Contacts of the helix formed by residues 358 - 373 (chain B) in PDB entry 4N41
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 PRO 358 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348B LEU* 4.7 2.2 - - + -
350B ARG* 4.7 5.6 - - - +
356B GLY 3.4 8.3 - - - +
357B TRP* 1.3 84.9 - - + +
359B GLU* 1.3 65.8 + - - +
360B PHE* 3.3 21.5 - - + -
361B LEU* 3.1 43.2 + - + +
362B ARG* 3.1 9.7 + - - +
409B LEU* 3.7 26.7 - - + -
439B LEU* 5.8 2.7 - - + -
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Residues in contact with GLU 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 TRP 3.3 4.1 + - - +
358B PRO* 1.3 71.9 - - - +
360B PHE* 1.3 61.9 + - + +
362B ARG* 3.4 32.9 + - - +
363B ARG* 2.9 36.3 + - + +
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Residues in contact with PHE 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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358B PRO* 3.9 21.5 - - + -
359B GLU* 1.3 77.9 - - + +
361B LEU* 1.3 91.8 + - + +
363B ARG* 3.6 19.3 + - - +
364B ALA* 2.9 29.3 + - - +
439B LEU* 4.6 17.3 - - + -
440B ARG* 4.4 2.7 - - - -
441B GLU* 3.3 66.9 - - + +
447B TRP* 3.9 27.7 - + + -
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Residues in contact with LEU 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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357B TRP* 4.7 9.2 - - + -
358B PRO* 3.1 42.7 + - + +
360B PHE* 1.3 96.4 - - + +
362B ARG* 1.3 59.9 + - - +
364B ALA* 3.3 3.9 + - - +
365B LEU* 2.9 37.6 + - + +
407B LEU* 4.2 23.6 - - + -
409B LEU* 4.7 3.4 - - + -
435B LEU* 4.2 13.0 - - + -
439B LEU* 5.0 1.8 - - + -
447B TRP* 3.6 33.0 - - + -
451B LEU* 4.5 13.6 - - + +
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Residues in contact with ARG 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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356B GLY* 6.0 0.4 - - - -
357B TRP* 3.3 60.0 + - + +
358B PRO 3.1 6.2 + - - +
359B GLU* 3.6 34.2 + - - +
361B LEU* 1.3 78.8 - - - +
363B ARG* 1.3 58.6 + - - +
365B LEU* 3.4 6.4 + - - +
366B LEU* 2.9 50.3 + - + +
378B LEU* 4.3 20.0 - - + +
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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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335B ARG* 6.0 1.6 - - - +
359B GLU* 2.9 27.8 + - + +
360B PHE* 3.6 26.3 + - - +
362B ARG* 1.3 78.2 - - - +
364B ALA* 1.3 58.5 + - - +
366B LEU* 3.2 7.3 + - - +
367B ARG* 2.9 31.5 + - + +
441B GLU* 3.4 26.3 + - - -
447B TRP* 6.3 1.2 - - - -
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Residues in contact with ALA 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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334B LEU* 4.1 10.0 - - + +
335B ARG* 6.3 0.7 - - - +
360B PHE 2.9 17.5 + - - +
361B LEU 3.3 4.2 + - - +
363B ARG* 1.3 75.6 - - - +
365B LEU* 1.3 65.5 + - - +
367B ARG* 3.3 6.3 + - - +
368B ALA* 2.9 24.7 + - - +
447B TRP* 3.8 29.4 - - + -
451B LEU* 4.2 6.7 - - + -
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Residues in contact with LEU 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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334B LEU* 5.9 0.9 - - + -
346B LEU* 4.6 11.2 - - + -
357B TRP* 3.5 36.8 - - + -
361B LEU* 2.9 22.1 + - + +
362B ARG* 3.8 4.9 - - - +
364B ALA* 1.3 75.0 - - - +
366B LEU* 1.3 57.1 + - - +
368B ALA* 3.2 4.1 + - + +
369B PHE* 2.9 38.0 + - + -
376B LEU* 3.8 14.1 - - + -
378B LEU* 4.4 10.5 - - + -
451B LEU* 4.0 27.6 - - + -
454B LEU* 4.9 7.2 - - + -
455B LEU* 4.4 29.8 - - + -
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Residues in contact with LEU 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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362B ARG* 2.9 39.5 + - + +
363B ARG* 3.6 6.5 - - - +
365B LEU* 1.3 74.9 - - - +
367B ARG* 1.3 59.8 + - - +
369B PHE* 3.9 1.9 - - + +
370B GLY* 2.9 26.0 + - - -
376B LEU* 4.3 24.2 - - + +
378B LEU* 5.6 3.8 - - + -
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Residues in contact with ARG 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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334B LEU 4.1 6.9 - - - +
335B ARG* 4.7 6.1 - - + +
363B ARG* 2.9 19.5 + - + +
364B ALA* 3.7 7.2 - - - +
366B LEU* 1.3 75.4 - - - +
368B ALA* 1.3 58.8 + - - +
370B GLY* 3.3 1.4 + - - -
371B ALA* 2.9 30.5 + - - +
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Residues in contact with ALA 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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333B ALA 4.8 0.9 - - - -
334B LEU* 3.2 34.1 + - + +
337B GLY* 4.3 0.9 - - - -
338B PHE* 3.6 24.5 - - + -
364B ALA 2.9 16.3 + - - +
365B LEU* 3.4 7.6 - - - +
367B ARG* 1.3 78.6 - - - +
369B PHE* 1.3 57.1 + - + +
371B ALA* 3.4 3.4 + - - +
372B SER* 2.5 34.2 + - - -
455B LEU* 5.3 0.9 - - + -
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Residues in contact with PHE 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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338B PHE* 4.2 10.1 - + - -
342B GLN 4.1 3.8 - - - -
344B THR* 3.5 34.3 - - + -
346B LEU* 4.4 1.6 - - + -
365B LEU* 2.9 28.4 + - + +
366B LEU* 4.3 3.6 - - + +
368B ALA* 1.3 75.5 - - + +
370B GLY* 1.3 64.4 + - - +
372B SER* 3.7 4.7 - - - -
373B GLY* 3.1 3.5 + - - -
374B ALA* 3.0 50.6 + - + +
375B SER 3.7 17.3 - - - -
376B LEU* 3.7 35.9 - - + -
455B LEU* 3.5 33.9 - - + -
460B LEU* 3.8 14.1 - - + -
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Residues in contact with GLY 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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366B LEU 2.9 19.0 + - - -
367B ARG* 3.6 2.2 - - - -
368B ALA 3.2 0.2 - - - -
369B PHE* 1.3 77.0 - - - +
371B ALA* 1.3 60.6 + - - +
372B SER 3.2 1.0 + - - -
373B GLY* 3.2 12.2 + - - -
374B ALA 5.4 0.2 - - - -
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Residues in contact with ALA 371 (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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324B ARG* 4.4 5.9 - - - +
335B ARG 3.3 27.1 - - - +
336B VAL 3.5 20.0 - - - +
337B GLY* 4.0 4.3 - - - +
367B ARG 2.9 14.0 + - - +
368B ALA 4.0 2.0 - - - +
370B GLY* 1.3 74.6 - - - +
372B SER* 1.3 58.4 + - - +
373B GLY 3.3 0.4 + - - -
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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
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324B ARG* 5.0 3.6 - - - -
337B GLY* 3.3 3.9 - - - -
338B PHE* 3.0 48.5 + - - +
341B ALA* 4.1 15.1 + - - +
368B ALA 2.5 22.7 + - - -
369B PHE* 3.9 6.5 - - - -
370B GLY 3.1 1.2 - - - -
371B ALA* 1.3 78.0 - - - +
373B GLY* 1.3 63.3 + - - +
374B ALA* 3.6 2.9 + - - +
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Residues in contact with GLY 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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341B ALA 5.7 0.2 - - - +
369B PHE 3.1 4.5 + - - -
370B GLY 3.2 10.4 + - - -
371B ALA 3.3 1.0 - - - -
372B SER* 1.3 80.8 - - - +
374B ALA* 1.3 58.0 + - - +
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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