Contacts of the strand formed by residues 358 - 364 (chain A) in PDB entry 2EJU
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 SER 358 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A GLU 4.7 4.5 - - - -
193A HIS* 5.1 2.7 - - - -
321A PHE* 4.1 19.7 - - - -
323A ASP* 3.4 19.0 + - - -
354A ARG* 5.9 0.3 - - - +
355A THR* 2.8 25.5 + - - +
356A HIS 3.2 3.2 - - - -
357A PHE* 1.3 83.3 - - - +
359A PRO* 1.3 76.9 - - - +
360A THR* 3.5 6.6 + - - -
361A GLY 3.3 14.7 + - - +
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Residues in contact with PRO 359 (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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193A HIS* 6.5 0.7 - - + -
338A VAL* 4.4 8.7 - - - +
354A ARG* 4.6 13.2 + - - +
355A THR 4.9 0.9 - - - +
358A SER* 1.3 91.1 - - - +
360A THR* 1.3 69.1 + - + +
361A GLY 3.4 3.1 + - - +
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Residues in contact with THR 360 (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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323A ASP* 2.8 31.9 + - - -
324A THR* 3.2 27.6 + - - -
325A HIS* 4.4 21.1 - - + +
338A VAL* 4.0 18.4 - - + +
358A SER* 3.2 3.8 + - - -
359A PRO* 1.3 87.0 - - + +
361A GLY* 1.3 62.0 + - - +
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Residues in contact with GLY 361 (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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321A PHE* 3.7 22.4 - - - -
322A TYR 3.6 6.3 - - - -
323A ASP* 4.2 1.3 - - - -
338A VAL* 4.9 2.1 - - - +
354A ARG* 3.9 5.4 - - - +
355A THR* 3.6 23.9 + - - +
358A SER* 3.3 14.0 + - - +
359A PRO 3.4 2.8 - - - +
360A THR* 1.3 81.2 - - - +
362A ILE* 1.3 65.7 + - - +
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Residues in contact with ILE 362 (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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321A PHE* 3.2 6.1 - - - +
322A TYR* 2.9 38.0 + - - +
324A THR* 3.8 18.2 - - - +
338A VAL* 4.0 27.1 - - + +
341A ILE* 3.6 34.8 - - + -
342A ILE* 4.0 15.0 - - + -
345A LEU* 4.3 11.9 - - + -
352A ALA* 4.4 2.0 - - + -
353A THR 3.5 8.1 - - - +
361A GLY* 1.3 78.6 - - - +
363A LYS* 1.3 73.8 + - - +
364A THR* 3.8 4.9 + - - +
371A PHE* 4.1 15.0 - - + -
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Residues in contact with LYS 363 (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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194A GLU* 2.7 34.9 + - - -
198A ARG* 4.5 1.4 - - - +
315A GLU* 3.7 23.6 - - + -
316A LEU* 3.6 28.3 - - + +
317A ASP* 5.8 0.2 + - - -
318A ILE* 2.7 28.7 + - + +
320A LEU 3.0 20.1 + - - +
321A PHE* 4.0 7.0 - - + -
352A ALA* 3.1 4.3 - - - -
353A THR* 2.9 44.8 + - - +
355A THR* 3.7 24.2 - - - +
357A PHE* 4.4 2.5 - - - -
362A ILE* 1.3 72.5 - - - +
364A THR* 1.3 60.2 + - - +
601A GOL 4.3 3.9 + - - -
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Residues in contact with THR 364 (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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316A LEU* 3.8 9.4 - - - +
318A ILE* 3.8 15.4 - - - +
320A LEU 5.4 0.6 + - - -
321A PHE* 5.5 1.0 - - - +
322A TYR* 3.8 34.7 - - + -
345A LEU* 3.9 9.6 - - - +
350A TYR* 4.2 2.4 - - - +
351A GLU 2.7 19.6 + - - -
352A ALA* 4.0 6.7 - - - +
362A ILE* 3.8 3.5 + - + +
363A LYS* 1.3 76.2 - - - +
365A SER* 1.3 64.2 + - - +
366A ALA* 3.1 28.5 + - + +
371A PHE* 4.2 11.7 - - + -
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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