Contacts of the strand formed by residues 301 - 306 (chain B) in PDB entry 2EZT
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 TYR 301 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208B THR* 3.8 29.6 - - + -
278B ASP 3.0 4.8 + - - -
279B VAL* 3.4 23.6 - - + +
280B VAL 3.2 23.6 + - - -
299B THR* 3.3 6.7 - - - +
300B ARG* 1.3 130.3 + - + +
302B PHE* 1.3 61.3 + - - +
303B LEU* 4.0 2.0 - - + -
319B ASP* 3.2 25.1 - - + +
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Residues in contact with PHE 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B VAL* 3.7 15.0 - - + -
282B PHE* 3.4 49.1 - + + -
296B PHE* 3.7 43.3 - + + -
299B THR* 4.6 3.4 - - + -
300B ARG 4.3 0.4 + - - -
301B TYR* 1.3 72.7 - - - +
303B LEU* 1.3 62.7 + - - +
304B GLN* 4.7 5.6 - - + -
315B ARG* 5.2 0.7 - - + -
316B HIS* 3.8 34.1 - - + +
317B LYS 3.4 15.9 - - - +
318B THR* 3.3 31.2 - - + +
319B ASP* 2.8 33.6 + - - +
320B ILE 3.6 2.1 + - - -
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Residues in contact with LEU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B LEU* 3.4 41.1 - - + +
208B THR* 3.8 19.1 - - + -
209B LEU* 3.8 24.9 - - + +
279B VAL* 3.9 18.4 - - + -
280B VAL 2.9 13.3 + - - +
281B LEU* 4.0 8.1 - - + -
282B PHE* 2.7 36.7 + - - +
301B TYR* 4.7 1.3 - - + -
302B PHE* 1.3 79.3 - - - +
304B GLN* 1.3 58.0 + - - +
319B ASP* 4.5 4.7 - - + -
320B ILE* 3.4 33.2 - - + +
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Residues in contact with GLN 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B LEU* 4.0 2.2 - - - +
281B LEU* 4.5 0.2 - - - -
282B PHE* 3.2 32.4 - - + +
285B ASN 4.7 3.0 + - - -
302B PHE* 4.7 3.8 - - + -
303B LEU* 1.3 76.9 - - - +
305B ILE* 1.3 75.8 + - - +
306B ASP* 3.9 14.1 + - - +
311B LYS* 2.8 28.6 + - - +
312B LEU* 3.5 11.4 - - + -
313B GLY* 3.0 27.1 + - - -
314B LYS 5.0 0.6 - - - +
315B ARG* 5.8 1.2 - - - +
318B THR* 3.9 14.3 + - + -
320B ILE 2.8 11.2 + - - +
321B ALA* 3.4 8.3 - - + +
322B VAL* 2.8 27.3 + - - +
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Residues in contact with ILE 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B LEU* 4.2 8.1 - - + -
281B LEU* 3.8 21.8 - - + -
282B PHE 3.0 7.8 + - - +
283B VAL* 3.5 18.1 - - + -
284B GLY* 2.8 29.5 + - - -
304B GLN* 1.3 78.7 - - - +
306B ASP* 1.3 64.4 + - - +
322B VAL* 3.5 9.9 - - + +
324B ALA* 3.8 18.2 - - + +
326B ALA* 4.0 16.4 - - - -
329B THR* 3.6 41.3 - - + +
330B LEU* 4.3 7.6 - - + -
333B ILE* 4.2 14.4 - - + -
1615B FAD 4.3 0.3 + - - -
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Residues in contact with ASP 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B GLY* 4.0 0.3 - - - -
285B ASN 3.8 15.2 + - - +
304B GLN* 3.9 17.6 + - - +
305B ILE* 1.3 74.4 - - - +
307B ILE* 1.3 70.2 + - - +
308B ASP* 2.9 13.6 + - - +
311B LYS* 3.7 14.6 - - + +
312B LEU* 4.3 8.8 - - + +
322B VAL 3.2 6.1 + - - +
323B LEU* 3.3 12.6 - - - +
324B ALA 3.0 23.6 + - - -
1615B FAD 2.8 55.0 + - - -
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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
------------------------------------------------------------
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