Contacts of the strand formed by residues 209 - 216 (chain A) in PDB entry 4AOR
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 LYS 209 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A ILE* 4.4 0.2 - - - -
127A SER* 3.5 14.1 - - - +
128A LEU 3.5 20.4 - - - +
129A PRO* 3.9 20.4 - - + -
130A THR* 4.4 24.2 + - - +
205A VAL* 3.3 6.2 - - - +
206A CYS 2.9 30.7 + - - +
207A SER* 3.9 12.4 + - - +
208A GLY* 1.3 88.0 - - - +
210A LEU* 1.3 59.5 + - - +
211A GLN* 3.1 14.3 + - - +
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Residues in contact with LEU 210 (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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51A SER* 3.6 36.1 - - - +
53A ILE* 4.3 11.2 - - + -
59A VAL* 4.1 27.1 - - + -
126A ILE* 4.0 12.0 - - + +
127A SER 3.0 17.5 + - - +
128A LEU* 4.7 3.4 - - + -
129A PRO* 3.1 22.0 - - + +
203A PRO* 3.7 11.7 - - + -
204A VAL 3.7 8.5 - - - +
205A VAL* 4.0 6.1 - - + -
209A LYS* 1.3 69.6 - - - +
211A GLN* 1.3 56.6 + - - +
212A GLY 3.5 24.2 - - - +
213A ILE* 5.3 0.4 - - + -
232A VAL* 3.4 19.0 - - + +
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Residues in contact with GLN 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A PRO* 3.5 25.1 - - - +
130A THR 5.4 0.2 - - - +
131A SER* 3.0 24.5 + - - +
132A CYS 4.2 0.4 - - - -
133A ALA* 3.8 27.0 + - + +
165A ILE* 5.1 0.7 - - + -
184A PHE* 3.3 19.9 - - + -
204A VAL 2.9 5.1 + - - -
206A CYS* 3.8 36.8 + - + +
209A LYS* 3.1 17.4 + - - +
210A LEU* 1.3 73.2 - - - +
212A GLY* 1.3 58.9 + - - +
231A LYS* 3.8 1.2 - - - +
232A VAL* 2.9 26.2 + - - -
233A CYS* 3.8 11.3 - - - +
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Residues in contact with GLY 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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184A PHE* 3.7 9.6 - - - -
202A GLY 3.8 0.5 - - - +
203A PRO 3.8 0.3 - - - -
204A VAL* 3.0 40.3 + - - +
210A LEU* 3.5 13.4 - - - +
211A GLN* 1.3 81.7 - - - +
213A ILE* 1.3 65.7 + - - +
229A TYR* 4.5 0.2 - - - -
230A THR 3.2 8.3 - - - -
232A VAL* 3.7 1.5 - - - +
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Residues in contact with ILE 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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59A VAL* 3.5 20.0 - - + -
60A SER 3.5 4.0 - - - +
61A ALA* 3.8 15.0 - - + +
107A ASP 4.0 4.7 - - - +
108A ILE* 3.5 41.1 - - + -
201A GLY* 3.6 31.9 - - - +
202A GLY 3.3 4.3 - - - +
210A LEU* 5.3 1.3 - - + -
212A GLY* 1.3 78.2 - - - +
214A VAL* 1.3 72.6 + - - +
215A SER* 3.1 3.3 + - - -
229A TYR* 3.3 7.5 - - - +
230A THR* 3.1 33.8 + - - +
232A VAL* 3.6 13.0 - - + -
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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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61A ALA* 4.1 3.8 - - - +
141A ILE* 4.1 18.8 - - + -
142A SER 4.9 2.2 - - - +
195A SER* 3.5 23.8 - - - +
199A ASP* 3.3 39.0 - - + +
200A SER* 3.7 5.5 - - - +
201A GLY 2.9 22.4 + - - +
202A GLY* 3.0 20.3 + - - +
203A PRO 4.6 1.1 - - - +
204A VAL* 4.5 0.4 - - + +
213A ILE* 1.3 75.5 - - - +
215A SER* 1.3 60.7 + - - +
229A TYR* 3.5 21.0 - - + -
32D ARG* 3.9 12.1 - - + -
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Residues in contact with SER 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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63A HIS* 3.3 23.0 - - - -
104A LEU* 4.7 2.1 + - - +
107A ASP* 2.7 28.9 + - - +
200A SER* 3.8 0.9 + - - -
213A ILE* 3.1 8.6 + - - -
214A VAL* 1.3 76.1 - - - +
216A TRP* 1.3 81.2 + - - +
228A VAL 3.4 14.2 + - - -
229A TYR* 4.4 1.1 - - - -
230A THR* 3.8 13.2 - - - -
31D LEU* 3.8 0.7 - - - -
32D ARG* 3.3 17.6 + - - +
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Residues in contact with TRP 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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104A LEU* 3.6 24.6 - - + +
175A TYR* 3.7 37.9 - + - -
178A GLN* 3.8 30.1 - - + -
179A ILE* 4.0 3.1 - - + -
183A MET* 3.6 20.3 - - + +
215A SER* 1.3 103.9 - - - +
217A GLY* 1.3 71.6 + - - +
228A VAL* 2.8 64.2 + - + +
1254A IMD 3.5 34.1 - + - -
30D ILE* 3.2 28.9 - - + +
31D LEU* 4.4 0.7 - - - -
32D ARG* 3.7 15.3 + - - +
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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