Contacts of the helix formed by residues 353 - 363 (chain B) in PDB entry 4B92
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 ASP 353 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B SER 3.8 2.1 - - - +
350B GLY* 3.1 17.9 + - - +
352B GLN* 1.3 79.5 - - - +
354B ARG* 1.3 58.5 + - - +
355B MET 3.2 1.7 + - - -
356B SER* 3.2 4.4 + - - -
357B VAL* 2.8 51.8 + - + +
413B ILE* 3.9 13.6 - - + +
418B GLN* 5.7 0.5 - - - +
420B GLN* 2.8 23.2 + - - -
425B ASN* 2.8 26.9 + - - +
427B TYR* 3.6 19.4 - - + -
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Residues in contact with ARG 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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62B GLY* 3.7 4.2 - - - -
63B ILE 3.1 41.2 + - - +
64B ASP* 3.4 15.3 + - - +
94B THR* 2.9 24.9 + - - -
273B THR* 3.4 24.9 - - - +
322B VAL* 3.0 31.4 + - + +
323B ALA* 3.6 20.0 - - - +
324B SER* 3.7 2.9 - - - +
350B GLY 3.3 12.3 + - - +
351B VAL 4.3 6.3 - - - +
352B GLN 3.4 2.2 - - - -
353B ASP* 1.3 76.3 - - - +
355B MET* 1.3 71.2 + - + +
358B ILE* 3.0 38.4 + - + +
377B THR* 3.2 23.4 + - + +
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Residues in contact with MET 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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59B ILE* 3.5 30.7 - - + -
60B PRO 4.8 0.2 - - - +
62B GLY* 4.0 11.0 - - - +
92B GLY 3.3 25.9 + - - +
93B GLY 3.5 17.3 - - - +
94B THR* 3.7 15.0 - - - +
353B ASP 3.3 0.6 - - - -
354B ARG* 1.3 95.6 - - + +
356B SER* 1.3 59.5 + - - +
358B ILE* 4.8 0.4 - - - -
359B TRP* 3.0 28.9 + - - +
373B PHE* 3.4 19.3 - - + -
377B THR* 3.7 30.3 - - - +
405B TRP* 3.8 14.4 - - + -
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Residues in contact with SER 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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92B GLY 4.9 1.3 + - - -
352B GLN 5.1 2.5 + - - -
353B ASP* 3.2 9.0 + - - -
355B MET* 1.3 76.1 - - - +
357B VAL* 1.3 66.7 + - - +
359B TRP* 3.1 3.0 + - - +
360B GLU* 3.0 24.4 + - - +
405B TRP* 3.6 12.5 - - - -
411B LYS* 5.8 3.5 - - - +
413B ILE* 5.3 3.1 - - - -
432B CYS* 4.0 18.2 - - - +
434B GLY 2.6 29.4 + - - +
435B VAL* 4.1 7.3 - - - +
436B PRO* 4.3 4.9 - - - +
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Residues in contact with VAL 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B THR* 3.6 22.4 - - + -
277B THR* 3.8 12.3 - - + -
353B ASP* 2.8 43.3 + - + +
356B SER* 1.3 72.7 - - - +
358B ILE* 1.3 62.8 + - - +
360B GLU* 3.3 1.9 + - - +
361B ARG* 3.0 22.9 + - - +
413B ILE* 3.8 12.6 - - + -
427B TYR* 3.7 27.1 - - + -
430B MET* 3.6 29.4 - - + -
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Residues in contact with ILE 358 (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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273B THR* 4.2 12.1 - - + -
276B ALA* 4.4 9.0 - - + -
277B THR* 4.7 2.2 - - + -
311B MET* 3.9 24.7 - - + -
314B LEU* 4.6 2.5 - - + -
322B VAL* 3.8 38.1 - - + -
354B ARG* 3.0 22.4 + - + +
355B MET 4.0 2.0 - - - +
357B VAL* 1.3 78.8 - - - +
359B TRP* 1.3 55.6 + - - +
362B GLY* 2.7 31.3 + - - +
363B VAL 3.7 0.2 + - - -
368B MET* 4.9 9.2 - - + -
373B PHE* 3.8 21.6 - - + -
376B VAL* 4.6 7.4 - - + -
377B THR* 4.3 10.8 - - + -
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Residues in contact with TRP 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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18B VAL* 6.4 0.2 - - + -
57B LEU* 3.2 33.4 - - + -
59B ILE* 5.7 2.0 - - + -
355B MET 3.0 18.3 + - - +
356B SER 3.1 5.1 + - - +
358B ILE* 1.3 74.7 - - - +
360B GLU* 1.3 58.6 + - - +
363B VAL* 2.8 46.9 + - + +
364B VAL* 2.9 31.5 + - + +
370B GLU* 3.9 19.7 - - + -
373B PHE* 3.6 48.0 - + + -
405B TRP* 3.3 31.3 - + + +
407B PRO* 4.0 17.6 + - + +
433B HIS 4.4 3.8 + - - -
434B GLY* 3.6 23.7 - - - +
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Residues in contact with GLU 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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356B SER 3.0 11.4 + - - +
357B VAL* 3.5 9.2 - - - +
359B TRP* 1.3 79.6 - - + +
361B ARG* 1.3 81.9 + - - +
364B VAL* 3.2 24.2 - - - +
365B GLY* 2.9 26.2 + - - -
430B MET* 4.3 5.4 - - - -
431B ARG 3.5 20.9 - - - +
432B CYS* 4.4 7.9 - - - -
433B HIS* 3.1 45.9 + - - +
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Residues in contact with ARG 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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277B THR* 3.8 30.5 + - + +
311B MET* 3.8 20.8 - - + +
357B VAL 3.0 12.0 + - - +
360B GLU* 1.3 106.1 + - + +
362B GLY* 1.3 61.8 + - - +
365B GLY* 3.6 15.7 - - - +
367B LYS* 3.9 12.5 - - - +
430B MET* 3.9 33.7 - - + +
431B ARG 5.2 1.0 + - - -
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Residues in contact with GLY 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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311B MET* 3.7 23.4 - - - +
358B ILE 2.7 21.7 + - - -
361B ARG* 1.3 75.3 - - - +
363B VAL* 1.3 57.5 + - - -
367B LYS* 3.0 11.3 + - - +
368B MET* 3.0 38.6 + - - -
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Residues in contact with VAL 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B ILE 3.7 0.4 + - - -
359B TRP* 2.8 54.4 + - + +
362B GLY* 1.3 72.3 - - - -
364B VAL* 1.3 66.5 + - - +
365B GLY 3.2 0.9 - - - -
366B GLY* 3.0 14.9 + - - -
368B MET* 3.4 20.5 - - + +
369B ASP* 3.9 4.7 - - - +
370B GLU* 4.1 10.3 - - + +
373B PHE* 3.5 36.3 - - + -
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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