Contacts of the strand formed by residues 163 - 168 (chain B) in PDB entry 5CYP
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 ASN 163 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B HIS 3.0 22.3 + - - +
135B CYS* 3.7 5.9 - - + -
136B CYS* 2.7 34.3 + - - +
162B VAL* 1.3 75.3 - - - +
164B ILE* 1.3 58.9 + - - +
198B TYR* 4.3 17.5 - - + -
200B GLN* 3.5 16.8 + - - +
273B ILE* 3.2 22.1 + - + +
276B ILE* 3.6 9.4 - - - +
277B THR* 3.1 18.8 + - - +
281B HIS* 2.6 29.9 + - - -
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Residues in contact with ILE 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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136B CYS* 3.5 35.7 - - + +
138B TYR* 4.0 14.1 - - + -
155B MET* 3.8 31.4 - - + +
158B LEU* 3.6 37.2 - - + -
159B SER* 4.0 12.1 - - - +
162B VAL* 3.4 11.0 + - + +
163B ASN* 1.3 74.5 - - - +
165B VAL* 1.3 67.7 + - - +
166B PRO* 4.1 3.1 - - + -
195B ILE* 5.7 0.2 - - + -
196B ASP 5.1 1.2 + - - +
197B VAL* 3.5 14.9 - - + +
198B TYR 3.1 26.8 + - - +
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Residues in contact with VAL 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B CYS* 3.9 22.2 - - - -
136B CYS 2.9 9.1 + - - -
137B LEU* 3.3 26.0 - - + +
138B TYR 2.9 21.2 + - - -
164B ILE* 1.3 79.0 - - - +
166B PRO* 1.3 67.4 - - + +
167B VAL* 3.6 2.6 + - + +
198B TYR* 4.4 13.0 - - + +
216B PHE* 4.3 22.0 - - + -
220B ILE* 5.0 0.2 - - + -
222B PHE* 4.0 31.6 - - + -
261B LEU* 4.2 6.5 - - + -
265B LEU* 4.4 3.1 - - + -
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Residues in contact with PRO 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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138B TYR* 3.4 10.8 - - + +
140B ILE* 4.0 17.0 - - + -
155B MET* 3.6 28.9 - - + -
164B ILE* 3.8 7.2 - - - +
165B VAL* 1.3 92.0 - - + +
167B VAL* 1.3 60.4 + - - +
190B LEU* 3.8 6.5 - - + -
197B VAL* 3.7 16.2 - - + -
220B ILE* 3.7 23.3 - - + -
221B PRO* 3.4 11.9 - - + +
222B PHE* 3.3 17.8 + - - -
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Residues in contact with VAL 167 (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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39B LEU* 6.0 0.2 - - + -
137B LEU* 5.0 9.0 - - + -
138B TYR 2.6 16.7 + - - +
139B PHE* 3.9 24.0 - - + -
140B ILE* 2.6 35.5 + - - +
165B VAL* 4.4 6.3 - - + +
166B PRO* 1.3 75.2 - - - +
168B ILE* 1.3 64.1 + - - +
169B ALA 3.3 0.2 + - - -
221B PRO* 4.3 1.8 - - - -
222B PHE* 3.4 29.8 - - + +
224B VAL* 3.5 34.5 - - + -
261B LEU* 3.9 11.9 - - + -
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Residues in contact with ILE 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ILE* 3.8 5.4 - - + +
142B ALA* 4.5 2.5 - - + -
167B VAL* 1.3 70.5 - - - +
169B ALA* 1.3 70.7 + - - +
171B ALA* 3.8 12.6 + - + +
174B LEU* 4.3 13.7 - - + -
179B ARG* 4.7 5.8 - - + +
182B PHE* 3.7 39.7 - - + -
183B LYS* 3.7 24.2 - - + +
221B PRO* 3.6 39.3 - - + +
222B PHE 2.7 13.1 + - - +
223B ALA* 4.0 5.2 - - + -
224B VAL* 3.4 23.4 + - - +
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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