Contacts of the strand formed by residues 327 - 333 (chain B) in PDB entry 5H14
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 ALA 327 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321B SER 4.2 0.2 - - - +
322B LYS* 3.7 13.2 - - - +
323B SER 4.4 3.6 + - - +
325B GLU* 3.3 6.4 - - + +
326B ASN* 1.3 80.9 - - - +
328B ILE* 1.3 61.1 + - - +
329B VAL* 3.9 5.9 + - + +
355B ARG* 3.5 47.6 - - + +
356B PHE 3.3 4.5 - - - +
357B ASP* 3.7 8.3 - - - +
358B TYR* 3.2 21.3 + - - -
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Residues in contact with ILE 328 (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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320B LEU* 3.8 31.6 - - + -
321B SER 3.6 15.3 - - - +
322B LYS* 4.0 9.2 - - + -
327B ALA* 1.3 72.4 - - - +
329B VAL* 1.3 63.0 + - - +
355B ARG* 3.4 3.5 - - - -
356B PHE* 2.8 43.7 + - + +
358B TYR* 3.5 10.5 - - + +
368B PHE* 3.8 42.0 - - + -
377B LEU* 4.0 18.8 - - + -
379B LEU* 4.2 13.9 - - + -
389B TRP* 4.2 12.6 - - + -
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Residues in contact with VAL 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ILE* 3.8 22.2 - - + +
305B HIS* 3.7 25.1 - - + +
319B ILE 3.4 1.9 - - - +
320B LEU* 3.4 3.1 - - - -
321B SER 2.8 36.2 + - - +
325B GLU* 4.8 4.3 - - - +
327B ALA* 4.6 4.7 - - + +
328B ILE* 1.3 76.3 - - - +
330B CYS* 1.4 64.0 + - - +
331B TRP* 3.7 4.0 - - + -
352B ILE* 3.8 33.9 - - + -
354B GLY 3.8 3.8 - - - +
355B ARG* 4.1 23.6 - - + +
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Residues in contact with CYS 330 (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* 4.3 3.1 - - - -
318B LEU* 3.6 32.1 - - - -
319B ILE 3.1 6.7 - - - -
320B LEU* 3.5 19.3 - - + -
328B ILE 4.0 1.2 + - - -
329B VAL* 1.4 69.0 - - - +
331B TRP* 1.3 58.8 + - - +
352B ILE* 3.8 2.6 - - - +
353B LEU* 2.8 33.7 + - - -
354B GLY 2.9 20.0 + - - +
356B PHE* 4.4 4.4 - - + -
501B GOL 3.5 32.8 - - - -
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Residues in contact with TRP 331 (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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252B MET* 4.4 14.1 - - + -
260B LEU* 3.8 26.7 - - + -
299B PHE* 3.9 19.1 - + - -
301B THR* 3.7 14.8 - - + -
304B ILE* 3.5 35.8 - - + +
318B LEU* 3.6 2.9 - - - +
319B ILE* 2.8 61.6 + - + +
321B SER* 3.1 19.3 + - - -
329B VAL* 3.7 16.6 - - + -
330B CYS* 1.3 74.3 - - - +
332B LYS* 1.3 85.4 + - - +
333B PRO* 3.6 18.4 - - + -
350B VAL* 3.9 7.4 - - + -
351B THR 3.3 14.6 - - - +
352B ILE* 3.8 16.8 - - + -
353B LEU* 3.9 5.8 - - - -
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Residues in contact with LYS 332 (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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317B ASP 4.6 4.5 - - - +
318B LEU* 3.9 15.6 - - + +
319B ILE 5.0 0.2 - - - +
331B TRP* 1.3 85.6 - - - +
333B PRO* 1.3 81.3 - - + +
335B LYS 3.3 22.0 - - - +
336B MET* 2.9 25.1 + - - +
337B GLU 4.2 1.2 - - - -
338B ASP 2.8 26.8 + - - +
350B VAL* 3.6 0.2 - - - -
351B THR* 2.9 45.4 + - + +
353B LEU* 3.8 9.0 - - + -
41C MET* 4.0 25.4 - - - +
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Residues in contact with PRO 333 (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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252B MET* 4.6 7.4 - - + -
262B LEU* 5.6 0.9 - - + -
299B PHE* 3.7 38.8 - - + -
317B ASP 4.8 3.6 - - - +
319B ILE* 4.8 5.6 - - + -
331B TRP* 3.6 17.7 - - + -
332B LYS* 1.3 101.2 - - + +
334B GLY* 1.3 60.4 + - - +
335B LYS 4.3 0.2 - - - +
338B ASP* 4.3 1.9 - - - +
340B ILE* 3.7 29.7 - - + +
343B ILE* 4.0 26.1 - - + +
349B ASN 4.2 0.9 - - - +
350B VAL* 4.5 0.2 - - + -
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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