.4 - - + -
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Residues in contact with ASN 191 (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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5A HIS* 3.4 11.5 + - - -
154A HIS* 4.2 8.1 - - + -
189A ASP* 2.9 25.9 + - - +
190A VAL* 1.3 71.3 - - - +
192A THR* 1.3 60.5 + - - +
193A ALA* 3.0 31.8 + - - +
194A GLY 3.6 2.9 + - - -
202A VAL* 3.4 6.0 - - - -
203A TYR* 2.6 54.2 + - + -
222A GLY 3.5 5.6 - - - -
223A SER 3.8 0.9 - - - +
224A ASP* 2.7 31.2 + - - +
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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