Contacts of the helix formed by residues 358 - 373 (chain B) in PDB entry 4UFT
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 358 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330B PRO* 4.5 6.7 - - + +
331B LEU* 4.1 14.2 - - - +
334B SER* 3.1 22.5 + - - +
356B TYR 3.3 6.7 - - - +
357B PHE* 1.3 84.6 - - - +
359B PRO* 1.3 70.5 - - - +
360B ALA* 3.9 9.5 + - - +
361B TYR* 3.2 32.8 - - - +
362B PHE* 3.4 14.7 + - - +
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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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357B PHE* 3.7 21.7 - - + -
358B ASP* 1.3 85.9 - - - +
360B ALA* 1.3 65.2 + - + +
361B TYR 3.4 0.2 - - - -
362B PHE* 3.7 11.7 - - + +
363B ARG* 3.4 36.5 + - - +
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Residues in contact with ALA 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B ASP* 3.2 10.9 - - - +
359B PRO* 1.3 81.4 - - + +
361B TYR* 1.3 69.5 + - + +
363B ARG* 3.4 26.3 - - - +
364B LEU* 3.9 7.3 + - - +
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Residues in contact with TYR 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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288B GLU* 2.9 45.8 + - + +
289B PHE* 3.6 33.4 - + + -
331B LEU* 4.8 11.2 - - + +
334B SER* 3.9 10.1 - - - +
335B TYR* 4.1 12.0 - - + -
358B ASP* 3.2 33.6 + - - +
360B ALA* 1.3 85.1 - - + +
362B PHE* 1.3 64.3 + - - +
363B ARG 3.4 0.4 - - - -
364B LEU* 3.4 30.1 + - + +
365B GLY 3.4 9.2 + - - -
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Residues in contact with PHE 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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334B SER* 3.6 22.6 + - - +
337B MET* 3.8 27.6 - - + -
338B GLY* 3.6 29.1 - - - -
341B VAL* 4.5 13.0 - - + -
352B PHE* 5.3 12.8 - + - -
357B PHE* 3.7 29.6 - + + +
358B ASP 3.4 17.2 + - - +
359B PRO* 3.7 11.7 - - + +
360B ALA 3.4 0.4 - - - -
361B TYR* 1.3 77.8 - - - +
363B ARG* 1.3 66.6 + - + +
364B LEU 3.4 0.3 + - - -
365B GLY 3.4 9.0 + - - -
366B GLN* 3.6 20.6 + - - +
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Residues in contact with ARG 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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359B PRO* 3.4 20.6 + - - +
360B ALA* 3.4 18.7 - - - +
362B PHE* 1.3 81.6 - - + +
364B LEU* 1.3 62.5 + - - +
365B GLY 3.3 0.2 - - - -
366B GLN* 3.4 11.5 + - - +
367B GLU* 2.9 31.1 + - - +
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Residues in contact with LEU 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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283B ALA* 4.6 15.5 - - + +
289B PHE* 5.3 4.7 - - + -
335B TYR* 3.7 26.9 - - + -
360B ALA 4.1 4.9 - - - +
361B TYR* 3.4 36.3 + - + +
362B PHE 3.2 0.4 - - - -
363B ARG* 1.3 82.9 - - - +
365B GLY* 1.3 61.1 + - - +
367B GLU* 3.3 9.1 + - + +
368B MET* 3.2 27.7 + - + +
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Residues in contact with GLY 365 (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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335B TYR* 3.7 25.6 - - - -
339B VAL* 3.4 36.3 - - - +
361B TYR 3.4 5.0 + - - -
362B PHE 3.4 6.2 + - - -
363B ARG 3.3 0.4 - - - -
364B LEU* 1.3 80.1 - - - +
366B GLN* 1.3 59.9 + - - +
368B MET* 3.3 12.1 + - - +
369B VAL* 3.7 4.2 + - - +
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Residues in contact with GLN 366 (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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338B GLY 3.6 15.2 + - - +
341B VAL* 5.3 7.5 - - + +
342B GLU* 3.1 31.1 + - - +
362B PHE* 3.6 24.0 + - + +
363B ARG* 3.4 13.5 + - - +
364B LEU 3.3 0.4 - - - -
365B GLY* 1.3 75.7 - - - +
367B GLU* 1.3 62.6 + - - +
369B VAL* 3.3 18.9 - - - +
370B ARG* 3.5 27.2 - - - +
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Residues in contact with GLU 367 (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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363B ARG 2.9 17.7 + - - +
364B LEU* 3.4 11.0 - - + +
365B GLY 3.2 0.2 - - - -
366B GLN* 1.3 76.3 - - - +
368B MET* 1.3 64.9 + - + +
370B ARG* 3.3 22.4 + - - +
371B ARG* 3.2 56.8 + - - +
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Residues in contact with MET 368 (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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281B TYR* 4.8 16.1 - - + -
282B PRO* 4.1 22.0 - - + -
283B ALA* 3.7 41.7 - - + +
335B TYR* 4.4 8.3 - - - +
339B VAL* 4.8 3.1 - - + -
364B LEU* 3.2 20.7 + - + +
365B GLY 3.6 8.1 - - - +
366B GLN 3.3 0.4 - - - -
367B GLU* 1.3 79.6 - - - +
369B VAL* 1.3 61.6 + - - +
371B ARG* 3.5 6.8 + - - +
372B SER* 3.1 28.3 + - - -
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Residues in contact with VAL 369 (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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281B TYR* 3.4 31.2 - - + +
339B VAL* 3.5 31.2 - - + +
342B GLU* 3.4 40.2 - - + +
343B LEU* 4.1 5.6 - - + -
365B GLY 3.7 0.8 + - - +
366B GLN* 3.3 16.8 - - - +
368B MET* 1.3 76.3 - - - +
370B ARG* 1.3 62.9 + - + +
372B SER* 4.3 3.0 - - - -
373B ALA* 3.8 16.5 + - - +
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Residues in contact with ARG 370 (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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342B GLU* 6.0 3.4 - - + -
366B GLN* 3.5 29.4 - - + +
367B GLU* 3.3 34.4 + - - +
369B VAL* 1.3 82.8 - - + +
371B ARG* 1.3 68.4 + - + +
372B SER 3.5 0.2 - - - -
373B ALA* 4.3 11.1 - - - +
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Residues in contact with ARG 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B GLU* 3.2 51.9 + - - +
368B MET* 4.1 7.0 - - - +
370B ARG* 1.3 80.1 - - + +
372B SER* 1.3 65.5 + - - +
373B ALA* 4.5 1.7 - - - +
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Residues in contact with SER 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B TYR* 5.9 5.8 - - - -
368B MET* 3.1 19.1 + - - -
369B VAL* 4.5 4.0 - - - -
371B ARG* 1.3 80.5 - - - +
373B ALA* 1.3 69.0 + - - +
374B GLY* 2.9 27.1 + - - +
375B LYS* 4.0 12.6 - - - +
376B VAL* 3.8 14.6 + - - +
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Residues in contact with ALA 373 (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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369B VAL 3.8 11.8 + - - -
370B ARG 4.3 12.1 - - - +
371B ARG 3.6 1.8 - - - +
372B SER* 1.3 81.1 - - - +
374B GLY* 1.3 57.5 + - - +
375B LYS* 3.8 2.6 + - - +
389B GLU 5.6 0.5 - - - +
390B ASP 5.3 1.4 - - - +
391B ALA* 4.0 18.7 - - - +
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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