Contacts of the strand formed by residues 351 - 356 (chain B) in PDB entry 5ITZ
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 VAL 351 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296B PHE* 4.6 1.6 - - + -
315B VAL* 3.5 20.4 - - + -
332B MET* 3.5 27.6 - - + -
336B GLN* 3.4 42.6 + - + +
343B PHE* 3.5 37.5 - - + -
349B ASN* 3.2 7.7 - - - +
350B ASN* 1.3 85.0 + - - +
352B LYS* 1.3 66.6 + - - +
353B THR* 4.2 2.0 + - - +
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Residues in contact with LYS 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A PRO* 5.2 4.8 + - - +
178A SER* 5.8 1.3 - - - -
179A THR* 2.9 47.2 + - - +
180A ALA* 4.2 1.6 - - - +
315B VAL 2.8 7.7 + - - +
316B ALA* 3.4 2.6 - - - -
317B ALA* 2.9 27.9 + - - +
349B ASN* 3.7 28.7 + - - +
350B ASN 3.9 0.2 - - - -
351B VAL* 1.3 76.6 + - - +
353B THR* 1.3 67.5 + - - +
502B LOC 3.0 75.5 - - + +
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Residues in contact with THR 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ALA* 3.5 5.1 - - - +
319B PHE* 4.1 10.5 - - + -
325B MET* 4.6 3.8 - - + -
328B VAL* 3.8 26.9 - - + -
329B ASP* 4.5 11.7 - - - +
332B MET* 3.4 32.0 - - - +
351B VAL* 4.2 2.7 + - - +
352B LYS* 1.3 84.7 + - - +
354B ALA* 1.3 71.6 + - - +
355B VAL* 4.4 5.2 - - + -
502B LOC 4.4 4.9 - - - +
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Residues in contact with ALA 354 (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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241B CYS* 4.1 13.7 - - - -
247B GLN 5.3 4.5 - - - +
248B LEU* 4.1 12.6 - - + -
317B ALA 2.8 9.6 + - - +
318B ILE* 3.3 24.0 - - + +
319B PHE* 2.9 24.4 + - - -
353B THR* 1.3 75.5 - - - +
355B VAL* 1.3 69.0 + - - +
502B LOC 4.0 10.8 - - - +
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Residues in contact with VAL 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B CYS* 5.9 1.9 - - - -
247B GLN* 4.0 25.4 + - + +
318B ILE* 5.4 0.7 - - - -
319B PHE* 3.4 27.1 - - + +
321B GLY 6.1 1.1 - - - +
323B MET* 5.3 2.9 - - + -
325B MET* 3.2 50.5 - - + -
328B VAL* 4.8 1.6 - - + -
353B THR* 4.4 2.0 - - + -
354B ALA* 1.3 84.6 - - - +
356B CYS* 1.3 62.1 + - - +
357B ASP* 4.4 5.8 - - - +
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Residues in contact with CYS 356 (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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240B THR* 3.7 25.8 - - + -
241B CYS* 5.8 2.5 - - - -
244B PHE* 3.7 31.0 - - - -
245B PRO 5.4 4.9 - - - +
247B GLN* 4.7 4.0 - - - -
318B ILE* 5.0 1.6 - - + -
319B PHE 2.8 9.3 + - - +
320B ARG* 3.2 6.2 - - + -
321B GLY 2.9 26.2 + - - +
355B VAL* 1.3 75.7 - - - +
357B ASP* 1.3 63.4 + - - +
358B ILE* 3.5 26.9 - - - -
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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