Contacts of the helix formed by residues 358 - 372 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348A LEU* 4.6 1.3 - - + -
350A ARG* 4.5 7.2 - - - +
356A GLY 3.5 8.9 - - - +
357A TRP* 1.3 84.9 - - + +
359A GLU* 1.3 66.8 + - - +
360A PHE* 3.3 18.8 - - + -
361A LEU* 3.2 36.2 + - + +
362A ARG 3.2 9.0 + - - -
409A LEU* 3.6 30.5 - - + -
439A LEU* 5.1 4.7 - - + -
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Residues in contact with GLU 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A TRP 3.3 4.6 + - - +
358A PRO* 1.3 71.2 - - - +
360A PHE* 1.3 61.7 + - + +
362A ARG* 3.2 29.8 + - - +
363A ARG* 2.9 43.2 + - - +
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Residues in contact with PHE 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A PRO* 4.2 15.3 - - + -
359A GLU* 1.3 79.1 - - + +
361A LEU* 1.3 86.5 + - + +
363A ARG* 3.6 18.5 - - - +
364A ALA* 2.9 30.7 + - - +
439A LEU* 4.0 22.7 - - + -
440A ARG* 4.0 5.4 - - - -
441A GLU* 3.7 56.1 - - + +
447A TRP* 3.6 45.6 - + + -
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Residues in contact with LEU 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A TRP* 4.6 9.6 - - + -
358A PRO* 3.2 33.5 + - + +
360A PHE* 1.3 91.8 - - + +
362A ARG* 1.3 66.7 + - - +
364A ALA* 3.2 3.5 + - - +
365A LEU* 2.9 31.0 + - + +
407A LEU* 4.1 17.0 - - + -
409A LEU* 4.6 2.9 - - + -
435A LEU* 3.9 21.5 - - + -
439A LEU* 4.2 3.8 - - + -
447A TRP* 3.6 38.4 - - + -
451A LEU* 4.2 16.6 - - + +
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Residues in contact with ARG 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A TRP* 3.6 51.3 + - + +
358A PRO 3.2 6.6 + - - +
359A GLU* 3.2 28.4 + - - +
361A LEU* 1.3 79.7 - - - +
363A ARG* 1.3 58.9 + - - +
365A LEU* 3.3 3.3 + - - +
366A LEU* 2.9 49.0 + - + +
378A LEU* 3.9 32.4 + - + +
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Residues in contact with ARG 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A GLU* 2.9 34.7 + - - +
360A PHE* 3.6 29.0 + - - +
362A ARG* 1.3 78.4 - - - +
364A ALA* 1.3 56.4 + - - +
366A LEU* 3.3 7.1 + - - +
367A ARG* 2.9 31.0 + - + +
441A GLU* 2.6 31.5 + - - -
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Residues in contact with ALA 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A LEU* 4.3 10.9 - - + +
335A ARG* 6.3 0.7 - - - +
360A PHE 2.9 18.3 + - - +
361A LEU 3.8 2.9 - - - +
363A ARG* 1.3 76.3 - - - +
365A LEU* 1.3 64.0 + - - +
367A ARG* 3.3 5.9 + - - +
368A ALA* 2.9 24.8 + - - +
447A TRP* 3.6 29.6 - - + -
451A LEU* 4.2 7.9 - - + -
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Residues in contact with LEU 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A LEU* 5.9 1.3 - - + -
346A LEU* 4.6 8.3 - - + -
357A TRP* 3.7 32.3 - - + -
361A LEU 2.9 21.1 + - - +
362A ARG* 3.7 3.8 - - - +
364A ALA* 1.3 76.2 - - - +
366A LEU* 1.3 58.0 + - - +
368A ALA* 3.3 3.9 + - + +
369A PHE* 2.9 41.0 + - + -
376A LEU* 3.8 13.7 - - + -
378A LEU* 4.1 14.1 - - + -
451A LEU* 3.9 31.9 - - + -
454A LEU* 4.7 4.5 - - + -
455A LEU* 4.1 31.4 - - + -
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Residues in contact with LEU 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A ARG* 2.9 41.9 + - + +
363A ARG* 3.7 6.7 - - - +
365A LEU* 1.3 75.1 - - - +
367A ARG* 1.3 59.0 + - - +
369A PHE* 3.9 1.9 - - + +
370A GLY* 2.9 26.3 + - - -
376A LEU* 4.2 28.0 - - + +
378A LEU* 5.4 2.5 - - + -
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Residues in contact with ARG 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A LEU 4.3 6.5 - - - +
335A ARG* 5.7 2.2 - - + -
363A ARG* 2.9 18.9 + - + +
364A ALA* 3.8 7.0 - - - +
366A LEU* 1.3 75.8 - - - +
368A ALA* 1.3 58.1 + - - +
370A GLY* 3.2 1.4 + - - -
371A ALA* 2.9 32.2 + - - +
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Residues in contact with ALA 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A ALA 4.8 0.4 - - - -
334A LEU* 3.3 34.9 + - + +
337A GLY* 4.2 1.6 - - - -
338A PHE* 3.5 26.2 - - + -
364A ALA 2.9 16.3 + - - +
365A LEU* 3.6 7.4 - - - +
367A ARG* 1.3 78.5 - - - +
369A PHE* 1.3 59.6 + - + +
371A ALA* 3.5 4.5 + - - +
372A SER* 2.7 27.8 + - - -
455A LEU* 5.4 0.4 - - + -
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Residues in contact with PHE 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A PHE* 3.8 13.7 - + - -
341A ALA* 5.0 0.7 - - + -
342A GLN 3.9 6.1 - - - -
344A THR* 3.3 37.0 - - + -
365A LEU* 2.9 29.7 + - + +
366A LEU* 4.3 3.1 - - + +
368A ALA* 1.3 75.2 - - + +
370A GLY* 1.3 63.2 + - - +
372A SER* 3.2 5.0 + - - -
373A GLY 3.1 4.2 + - - -
374A ALA* 3.0 50.3 + - + +
375A SER 3.8 14.8 - - - -
376A LEU* 3.8 28.7 - - + -
455A LEU* 3.5 25.1 - - + -
460A LEU* 3.4 24.7 - - + -
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Residues in contact with GLY 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A LEU 2.9 18.6 + - - -
367A ARG* 3.6 1.6 - - - -
369A PHE* 1.3 75.1 - - - +
371A ALA* 1.3 63.9 - - - +
373A GLY* 3.1 13.6 + - - -
374A ALA 5.2 0.4 - - - -
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Residues in contact with ALA 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A ARG* 3.1 28.5 + - - -
335A ARG 3.5 25.6 - - - +
336A VAL 3.7 13.0 - - - +
337A GLY* 3.9 1.1 - - - +
367A ARG 2.9 15.6 + - - +
368A ALA 3.8 5.4 - - - +
370A GLY* 1.3 74.7 - - - +
372A SER* 1.3 58.7 + - - +
373A GLY 3.4 0.4 + - - -
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Residues in contact with SER 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A ARG* 3.1 23.8 + - - +
337A GLY* 3.3 2.4 - - - -
338A PHE* 2.9 34.9 + - - +
341A ALA* 3.8 26.1 + - - +
368A ALA 2.7 21.4 + - - -
369A PHE* 3.2 7.5 + - - -
370A GLY 3.1 0.8 - - - -
371A ALA* 1.3 74.3 - - - +
373A GLY* 1.3 64.6 + - - +
374A ALA* 4.3 2.8 - - - +
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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