Contacts of the strand formed by residues 350 - 357 (chain B) in PDB entry 5H15
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 350 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299B PHE* 4.2 5.4 - - + -
301B THR* 3.8 14.8 - - - +
303B ASP* 4.3 20.9 - - + +
304B ILE* 3.6 23.1 - - + -
331B TRP* 3.5 38.4 - - + -
332B LYS 3.7 3.4 - - - +
334B GLY 3.2 8.2 - - - +
335B LYS* 5.6 0.2 - - - -
348B SER 5.3 0.7 - - - +
349B ASN* 1.3 79.4 - - - +
351B THR* 1.3 60.6 + - - +
352B ILE* 4.3 8.1 + - + -
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Residues in contact with THR 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B TRP* 3.2 5.0 - - - -
332B LYS* 2.9 51.0 + - + +
334B GLY 2.7 19.5 + - - -
335B LYS* 3.3 2.4 - - - -
336B MET* 3.1 55.6 + - + -
350B VAL* 1.3 73.6 + - - +
352B ILE* 1.3 66.0 + - - +
353B LEU* 3.7 13.7 + - + +
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Residues in contact with ILE 352 (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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303B ASP 4.5 10.8 - - - +
304B ILE* 4.2 27.8 - - + +
329B VAL* 3.8 25.4 - - + -
330B CYS 3.9 3.4 - - - +
331B TRP* 4.2 0.4 - - + -
336B MET* 5.4 2.4 - - - +
350B VAL* 4.2 7.1 + - + -
351B THR* 1.3 75.7 - - - +
353B LEU* 1.3 61.9 + - - +
354B GLY* 4.2 9.6 - - - +
355B ARG* 4.0 28.3 - - - +
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Residues in contact with LEU 353 (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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318B LEU* 3.6 37.9 - - + -
330B CYS* 2.9 19.3 + - - +
331B TRP 4.6 2.5 - - - -
332B LYS* 4.0 19.5 - - + -
336B MET* 3.9 23.8 - - + -
351B THR* 3.8 27.1 - - + +
352B ILE* 1.3 74.6 - - - +
354B GLY* 1.3 57.6 + - - +
396B PRO* 5.7 1.4 - - - +
41D MET* 4.3 15.9 - - + -
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Residues in contact with GLY 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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329B VAL* 3.7 6.8 - - - +
330B CYS* 2.8 36.3 + - - +
352B ILE* 3.7 6.1 - - - +
353B LEU* 1.3 78.4 - - - +
355B ARG* 1.3 61.9 + - - +
356B PHE* 5.2 0.4 - - - -
396B PRO* 4.4 14.4 - - - -
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Residues in contact with ARG 355 (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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304B ILE 4.9 7.9 + - - -
325B GLU* 6.0 4.0 - - - +
327B ALA* 3.7 21.6 - - + +
328B ILE 3.5 5.4 - - - +
329B VAL* 3.6 26.7 - - + +
352B ILE* 4.0 35.8 - - - +
354B GLY* 1.3 72.8 - - - +
356B PHE* 1.3 63.1 + - - +
357B ASP* 3.3 26.5 + - - +
396B PRO* 3.2 18.9 - - - +
397B HIS 5.1 0.2 + - - -
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Residues in contact with PHE 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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315B LEU* 5.4 3.4 - - + -
320B LEU* 4.1 20.9 - - + -
328B ILE* 2.8 51.7 + - + +
330B CYS* 4.2 13.7 - - + -
355B ARG* 1.3 72.1 - - - +
357B ASP* 1.4 60.6 + - - +
358B TYR* 3.4 10.4 - - - -
377B LEU* 3.9 13.0 - - + -
389B TRP* 3.7 46.2 - + + +
390B ASP 5.3 0.9 - - - -
391B LEU* 3.9 28.5 - - + -
393B VAL 5.7 2.0 - - - -
394B GLU 6.1 0.2 - - - -
396B PRO* 3.8 32.1 - - + -
399B ALA* 4.6 5.4 - - + -
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Residues in contact with ASP 357 (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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326B ASN 3.6 7.0 - - - +
327B ALA* 3.7 6.6 - - - +
355B ARG* 3.3 39.4 + - - +
356B PHE* 1.4 72.7 - - - +
358B TYR* 1.3 64.0 + - - +
387B TYR* 5.5 0.5 - - - -
389B TRP* 3.7 12.9 + - - +
400B LYS* 5.4 2.1 - - - +
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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