Contacts of the strand formed by residues 323 - 327 (chain A) in PDB entry 2FYT
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 ILE 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287A SER* 3.5 46.0 - - - +
288A MET* 3.8 13.0 - - + -
291A ALA* 3.8 18.6 - - + -
298A VAL* 3.3 14.1 - - + +
300A GLY 4.8 0.4 - - - +
314A ILE* 3.7 43.3 - - + +
319A LEU* 3.0 18.1 + - + +
320A GLU* 3.8 14.7 - - - +
322A THR* 1.3 79.6 - - - +
324A THR* 1.3 70.7 + - - +
325A LEU* 4.2 9.6 + - + +
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Residues in contact with THR 324 (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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297A LYS* 3.5 32.7 + - - +
298A VAL 2.8 11.1 + - - +
299A LEU* 3.5 8.8 - - - -
300A GLY 2.9 26.2 + - - +
322A THR 5.1 0.5 - - - -
323A ILE* 1.3 75.4 - - - +
325A LEU* 1.3 68.5 + - - +
326A ILE* 4.1 19.6 + - + +
336A PRO* 5.7 3.4 - - + -
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Residues in contact with LEU 325 (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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281A CYS* 4.0 20.9 - - + -
284A GLY* 5.2 1.8 - - - -
287A SER* 5.3 0.4 - - - +
300A GLY* 3.4 7.0 - - - +
307A LEU* 3.9 12.1 - - + +
310A ALA* 3.5 22.7 - - + +
311A MET* 3.2 54.4 - - + +
314A ILE* 4.0 20.4 - - + -
323A ILE* 4.2 12.8 - - + +
324A THR* 1.3 84.4 - - - +
326A ILE* 1.3 69.8 + - - +
327A LYS 4.4 0.2 + - - -
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Residues in contact with ILE 326 (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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299A LEU* 4.7 9.6 - - + -
300A GLY 2.8 10.6 + - - +
301A VAL* 3.3 19.7 - - + +
302A ASP 3.1 25.6 + - - -
307A LEU* 3.3 4.9 - - - +
324A THR* 4.1 19.3 - - + +
325A LEU* 1.3 85.6 - - - +
327A LYS* 1.3 61.9 + - - +
328A GLY 3.8 0.3 + - - -
333A VAL* 4.1 33.2 - - + -
334A HIS 4.3 10.5 - - - +
335A LEU* 4.4 8.7 - - + -
336A PRO* 4.4 16.4 - - + -
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Residues in contact with LYS 327 (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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302A ASP 3.3 10.3 - - - +
303A GLN 2.9 21.0 + - - +
304A SER 3.7 9.0 - - - +
305A GLU* 3.3 26.2 + - - -
307A LEU* 3.8 22.3 - - + +
308A TYR* 3.5 30.6 + - + +
326A ILE* 1.3 74.3 - - - +
328A GLY* 1.3 62.2 + - - +
333A VAL* 3.3 12.1 - - - +
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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