Contacts of the strand formed by residues 214 - 218 (chain A) in PDB entry 6YB9
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 TRP 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ILE* 4.0 20.0 - - + -
64A ILE* 3.9 25.4 - - + -
176A LEU* 4.3 12.1 - - + -
180A TRP* 3.6 37.9 - + - -
187A LEU* 3.6 23.1 - - + -
189A ASP 3.3 15.0 - - - +
190A MET* 4.0 5.8 - - + -
209A ILE* 3.8 26.9 - - + -
210A ASP 3.8 10.3 - - - -
211A ASN* 3.1 28.4 + - - +
212A ASP 3.4 1.1 - - - +
213A SER* 1.3 76.7 - - - +
215A ARG* 1.3 60.3 + - - +
216A LEU* 4.0 16.1 - - + +
227A ASP* 3.2 22.6 - - + +
228A LYS* 4.8 0.3 + - - +
232A ARG* 5.4 0.2 + - - -
252A VAL* 4.1 8.7 - - + -
256A VAL* 4.8 0.2 - - + -
502A OK8 3.4 12.5 + - - -
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Residues in contact with ARG 215 (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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105A THR* 3.8 20.9 + - - +
106A GLY* 3.9 14.0 - - - -
187A LEU* 3.6 7.8 - - - +
188A VAL* 3.0 38.5 + - + -
189A ASP* 2.8 48.1 + - - +
214A TRP* 1.3 74.1 - - - +
216A LEU* 1.3 60.5 - - - +
217A TRP* 4.2 11.7 - - - +
225A GLN* 5.7 0.2 - - - -
227A ASP* 3.4 20.9 - - - +
229A GLN* 3.0 37.4 + - + +
232A ARG* 4.5 3.2 - - - +
502A OK8 3.0 55.2 + - - +
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Residues in contact with LEU 216 (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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180A TRP* 3.7 52.9 - - + -
185A CYS* 3.8 29.8 - - + -
186A THR 3.6 9.0 - - - +
187A LEU* 4.2 8.5 - - + -
214A TRP* 4.0 26.0 - - + +
215A ARG* 1.3 68.8 - - - +
217A TRP* 1.3 67.2 + - - +
218A PRO* 3.6 2.9 - - + +
225A GLN* 3.5 0.3 - - - -
226A LYS* 3.1 28.8 + - + -
227A ASP* 3.2 12.1 + - + +
251A TRP* 5.0 4.0 - - + -
252A VAL* 4.2 17.9 - - + -
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Residues in contact with TRP 217 (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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103A ILE* 4.5 23.6 - - + -
105A THR* 4.5 10.1 - - + -
117A GLU* 4.2 13.0 - - + -
118A GLY* 6.3 0.2 - - - -
185A CYS* 4.4 1.3 - - - -
186A THR* 2.9 36.2 + - + +
188A VAL* 3.4 38.5 - - + +
215A ARG* 4.3 13.7 - - - +
216A LEU* 1.3 84.0 - - - +
218A PRO* 1.4 67.3 - - - +
220A GLY* 3.1 27.9 + - - -
221A ASP 3.7 14.8 - - - +
222A ARG* 3.6 46.9 - - + +
225A GLN* 3.8 23.4 + - + +
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Residues in contact with PRO 218 (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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184A ASN 3.7 8.5 - - - +
185A CYS* 4.2 6.4 - - - -
216A LEU* 3.6 8.1 - - + +
217A TRP* 1.4 79.8 - - - +
219A SER* 1.3 64.2 + - - +
221A ASP* 2.9 25.3 + - - +
224A GLN* 3.2 48.9 - - + +
226A LYS* 3.7 21.8 - - + +
251A TRP* 4.0 23.6 - - + -
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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