Contacts of the helix formed by residues 355 - 371 (chain D) in PDB entry 4R0C
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 GLN 355 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55D ILE* 3.3 27.5 - - + +
56D THR 3.3 25.4 - - - +
57D ALA* 4.5 0.4 - - - -
58D HIS* 4.2 10.4 + - + +
351D PHE 4.1 0.2 - - - -
352D ASN* 2.7 37.3 + - - -
353D TYR* 2.8 13.8 + - - +
354D SER* 1.3 75.5 + - - +
356D LEU* 1.3 59.6 - - - +
357D GLY 3.0 2.2 - - - +
358D LEU* 3.0 23.9 + - - +
359D LEU* 2.8 29.4 + - + +
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Residues in contact with LEU 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D LEU* 3.9 7.4 - - + -
35D LEU* 3.5 32.5 - - + -
36D THR* 3.9 17.7 - - + -
39D LEU* 3.7 30.1 - - + -
57D ALA* 4.0 8.3 - - + -
351D PHE* 3.9 16.7 - - + -
354D SER* 3.1 34.7 + - - +
355D GLN* 1.3 74.6 - - - +
357D GLY* 1.3 67.2 + - - +
359D LEU* 3.7 18.1 - - + +
360D LEU* 2.9 27.5 + - - +
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Residues in contact with GLY 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D ILE* 3.4 17.2 - - - +
351D PHE* 2.9 44.7 + - - -
352D ASN* 5.3 0.7 - - - -
356D LEU* 1.3 76.5 - - - +
358D LEU* 1.3 55.2 + - - +
360D LEU* 3.9 1.9 - - - +
361D ALA* 3.0 29.5 + - - +
409D PRO* 5.1 1.0 - - - +
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Residues in contact with LEU 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D HIS* 3.4 29.4 - - + +
49D PRO* 4.3 16.4 - - + -
55D ILE* 3.5 26.2 - - + -
193D ILE* 3.4 27.2 - - - +
194D ILE* 3.7 22.0 - - + -
352D ASN 5.6 0.2 + - - -
355D GLN* 3.0 31.4 + - - +
357D GLY* 1.3 74.2 - - - +
359D LEU* 1.3 63.7 + - - +
361D ALA* 3.4 1.2 + - + -
362D VAL* 3.1 23.9 + - - +
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Residues in contact with LEU 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LEU* 4.9 5.4 - - + -
44D VAL* 3.6 34.8 - - + +
45D THR 4.6 0.7 - - - -
46D ALA* 4.1 24.5 - - + +
55D ILE* 3.9 22.2 - - + +
57D ALA* 3.8 22.4 - - + +
355D GLN 2.8 15.9 + - - +
356D LEU* 3.7 20.2 - - + +
358D LEU* 1.3 76.7 - - - +
360D LEU* 1.3 63.2 + - - +
362D VAL* 3.1 7.2 + - - +
363D LYS* 3.1 22.7 + - - +
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Residues in contact with LEU 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351D PHE* 3.9 21.8 - - + -
356D LEU 2.9 18.4 + - - +
357D GLY 3.9 2.2 - - - +
359D LEU* 1.3 76.8 - - - +
361D ALA* 1.3 57.6 + - - +
363D LYS* 4.0 26.2 - - + +
364D GLY* 2.8 29.0 + - - -
405D PRO 5.5 0.4 - - - +
406D VAL* 4.3 35.4 - - + +
410D MET* 4.6 4.7 - - - +
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Residues in contact with ALA 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D ILE* 4.7 0.2 - - + -
194D ILE* 3.9 17.0 - - + -
357D GLY 3.0 17.6 + - - +
358D LEU* 3.6 6.3 - - - +
360D LEU* 1.3 77.7 - - - +
362D VAL* 1.3 57.5 + - - +
365D ALA* 3.1 30.5 + - - +
406D VAL 6.1 0.2 - - - -
409D PRO* 3.6 27.8 - - + -
410D MET* 3.5 12.6 - - - +
413D LEU* 3.3 6.9 - - + +
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Residues in contact with VAL 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D ALA* 4.7 13.9 - - + -
47D THR 3.9 11.9 - - - +
49D PRO* 3.8 35.0 - - + -
55D ILE* 4.7 6.3 - - + -
358D LEU* 3.1 16.1 + - + +
359D LEU 3.8 6.5 - - - +
361D ALA* 1.3 77.5 - - - +
363D LYS* 1.3 68.4 + - - +
365D ALA* 3.9 2.1 - - - +
366D ALA* 3.0 24.7 + - + +
413D LEU* 4.2 4.7 - - + -
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Residues in contact with LYS 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359D LEU 3.1 15.5 + - - +
360D LEU* 4.0 23.3 - - + +
362D VAL* 1.3 77.5 - - - +
364D GLY* 1.3 74.9 + - - +
366D ALA* 3.1 20.1 - - - +
367D TRP* 3.1 29.6 + - - +
410D MET* 5.4 4.2 - - - +
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Residues in contact with GLY 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360D LEU* 2.8 18.9 + - - -
363D LYS* 1.3 87.8 - - - +
365D ALA* 1.3 65.5 + - - +
367D TRP* 2.9 14.0 + - - +
368D LEU* 3.0 15.9 + - - +
410D MET* 3.5 26.2 - - - -
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Residues in contact with ALA 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361D ALA 3.1 20.4 + - - +
362D VAL* 3.9 3.4 - - - +
364D GLY* 1.3 73.7 - - - +
366D ALA* 1.3 57.0 + - - +
369D GLY* 2.9 29.1 + - - -
410D MET* 3.4 28.0 - - - +
413D LEU* 3.6 21.5 - - + +
414D LEU* 3.5 16.6 - - + +
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Residues in contact with ALA 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362D VAL* 3.0 17.3 + - + +
363D LYS* 3.1 15.5 - - - +
364D GLY 3.1 0.2 - - - -
365D ALA* 1.3 78.7 - - - +
367D TRP* 1.3 60.7 + - - +
369D GLY* 4.0 1.0 - - - -
370D ALA* 3.4 18.9 + - - +
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Residues in contact with TRP 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363D LYS* 3.1 25.9 + - - +
364D GLY* 2.9 10.3 + - - +
366D ALA* 1.3 76.3 - - - +
368D LEU* 1.3 98.8 + - + +
369D GLY 3.1 0.2 - - - -
370D ALA* 3.1 21.1 + - + +
371D LEU* 3.7 25.0 + - + +
410D MET* 6.0 0.9 - - + -
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Residues in contact with LEU 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364D GLY 3.0 6.8 + - - +
367D TRP* 1.3 102.4 - - + +
369D GLY* 1.3 62.7 + - - +
371D LEU* 3.1 37.7 + - + +
372D THR 4.2 1.2 + - - -
373D VAL* 5.2 2.6 + - - +
378D LEU* 4.1 22.9 - - + +
407D PHE* 5.7 4.3 - - + -
410D MET* 3.3 33.2 - - + -
411D LEU* 4.3 10.5 - - + -
414D LEU* 3.6 28.7 - - + -
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Residues in contact with GLY 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365D ALA 2.9 18.5 + - - -
366D ALA 4.0 2.7 - - - -
367D TRP 3.1 0.2 - - - -
368D LEU* 1.3 78.3 - - - +
370D ALA* 1.3 60.7 + - - +
371D LEU 3.3 1.2 + - - -
372D THR* 3.3 15.6 + - - +
414D LEU* 3.7 15.4 - - - +
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Residues in contact with ALA 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366D ALA 3.4 11.2 + - - +
367D TRP* 3.1 15.9 + - + +
369D GLY* 1.3 77.9 - - - +
371D LEU* 1.3 61.2 + - + +
372D THR* 3.1 11.2 + - - +
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Residues in contact with LEU 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367D TRP* 4.5 25.1 - - + +
368D LEU* 3.1 41.3 + - + +
370D ALA* 1.3 74.7 - - + +
372D THR* 1.3 75.1 + - - +
373D VAL* 3.3 23.7 + - + +
378D LEU* 4.2 14.8 - - + -
381D LEU* 5.6 5.8 - - + -
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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