Contacts of the strand formed by residues 358 - 364 (chain B) in PDB entry 2YTZ
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190B GLU 4.8 3.1 - - - -
321B PHE* 3.8 16.6 - - - -
323B ASP* 2.8 26.7 + - - -
355B THR* 2.9 18.9 + - - +
356B HIS 3.2 2.6 - - - -
357B PHE* 1.3 84.5 - - - +
359B PRO* 1.3 76.2 - - - +
360B THR* 3.3 9.2 + - - -
361B GLY* 3.1 17.7 + - - +
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Residues in contact with PRO 359 (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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311B MET* 6.5 1.1 - - + -
338B VAL* 3.9 13.0 - - - +
354B ARG* 4.3 10.2 + - - +
355B THR 4.8 1.1 - - - +
356B HIS 5.7 0.4 - - - +
358B SER* 1.3 88.6 - - - +
360B THR* 1.3 68.4 + - + +
361B GLY 4.7 1.9 - - - +
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Residues in contact with THR 360 (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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323B ASP* 3.0 24.1 + - - -
324B THR* 3.0 32.0 + - - -
325B HIS* 3.5 37.6 - - + +
338B VAL* 4.1 14.0 - - + +
358B SER* 3.3 2.6 + - - -
359B PRO* 1.3 86.4 - - + +
361B GLY* 1.3 60.8 + - - +
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Residues in contact with GLY 361 (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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321B PHE* 3.7 21.1 - - - -
322B TYR 3.4 7.2 - - - -
323B ASP* 4.1 1.3 - - - -
338B VAL* 4.5 3.3 - - - +
354B ARG* 4.1 3.1 - - - +
355B THR* 3.4 24.0 + - - +
358B SER* 3.1 17.3 + - - +
359B PRO 4.7 1.0 - - - +
360B THR* 1.3 80.2 - - - +
362B ILE* 1.3 65.2 + - - +
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Residues in contact with ILE 362 (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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321B PHE* 3.2 7.1 - - - +
322B TYR* 2.8 36.3 + - - +
324B THR* 3.5 21.8 - - - +
338B VAL* 3.7 27.1 - - + +
341B ILE* 3.9 25.4 - - + -
342B ILE* 3.5 28.7 - - + -
345B LEU* 4.3 11.2 - - + -
352B ALA* 4.3 0.2 - - + -
353B THR 3.7 2.5 - - - +
360B THR 4.3 0.4 - - - +
361B GLY* 1.3 80.8 - - - +
363B LYS* 1.3 71.4 + - - +
364B THR* 3.7 5.2 + - - +
371B PHE* 4.1 15.0 - - + -
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Residues in contact with LYS 363 (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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194B GLU* 2.9 31.8 + - - -
198B ARG* 4.6 1.0 - - - +
281B LEU* 5.6 0.4 - - - +
315B GLU* 3.6 20.3 + - + -
316B LEU* 3.8 22.8 + - + +
318B ILE* 2.7 32.9 + - + +
320B LEU 3.1 21.6 + - - +
321B PHE* 3.8 7.9 - - + -
352B ALA* 2.9 6.4 - - - +
353B THR* 2.9 48.4 + - - +
355B THR* 3.7 23.3 - - - +
357B PHE* 4.2 4.2 - - - -
362B ILE* 1.3 70.2 - - - +
364B THR* 1.3 61.8 + - - +
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Residues in contact with THR 364 (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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259B PHE* 5.9 2.4 - - - -
316B LEU* 4.1 4.9 - - - +
318B ILE* 3.6 18.9 - - - +
320B LEU 5.3 1.2 + - - -
321B PHE* 5.5 0.8 - - - +
322B TYR* 3.6 36.2 - - + -
345B LEU* 4.0 10.3 - - + +
350B TYR* 4.3 0.9 - - - +
351B GLU 2.7 19.9 + - - -
352B ALA* 4.2 6.3 - - - -
362B ILE* 3.7 4.0 + - + +
363B LYS* 1.3 75.3 - - - +
365B SER* 1.3 60.7 + - - +
366B ALA* 3.0 27.5 + - + +
371B PHE* 4.4 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