Contacts of the helix formed by residues 432 - 449 (chain D) in PDB entry 1M7X
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 ASN 432 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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359D HIS* 5.5 4.7 - - - -
374D ILE* 3.7 27.5 - - - +
377D TYR* 4.9 5.1 - - - -
410D MET 3.3 24.7 + - - +
411D ILE 2.6 12.6 + - - +
413D ARG* 3.5 30.0 + - + +
430D ARG 3.9 1.2 + - - -
431D GLU* 1.3 70.1 - - - +
433D LEU* 1.3 58.4 + - - +
434D GLU* 3.3 12.3 + - - +
435D ALA* 2.9 31.7 + - - +
436D ILE* 2.9 30.4 + - - +
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Residues in contact with LEU 433 (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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413D ARG* 3.8 9.0 - - - +
431D GLU* 3.2 28.5 + - + +
432D ASN* 1.3 71.1 + - - +
434D GLU* 1.3 57.0 + - + +
436D ILE* 3.3 9.7 + - + +
437D GLU* 2.7 38.0 + - - +
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Residues in contact with GLU 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359D HIS* 3.2 31.1 + - - -
376D ASN* 3.4 4.6 - - - +
377D TYR* 3.8 8.8 + - + +
378D GLY* 3.3 35.4 + - - +
413D ARG* 5.2 6.9 + - - +
432D ASN* 3.3 7.7 + - - +
433D LEU* 1.3 79.2 - - + +
435D ALA* 1.3 52.0 + - - +
437D GLU* 3.7 5.8 - - - +
438D PHE* 2.8 33.8 + - - +
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Residues in contact with ALA 435 (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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377D TYR* 3.9 22.4 - - + +
410D MET* 3.2 35.6 - - + +
432D ASN* 2.9 23.6 + - - +
434D GLU* 1.3 75.1 - - - +
436D ILE* 1.3 61.5 + - - +
438D PHE* 3.1 5.3 + - - +
439D LEU* 2.9 34.7 + - - +
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Residues in contact with ILE 436 (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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411D ILE* 3.3 35.7 - - + -
431D GLU* 4.1 30.3 - - + +
432D ASN 2.9 23.6 + - - +
433D LEU* 3.8 11.0 - - + +
435D ALA* 1.3 71.7 - - - +
437D GLU* 1.3 63.9 + - - +
438D PHE 3.3 0.2 + - - -
439D LEU* 3.3 5.2 + - - +
440D ARG* 3.1 60.2 + - - +
463D PHE* 4.3 16.6 - - + -
475D LEU* 4.2 11.4 - - + +
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Residues in contact with GLU 437 (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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433D LEU 2.7 19.0 + - - +
434D GLU* 3.8 6.7 - - - +
436D ILE* 1.3 79.2 - - - +
438D PHE* 1.3 60.4 + - - +
440D ARG* 3.5 30.2 + - - +
441D ASN* 3.1 44.4 + - - +
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Residues in contact with PHE 438 (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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336D TRP* 4.5 5.6 - + - -
338D PRO* 4.4 13.5 - - + -
377D TYR* 3.7 38.1 - + + +
383D SER* 3.7 32.3 - - - -
386D LEU* 3.4 36.8 - - + -
387D VAL* 3.9 11.2 - - + -
410D MET* 4.3 10.1 - - + -
434D GLU 2.8 16.5 + - - +
435D ALA 3.1 7.6 + - - +
437D GLU* 1.3 76.3 - - - +
439D LEU* 1.3 72.6 + - + +
441D ASN* 2.9 9.9 + - + +
442D THR* 2.8 46.4 + - - -
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Residues in contact with LEU 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336D TRP* 6.2 1.6 - - + -
338D PRO* 5.5 1.8 - - + -
404D VAL* 4.8 9.0 - - + -
407D VAL* 4.0 17.7 - - + -
410D MET* 3.8 31.9 - - + -
411D ILE* 3.7 29.4 - - + -
435D ALA 2.9 14.7 + - - +
436D ILE* 3.7 6.3 - - - +
438D PHE* 1.3 83.1 - - + +
440D ARG* 1.3 63.7 + - - +
442D THR* 3.3 5.5 + - - -
443D ASN* 3.1 27.4 + - - +
475D LEU* 4.1 12.3 - - + -
477D PHE* 3.6 33.7 - - + -
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Residues in contact with ARG 440 (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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436D ILE* 3.1 40.1 + - - +
437D GLU* 3.5 33.5 + - - +
438D PHE 3.2 0.2 - - - -
439D LEU* 1.3 77.4 - - - +
441D ASN* 1.3 57.7 + - - +
443D ASN* 3.3 0.9 + - - +
444D ARG* 2.9 26.4 + - - +
463D PHE* 4.9 5.9 - - - -
470D GLN* 3.4 30.5 + - + +
473D GLY 3.0 22.2 + - - -
474D GLY* 3.2 14.7 - - - -
475D LEU* 3.1 29.6 - - + +
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Residues in contact with ASN 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383D SER* 5.7 3.6 - - - +
387D VAL* 5.8 1.1 - - + -
437D GLU* 3.1 40.3 + - - +
438D PHE* 2.9 12.9 + - + +
440D ARG* 1.3 75.6 - - - +
442D THR* 1.3 63.0 + - - +
444D ARG* 2.7 40.0 + - - +
445D ILE* 2.8 44.1 + - + +
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Residues in contact with THR 442 (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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336D TRP* 3.7 33.0 - - + -
387D VAL* 3.7 17.1 - - + +
390D ALA* 4.8 2.2 - - + -
438D PHE* 2.8 43.0 + - - -
439D LEU* 3.6 12.1 - - - -
440D ARG 3.3 0.2 - - - -
441D ASN* 1.3 78.0 - - - +
443D ASN* 1.3 60.0 + - - +
445D ILE* 3.4 2.3 + - - +
446D LEU* 2.9 50.8 + - + +
455D THR* 6.0 0.2 - - + -
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Residues in contact with ASN 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439D LEU 3.1 8.5 + - - +
440D ARG 3.6 3.6 - - - +
442D THR* 1.3 81.1 - - - +
444D ARG* 1.3 52.6 + - - +
446D LEU* 2.5 31.0 - - - +
447D GLY* 4.7 0.2 - - - -
455D THR* 2.4 46.0 + - - +
470D GLN* 3.7 8.7 - - - +
475D LEU 2.5 29.5 - - - +
476D GLY 3.7 12.7 + - - +
477D PHE* 3.5 22.3 + - - +
478D TRP* 4.7 6.7 + - - +
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Residues in contact with ARG 444 (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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440D ARG 2.9 14.3 + - - +
441D ASN* 2.7 35.0 + - - +
443D ASN* 1.3 73.6 - - - +
445D ILE* 1.3 82.3 + - - +
446D LEU 2.4 17.8 - - - +
448D GLU* 3.0 51.7 + - - +
470D GLN* 3.6 14.1 + - + +
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Residues in contact with ILE 445 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D LEU* 4.2 27.4 - - + -
380D ARG* 5.8 6.1 - - - +
383D SER* 6.0 0.7 - - - +
387D VAL* 3.8 38.1 - - + -
391D LEU* 4.3 7.2 - - + -
441D ASN* 2.8 30.9 + - + +
442D THR 3.8 3.1 - - - +
444D ARG* 1.3 95.9 - - - +
446D LEU* 1.3 57.7 + - - +
448D GLU* 3.3 9.7 - - - +
449D GLN* 2.8 49.9 + - + +
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Residues in contact with LEU 446 (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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336D TRP* 5.4 0.4 - - + -
387D VAL* 5.5 0.2 - - + -
390D ALA* 4.2 18.2 - - + -
391D LEU* 3.7 38.8 - - + -
394D ILE* 4.2 7.9 - - + -
402D LEU* 4.4 8.5 - - + -
442D THR* 2.9 41.7 + - + +
443D ASN* 2.5 16.7 - - - +
444D ARG 2.4 23.2 - - - +
445D ILE* 1.3 72.4 - - + +
447D GLY* 1.3 59.1 + - - +
448D GLU 2.8 5.4 - - - -
450D VAL* 3.8 13.9 - - + -
453D ALA 5.2 3.1 - - - +
455D THR* 3.8 28.9 - - + -
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Residues in contact with GLY 447 (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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443D ASN 4.7 0.2 - - - -
446D LEU* 1.3 71.9 - - - +
448D GLU* 1.3 57.7 + - - +
449D GLN 3.4 0.7 - - - -
450D VAL* 3.4 15.8 - - - +
451D SER* 3.1 41.0 - - - -
452D GLY 4.8 1.3 - - - -
453D ALA 4.8 5.6 + - - -
478D TRP* 5.5 12.6 - - - -
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Residues in contact with GLU 448 (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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444D ARG* 3.0 54.0 + - - +
445D ILE* 3.3 6.9 - - - +
446D LEU 2.6 7.1 + - - -
447D GLY* 1.3 74.0 - - - +
449D GLN* 1.3 72.5 + - + +
451D SER* 5.4 1.4 - - - -
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Residues in contact with GLN 449 (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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119D LEU* 3.1 28.3 - - + +
120D ARG* 2.7 33.3 + - - +
391D LEU* 3.9 19.7 - - + -
395D GLU* 5.1 3.2 - - - +
445D ILE* 2.8 27.2 + - + +
448D GLU* 1.3 90.7 + - + +
450D VAL* 1.3 61.4 + - - +
451D SER 3.6 1.8 + - - -
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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
------------------------------------------------------------
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