Contacts of the strand formed by residues 245 - 252 (chain A) in PDB entry 2O07
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 GLN 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A CYS* 3.7 20.8 - - - +
210A GLN* 2.9 45.9 - - - +
211A TRP* 3.3 12.2 - - + -
233A TYR* 5.1 0.4 + - - -
235A TYR* 3.5 14.9 - - + +
236A CYS 3.2 17.7 - - - +
237A THR* 4.1 5.2 - - + -
238A ILE* 3.6 8.8 + - - -
241A TYR* 4.1 5.3 + - - +
242A PRO 3.3 14.6 + - - +
243A SER 4.2 6.3 - - - +
244A GLY* 1.3 79.4 - - - +
246A ILE* 1.3 64.7 + - - +
237B THR* 3.1 36.4 + - + +
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Residues in contact with ILE 246 (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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79A TYR* 3.6 29.2 - - + -
206A GLN* 3.6 35.2 - - + +
208A GLU* 4.3 14.8 - - - +
209A CYS* 4.5 5.4 - - + +
233A TYR* 4.5 0.7 - - - -
235A TYR* 3.3 4.7 - - - -
236A CYS* 3.0 27.8 + - - -
238A ILE* 4.3 5.8 - - + -
241A TYR* 3.8 26.7 - - + -
242A PRO* 6.2 0.4 - - + -
245A GLN* 1.3 77.8 - - - +
247A GLY* 1.3 68.7 + - - +
248A PHE* 3.9 8.6 - - + -
601A SPD 4.3 15.0 - - + -
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Residues in contact with GLY 247 (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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206A GLN* 3.7 1.6 - - - -
207A GLY* 2.6 28.7 + - - -
208A GLU 3.1 13.4 + - - -
233A TYR* 3.4 17.4 + - - -
234A ALA 3.0 13.0 - - - -
235A TYR* 3.8 0.9 - - - -
246A ILE* 1.3 80.7 - - - +
248A PHE* 1.3 67.7 + - - -
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Residues in contact with PHE 248 (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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79A TYR* 3.6 33.2 - + - -
82A MET* 3.9 19.7 - - + -
83A ILE* 3.7 31.2 - - + -
86A LEU* 3.6 22.4 - - + -
204A CYS* 3.7 17.7 - - - -
205A CYS 3.3 9.2 - - - -
206A GLN* 4.5 1.1 - - - -
207A GLY* 4.2 0.2 - - - -
232A ALA 3.8 0.2 - - - +
233A TYR* 3.3 14.2 - - - -
234A ALA* 2.7 42.4 + - + +
235A TYR* 4.1 0.7 - - - -
236A CYS* 3.7 37.0 - - + -
246A ILE* 3.9 10.1 - - + -
247A GLY* 1.3 78.4 - - - -
249A MET* 1.3 59.9 + - - +
250A LEU* 3.8 3.1 + - + +
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Residues in contact with MET 249 (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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190A TYR* 3.7 39.0 - - + +
203A LEU* 3.8 1.2 - - - +
204A CYS* 3.2 6.2 - - - -
205A CYS* 2.9 33.9 + - + +
207A GLY* 3.9 12.0 - - - +
217A ILE* 4.8 5.2 - - + +
220A MET* 4.3 11.9 - - + -
221A ARG* 4.2 26.7 - - + +
224A CYS* 4.1 6.5 - - - -
231A VAL* 3.5 29.2 - - + -
232A ALA 3.8 6.1 - - - +
233A TYR* 4.9 13.7 - - + -
248A PHE* 1.3 71.8 - - - +
250A LEU* 1.3 62.6 - - - +
251A CYS* 3.9 11.2 - - - -
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Residues in contact with LEU 250 (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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86A LEU* 4.1 11.4 - - + -
87A PRO* 4.0 19.1 - - + -
203A LEU 3.3 9.0 - - - +
204A CYS* 3.7 30.3 - - + -
231A VAL* 3.3 5.0 - - - +
232A ALA* 2.9 35.4 + - + +
234A ALA* 4.1 13.7 - - + +
248A PHE* 4.6 4.7 - - + +
249A MET* 1.3 75.6 - - - +
251A CYS* 1.3 63.6 + - - +
259A PHE* 3.9 31.8 - - + -
288A PHE* 3.5 37.5 - - + -
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Residues in contact with CYS 251 (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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190A TYR* 4.4 0.2 - - - -
197A LEU* 5.1 0.7 - - - +
202A VAL* 3.3 3.1 - - - -
203A LEU* 2.8 58.0 + - + +
224A CYS* 3.7 38.6 - - - -
228A PHE* 3.6 27.4 - - + -
230A VAL 3.3 5.2 - - - +
231A VAL* 4.3 3.4 - - - -
249A MET* 3.9 7.4 - - - -
250A LEU* 1.3 80.5 - - - +
252A SER* 1.3 58.9 + - - +
259A PHE* 3.6 4.8 - - - -
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Residues in contact with SER 252 (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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197A LEU* 5.9 0.2 - - - -
201A GLY 3.6 4.4 + - - -
202A VAL* 3.5 10.5 - - - +
228A PHE* 3.5 9.3 - - - +
229A PRO* 3.1 23.4 - - - +
230A VAL* 2.9 13.3 + - - -
251A CYS* 1.3 74.0 - - - +
253A LYS* 1.3 57.8 + - - +
254A ASN* 3.0 16.7 + - - +
257A THR* 2.7 38.7 + - - -
259A PHE* 3.7 13.7 - - - -
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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