Contacts of the strand formed by residues 321 - 325 (chain B) in PDB entry 2E4Y
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 321 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B ILE* 4.2 17.5 - - + -
208B PHE* 5.4 1.6 - - + -
210B TRP* 4.6 8.7 - - + -
296B THR* 5.5 3.0 - - + +
297B TRP 2.5 17.3 + - - +
298B VAL* 2.9 21.9 - - + +
299B ALA 2.8 22.3 + - - +
319B GLY 5.3 0.4 - - - +
320B ALA* 1.3 78.7 - - - +
322B THR* 1.3 65.2 + - - +
323B LEU* 5.6 1.3 - - + -
468B VAL* 4.0 22.4 - - + -
469B PHE 3.1 15.5 - - - +
470B ASN* 4.7 4.3 - - + +
483B VAL* 5.8 0.9 - - + -
492B LEU* 5.8 1.6 - - + -
497B ILE* 4.4 17.0 - - + -
499B TRP* 3.6 37.0 - - + -
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Residues in contact with THR 322 (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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297B TRP 4.8 2.0 - - - +
299B ALA* 3.2 32.1 - - + -
303B TRP* 3.5 31.4 - - + +
304B GLY 2.7 25.4 + - - -
320B ALA* 4.2 2.5 + - + -
321B ILE* 1.3 79.7 - - - +
323B LEU* 1.3 63.8 + - - +
469B PHE* 2.8 43.5 + - - +
471B LEU* 5.6 1.3 + - + +
480B TYR* 3.6 13.1 - - + -
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Residues in contact with LEU 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B GLN* 4.1 20.0 - - + +
200B ALA* 3.9 24.7 - - + +
201B MET* 3.4 36.3 - - + +
204B ILE* 4.2 8.5 - - + -
299B ALA 2.9 12.5 + - - +
301B ASP* 3.0 25.8 + - - -
304B GLY* 3.4 10.4 - - - -
321B ILE* 5.7 1.3 - - + -
322B THR* 1.3 74.6 - - - +
324B GLU* 1.3 61.8 + - - +
466B TYR* 4.8 8.5 - - + -
467B ASN 3.4 15.9 - - - +
468B VAL* 3.5 34.8 - - + -
486B TRP* 5.8 0.4 - - + -
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Residues in contact with GLU 324 (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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64B ARG* 4.0 12.8 + - - -
301B ASP* 3.6 9.5 - - - +
304B GLY* 3.8 19.5 - - - -
305B ALA* 4.0 10.6 + - + +
306B GLN* 5.8 0.2 - - - +
323B LEU* 1.3 75.6 - - - +
325B LEU* 1.3 84.7 + - - +
387B GLU* 4.9 0.9 - - - +
388B SER* 3.1 37.3 + - - +
389B LYS* 3.0 27.1 + - - +
466B TYR* 3.1 9.1 - - - +
467B ASN* 2.7 35.1 + - + +
469B PHE* 4.6 17.7 - - + -
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Residues in contact with LEU 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B THR* 4.5 10.3 - - + -
191B VAL* 3.7 37.2 - - + -
192B PRO* 4.1 12.8 - - + -
197B GLN* 5.2 2.9 - - - +
301B ASP* 5.1 5.4 - - + +
324B GLU* 1.3 102.0 + - + +
326B ALA* 1.3 62.5 + - - +
327B SER* 3.2 9.9 + - - -
388B SER* 3.9 0.7 + - - +
389B LYS* 4.0 16.6 - - - +
392B PHE* 3.7 23.1 - - + -
465B ARG 3.7 2.7 - - - +
466B TYR* 3.2 37.5 - - + -
467B ASN* 3.8 7.0 + - - -
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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
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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