Contacts of the helix formed by residues 417 - 430 (chain D) in PDB entry 5MG3
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 ALA 417 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331D SER* 3.5 21.0 - - - +
339D PRO* 5.5 4.7 - - + -
411D ILE* 3.6 23.1 - - + +
413D ASN* 5.2 1.3 - - - +
415D ASN 3.7 4.4 + - - +
416D GLU* 1.3 77.8 - - - +
418D ARG* 1.4 62.4 + - - +
419D GLN* 3.5 2.4 - - - +
420D LEU* 3.7 9.5 + - - +
421D SER* 2.6 37.1 + - - -
508E PHE* 3.0 5.7 + - - -
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Residues in contact with ARG 418 (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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330D THR* 5.3 1.8 + - - -
331D SER* 5.1 14.3 + - - +
417D ALA* 1.4 75.0 - - - +
419D GLN* 1.4 50.2 + - - +
421D SER* 3.1 8.9 + - - -
422D LEU* 2.8 38.2 + - + +
505E GLY 2.9 23.4 + - - -
506E LEU* 3.3 24.1 + - - +
507E ARG* 3.6 17.0 - - - +
508E PHE* 2.7 36.0 + - - +
212Y GLN 4.7 1.6 + - - -
214Y ASP* 2.6 43.9 + - - -
215Y LEU* 3.6 29.1 - - - +
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Residues in contact with GLN 419 (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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232D ASN* 4.3 2.6 + - - -
297D ARG* 4.5 3.8 + - - +
416D GLU* 5.7 5.1 - - + +
417D ALA 3.5 0.2 - - - -
418D ARG* 1.4 73.9 - - - +
420D LEU* 1.4 60.9 + - - +
422D LEU* 3.6 5.6 + - - +
423D LEU* 3.2 21.0 + - - +
507E ARG 3.7 16.2 - - - +
508E PHE* 4.0 28.7 + - - +
534G LEU* 3.9 11.3 - - - +
535G GLY* 3.4 15.0 + - - -
539G SER* 3.3 18.6 - - - -
540G ASN* 2.9 46.6 + - - +
44Y ILE* 4.4 18.5 + - + +
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Residues in contact with LEU 420 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294D ALA* 3.6 34.8 - - + +
295D SER* 6.3 0.2 - - - -
297D ARG* 3.6 24.6 - - + +
298D VAL* 4.2 8.3 - - + -
341D VAL* 4.7 6.3 - - + -
394D ASN* 5.5 1.6 - - - +
411D ILE* 3.6 40.6 - - + -
413D ASN* 4.1 16.2 - - - +
417D ALA* 3.7 11.6 + - - +
418D ARG 3.4 0.4 - - - -
419D GLN* 1.4 75.7 - - - +
421D SER* 1.3 65.4 + - - +
423D LEU* 3.4 19.3 + - + +
424D LEU* 4.0 16.0 + - + +
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Residues in contact with SER 421 (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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329D SER* 2.8 34.0 + - - +
330D THR* 4.4 14.1 - - - +
331D SER* 3.5 28.6 + - - -
341D VAL* 4.8 13.0 - - - +
417D ALA 2.6 22.4 + - - -
418D ARG* 3.1 17.1 + - - +
420D LEU* 1.3 74.9 - - - +
422D LEU* 1.3 63.3 + - - +
424D LEU* 3.8 3.6 + - - +
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Residues in contact with LEU 422 (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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229D GLN* 3.9 41.1 - - + +
232D ASN* 3.6 19.7 - - - +
418D ARG 2.8 19.7 + - - +
419D GLN 4.0 2.9 - - - +
421D SER* 1.3 75.1 - - - +
423D LEU* 1.4 59.6 + - - +
424D LEU 3.0 1.0 + - - -
425D ARG* 3.3 29.4 - - + +
426D ALA* 2.9 27.3 + - + +
507E ARG* 5.8 2.9 - - - -
539G SER* 4.0 19.5 - - - +
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Residues in contact with LEU 423 (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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232D ASN* 3.8 17.8 - - + +
233D ILE* 3.6 35.3 - - + +
236D ASN* 4.1 13.2 - - - +
294D ALA* 4.5 14.6 - - + -
297D ARG* 3.6 41.1 - - - +
369D PHE* 4.4 2.9 - - - -
393D ILE* 4.6 11.2 - - + -
419D GLN 3.2 13.9 + - - +
420D LEU* 3.6 11.7 - - + +
421D SER 3.4 0.8 - - - -
422D LEU* 1.4 74.1 - - - +
424D LEU* 1.4 59.3 + - + +
426D ALA* 3.6 6.8 - - - +
427D GLY* 2.9 25.5 + - - -
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Residues in contact with LEU 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294D ALA* 5.4 1.6 - - + -
326D ILE* 5.1 3.2 - - - +
329D SER* 3.7 10.3 - - - +
341D VAL* 3.8 29.4 - - + -
343D ILE* 4.2 16.4 - - + -
367D THR* 4.2 24.5 - - + +
369D PHE* 3.7 11.4 - - + -
393D ILE* 4.3 17.3 - - + -
394D ASN* 3.7 25.8 - - + +
408D ILE* 4.1 15.3 - - + -
420D LEU* 4.3 14.8 - - + +
421D SER 3.8 1.9 + - - +
422D LEU 3.0 1.4 + - - -
423D LEU* 1.4 77.9 - - + +
425D ARG* 1.3 57.2 + - - +
427D GLY 3.6 0.5 + - - -
428D ALA* 3.1 25.5 + - - +
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Residues in contact with ARG 425 (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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326D ILE* 4.9 4.9 - - + +
327D THR 3.6 12.9 + - - -
328D ASP* 2.7 46.4 + - - +
329D SER* 3.1 32.3 + - - +
421D SER 4.1 1.1 - - - +
422D LEU* 3.3 34.2 - - + +
424D LEU* 1.3 72.2 - - - +
426D ALA* 1.4 56.9 + - - +
428D ALA* 4.2 6.1 - - - -
429D LEU* 2.8 63.3 + - + +
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Residues in contact with ALA 426 (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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229D GLN 3.8 14.4 - - - +
230D ASN* 4.0 13.8 - - - -
232D ASN* 3.1 29.4 - - - +
233D ILE* 3.8 7.0 - - + -
422D LEU* 2.9 23.0 + - + +
423D LEU* 3.6 5.2 - - - +
425D ARG* 1.4 70.8 - - - +
427D GLY* 1.3 55.9 + - - +
430D ILE* 3.0 35.9 + - - +
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Residues in contact with GLY 427 (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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233D ILE* 3.9 18.2 - - - +
277D ALA* 5.2 3.6 + - - +
279D LEU* 4.0 4.7 - - - +
369D PHE* 3.5 34.7 - - - -
423D LEU 2.9 17.1 + - - -
425D ARG 3.4 0.2 - - - -
426D ALA* 1.3 72.0 - - - +
428D ALA* 1.3 61.0 - - - +
430D ILE* 3.3 14.0 - - - +
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Residues in contact with ALA 428 (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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279D LEU* 3.6 33.5 - - + +
324D ASP* 5.2 1.4 - - - +
326D ILE* 3.7 37.5 - - + -
369D PHE* 3.6 2.6 - - + -
424D LEU 3.1 17.4 + - - +
425D ARG* 3.9 5.8 - - - +
426D ALA 3.4 0.2 - - - -
427D GLY* 1.3 78.9 - - - +
429D LEU* 1.4 69.2 + - + +
430D ILE* 3.4 5.3 + - - +
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Residues in contact with LEU 429 (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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230D ASN* 4.2 9.6 + - - +
324D ASP* 6.1 2.7 - - - +
326D ILE* 4.1 22.4 - - + +
327D THR* 4.9 6.5 - - - +
425D ARG* 2.8 60.2 + - + +
428D ALA* 1.4 81.3 - - + +
430D ILE* 1.4 64.4 - - - +
431D ALA* 3.5 3.3 + - - +
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Residues in contact with ILE 430 (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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230D ASN* 3.5 19.4 - - + +
233D ILE* 3.5 26.9 - - + -
234D LEU* 4.8 6.7 - - + -
274D GLY 6.1 0.7 - - - +
276D THR* 3.5 24.3 - - + +
426D ALA 3.0 19.6 + - - +
427D GLY* 3.3 21.3 - - - +
428D ALA 4.3 4.7 - - - +
429D LEU* 1.4 77.5 - - - +
431D ALA* 1.4 73.7 + - - +
432D PRO* 4.8 0.7 - - + -
433D ILE* 3.7 30.1 - - + +
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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