Contacts of the strand formed by residues 295 - 302 (chain A) in PDB entry 6FD3
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 GLY 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291A GLN* 3.4 4.2 - - - +
292A GLY 3.1 24.9 + - - -
294A SER* 1.3 76.6 - - - +
296A THR* 1.3 59.8 + - - -
297A VAL* 4.3 1.1 + - - +
312A LYS* 4.3 8.5 - - - +
313A GLN 3.2 13.5 - - - -
314A MET* 3.8 8.7 - - - +
603A ADP 2.7 17.3 + - - +
604A EDO 3.3 7.6 - - - -
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Residues in contact with THR 296 (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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288A LYS* 3.8 24.2 - - + -
290A GLY 3.6 11.2 - - - +
291A GLN* 3.6 14.7 + - + +
295A GLY* 1.3 72.9 - - - -
297A VAL* 1.3 60.4 + - - +
298A TYR* 3.6 33.9 - - + +
311A ILE 3.6 2.1 - - - +
313A GLN* 2.8 37.7 + - - +
604A EDO 3.0 20.3 + - - -
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Residues in contact with VAL 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LYS* 3.6 4.3 - - - +
289A ILE* 2.8 46.7 + - + -
290A GLY 2.9 12.3 + - - +
295A GLY 4.8 0.2 - - - +
296A THR* 1.3 77.6 - - - +
298A TYR* 1.3 62.2 + - - +
310A ALA* 4.2 7.4 - - + -
311A ILE 3.3 9.4 - - - +
312A LYS* 4.0 22.2 - - + -
357A MET* 5.2 0.9 - - + -
603A ADP 3.4 63.9 - - + +
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Residues in contact with TYR 298 (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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286A PHE* 3.8 26.9 - + + -
287A GLU* 3.1 8.7 - - - +
288A LYS* 3.5 33.4 - - + +
289A ILE* 4.1 3.8 - - - -
296A THR* 3.6 33.3 - - + +
297A VAL* 1.3 75.5 - - - +
299A THR* 1.3 69.8 + - - +
310A ALA* 3.2 6.1 - - - +
311A ILE* 2.8 36.9 + - + +
313A GLN* 3.3 43.8 + - + -
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Residues in contact with THR 299 (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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285A ARG 3.5 2.3 + - - +
286A PHE* 3.2 5.4 - - - -
287A GLU* 2.8 53.6 + - - +
289A ILE* 3.8 16.6 - - + +
298A TYR* 1.3 75.4 - - - +
300A ALA* 1.3 62.7 + - - +
308A GLU* 3.8 18.8 + - - +
309A VAL 3.3 5.8 - - - +
359A TYR* 3.4 49.1 - - + +
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Residues in contact with ALA 300 (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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283A TYR* 4.0 8.1 - - + -
284A THR 3.5 13.2 - - - +
285A ARG 3.7 4.3 - - - -
286A PHE* 3.9 15.3 - - + -
298A TYR 4.1 0.2 + - - -
299A THR* 1.3 77.5 - - - +
301A LEU* 1.3 64.4 + - - +
308A GLU* 3.4 5.9 - - - +
309A VAL* 2.9 33.4 + - + +
311A ILE* 3.9 28.3 - - + -
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Residues in contact with LEU 301 (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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283A TYR* 3.2 7.0 - - - -
284A THR* 2.8 43.3 + - + +
285A ARG* 3.9 33.0 - - + +
300A ALA* 1.3 74.1 - - - +
302A ASP* 1.3 67.2 + - - +
303A ILE 3.2 0.7 + - - -
306A GLY* 3.7 22.9 - - - +
307A GLN 3.4 2.0 - - - +
308A GLU* 3.8 28.3 - - + +
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Residues in contact with ASP 302 (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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282A LYS* 4.1 3.1 - - - +
283A TYR* 3.7 32.7 + - + -
300A ALA 4.1 0.2 + - - -
301A LEU* 1.3 71.1 - - - +
303A ILE* 1.3 59.4 + - - +
304A ALA* 2.9 22.1 + - - +
305A THR* 3.3 31.4 + - - +
306A GLY* 2.8 30.5 + - - -
307A GLN* 2.9 23.3 + - + +
309A VAL* 4.8 3.8 - - + +
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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