Contacts of the strand formed by residues 211 - 216 (chain A) in PDB entry 6PAU
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 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A THR* 3.7 4.2 - - - -
161A LEU* 3.0 40.9 + - + +
163A LEU* 4.0 13.7 - - + +
201A LEU* 2.8 41.8 + - + +
202A ARG* 3.9 11.8 + - + -
206A TRP* 3.7 29.1 - + - +
207A LEU 4.1 5.9 + - - -
208A LEU* 3.1 11.8 + - - +
209A GLN 4.6 0.9 - - - -
210A TRP* 1.3 83.4 - - - +
212A CYS* 1.3 59.5 + - - +
213A GLY 3.6 0.2 + - - -
225A PHE* 3.7 20.2 - + + -
226A ILE 4.0 0.9 - - - -
227A SER* 4.2 13.9 - - - -
228A ALA 4.5 8.1 + - - -
229A ILE* 4.8 0.2 - - - +
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Residues in contact with CYS 212 (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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158A TRP* 3.4 37.5 - - - -
159A ASP 4.4 1.1 - - - -
209A GLN 4.5 0.2 - - - +
211A HIS* 1.3 70.0 - - - +
213A GLY* 1.3 59.2 + - - +
225A PHE* 3.3 5.3 - - - -
226A ILE* 2.9 51.6 + - + +
263A LEU* 3.8 7.3 - - - +
266A GLU* 3.9 9.6 - - - -
267A ILE* 4.4 12.6 - - + -
270A ARG* 3.7 31.0 - - - +
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Residues in contact with GLY 213 (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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158A TRP* 3.7 7.3 - - - -
159A ASP* 2.9 41.0 + - - -
161A LEU* 4.3 8.0 - - - +
211A HIS 3.6 2.2 + - - -
212A CYS* 1.3 73.4 - - - +
214A VAL* 1.3 67.0 + - - +
222A LEU* 4.3 3.8 - - - -
224A GLY 3.3 10.3 - - - -
225A PHE* 4.1 6.9 - - - -
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Residues in contact with VAL 214 (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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152A LEU* 3.9 12.3 - - + -
156A PHE* 3.9 33.9 - - + -
157A MET 3.4 10.1 - - - +
158A TRP* 3.5 29.6 - - + -
213A GLY* 1.3 77.3 - - - +
215A ARG* 1.3 58.5 + - - +
222A LEU* 3.5 3.9 - - - +
223A VAL* 2.8 32.9 + - + +
224A GLY* 2.9 21.0 + - - -
259A VAL* 4.4 8.1 - - + -
263A LEU* 3.8 21.8 - - + -
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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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156A PHE* 3.4 5.3 - - - +
157A MET* 2.9 50.9 + - + +
159A ASP* 2.5 41.0 + - + +
161A LEU* 4.0 16.4 - - - +
168A VAL* 4.3 10.5 - - - +
171A GLU* 2.8 41.2 + - - +
214A VAL* 1.3 76.9 - - - +
216A VAL* 1.3 63.6 + - - +
220A LYS* 2.8 44.9 + - - +
221A LYS 3.0 9.0 - - - +
222A LEU* 3.9 16.1 - - + +
223A VAL* 4.0 5.2 - - - -
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Residues in contact with VAL 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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155A GLY* 3.5 11.9 - - - +
156A PHE* 4.6 2.0 - - + +
215A ARG* 1.3 71.8 - - - +
217A SER* 1.3 60.0 + - - +
218A SER* 3.6 17.5 - - - +
219A ASN* 3.3 23.6 - - - +
220A LYS* 2.7 35.3 + - - +
221A LYS* 2.8 15.2 + - + +
223A VAL* 3.6 32.5 - - + -
254A LEU* 3.8 17.9 - - + -
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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