Contacts of the helix formed by residues 432 - 449 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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359B HIS* 5.8 5.1 - - - -
374B ILE* 5.2 12.3 - - - +
377B TYR* 5.4 5.5 - - - -
410B MET 3.5 20.8 + - - +
411B ILE 2.9 9.8 + - - +
413B ARG* 3.5 32.4 + - + +
431B GLU* 1.3 68.2 - - - +
433B LEU* 1.3 62.8 + - - +
434B GLU* 3.3 9.0 + - - +
435B ALA* 2.9 30.9 + - - +
436B ILE* 3.2 13.9 + - - +
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Residues in contact with LEU 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B ARG* 4.3 5.7 - - - +
425B ASN* 3.9 21.3 - - + +
426B GLU* 3.3 39.5 - - + +
427B PHE* 4.6 13.9 - - + -
431B GLU* 3.2 25.5 + - + +
432B ASN* 1.3 72.2 - - - +
434B GLU* 1.3 61.7 + - + +
436B ILE* 3.4 11.9 + - + +
437B GLU* 3.0 31.4 + - - +
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Residues in contact with GLU 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B HIS* 4.3 9.7 + - - -
376B ASN* 3.9 12.0 + - - -
377B TYR* 4.0 8.3 - - + +
378B GLY* 3.7 33.2 - - - +
413B ARG* 5.7 3.8 - - - +
432B ASN* 3.0 7.0 + - - +
433B LEU* 1.3 78.4 - - + +
435B ALA* 1.3 59.9 + - - +
437B GLU* 3.5 6.3 + - - +
438B PHE* 2.9 27.9 + - - +
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Residues in contact with ALA 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B TYR* 3.8 29.5 - - + -
410B MET* 3.3 36.1 - - + +
411B ILE 4.5 0.2 - - - +
432B ASN* 2.9 18.2 + - - +
434B GLU* 1.3 74.3 - - - +
436B ILE* 1.3 68.6 + - - +
438B PHE* 3.1 4.8 + - - +
439B LEU* 3.1 28.9 + - - +
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Residues in contact with ILE 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B ILE* 3.8 30.7 - - + +
431B GLU* 3.8 34.1 - - + -
432B ASN 3.2 9.1 + - - +
433B LEU* 3.6 14.8 - - + +
435B ALA* 1.3 81.1 - - - +
437B GLU* 1.3 63.5 + - - +
439B LEU* 3.1 5.9 + - - +
440B ARG* 3.0 57.2 + - - +
463B PHE* 4.5 12.8 - - + -
475B LEU* 4.0 12.0 - - + +
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Residues in contact with GLU 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B LEU 3.0 15.3 + - - +
434B GLU* 3.7 7.6 - - - +
435B ALA 3.2 0.2 - - - -
436B ILE* 1.3 79.7 - - - +
438B PHE* 1.3 58.0 + - - +
440B ARG* 3.2 36.9 + - + +
441B ASN* 2.8 34.0 + - + +
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Residues in contact with PHE 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B TRP* 4.3 8.1 - + - -
338B PRO* 3.9 17.5 - - + -
377B TYR* 3.4 44.9 - + + +
383B SER* 4.2 17.3 - - - -
386B LEU* 3.5 37.9 - - + -
387B VAL* 3.9 11.4 - - + -
410B MET* 4.0 3.1 - - + -
434B GLU 2.9 16.0 + - - +
435B ALA 3.1 7.4 + - - +
437B GLU* 1.3 76.4 - - - +
439B LEU* 1.3 74.1 + - + +
441B ASN* 3.6 4.5 - - + +
442B THR* 2.7 56.8 + - - -
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Residues in contact with LEU 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B TRP* 6.0 1.6 - - + -
338B PRO* 5.2 1.8 - - + -
404B VAL* 4.9 7.6 - - + -
407B VAL* 3.6 31.0 - - + -
410B MET* 3.5 33.0 - - + -
411B ILE* 4.0 14.8 - - + -
435B ALA 3.1 14.2 + - - +
436B ILE 3.5 5.6 - - - +
438B PHE* 1.3 89.1 - - + +
440B ARG* 1.3 62.2 + - - +
442B THR* 3.7 5.9 - - + -
443B ASN* 2.9 32.0 + - - +
475B LEU* 3.9 10.8 - - + -
477B PHE* 4.4 26.9 - - + -
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Residues in contact with ARG 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B ILE* 3.0 31.1 + - - +
437B GLU* 3.2 41.4 + - - +
439B LEU* 1.3 77.6 - - - +
441B ASN* 1.3 58.4 + - - +
444B ARG* 3.0 15.8 + - - +
463B PHE* 4.8 7.9 - - - -
470B GLN* 2.8 44.5 + - + +
473B GLY 2.8 25.8 + - - -
474B GLY* 3.0 15.3 - - - -
475B LEU* 3.0 28.7 - - - +
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Residues in contact with ASN 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B SER* 4.9 5.5 + - - -
387B VAL* 4.7 7.4 - - + +
437B GLU* 2.8 18.7 + - + +
438B PHE* 3.6 4.7 - - + +
440B ARG* 1.3 75.7 - - - +
442B THR* 1.3 67.6 + - - +
444B ARG* 2.4 45.6 + - - +
445B ILE* 2.8 52.9 + - - +
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Residues in contact with THR 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B TRP* 4.0 31.4 - - + -
387B VAL* 3.7 16.3 - - + +
390B ALA* 5.0 1.3 - - + -
438B PHE* 2.7 48.1 + - - -
439B LEU* 3.7 8.7 - - + -
441B ASN* 1.3 77.3 - - - +
443B ASN* 1.3 60.8 + - - +
445B ILE* 3.5 3.6 + - - +
446B LEU* 2.8 50.5 + - + +
455B THR* 5.8 0.4 - - + -
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Residues in contact with ASN 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B LEU* 2.9 17.9 + - - +
442B THR* 1.3 78.1 - - - +
444B ARG* 1.3 66.6 + - - +
446B LEU* 3.6 6.9 - - - +
447B GLY* 3.5 12.6 + - - -
455B THR* 2.5 39.2 + - - +
470B GLN* 3.9 5.6 - - - +
475B LEU 2.7 29.5 + - - +
476B GLY 3.6 14.5 - - - +
477B PHE* 3.6 27.8 - - - -
478B TRP* 3.8 10.1 - - + -
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Residues in contact with ARG 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B ARG 3.0 12.0 + - - +
441B ASN* 2.4 47.7 + - - +
443B ASN* 1.3 75.1 - - - +
445B ILE* 1.3 80.0 + - - +
447B GLY* 2.9 13.2 + - - -
448B GLU* 3.1 41.0 + - + +
470B GLN* 3.6 10.0 + - - +
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Residues in contact with ILE 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B HIS* 5.6 3.1 - - + -
119B LEU* 3.7 32.3 - - + -
387B VAL* 3.9 24.7 - - + -
391B LEU* 4.4 7.2 - - + -
441B ASN* 2.8 46.3 + - - +
442B THR 3.9 2.9 - - - +
444B ARG* 1.3 86.2 - - - +
446B LEU* 1.3 55.5 + - + +
447B GLY 2.9 2.1 + - - -
448B GLU* 2.9 13.6 + - - +
449B GLN* 2.7 53.3 + - + +
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Residues in contact with LEU 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B TRP* 5.6 0.2 - - + -
387B VAL* 4.6 4.5 - - + +
390B ALA* 3.9 29.4 - - + -
391B LEU* 3.4 30.1 - - + +
394B ILE* 4.4 7.9 - - + -
402B LEU* 4.1 8.7 - - + -
442B THR* 2.8 29.8 + - + +
443B ASN* 3.6 8.3 - - - +
444B ARG 3.2 0.2 - - - -
445B ILE* 1.3 77.6 - - + +
447B GLY* 1.3 54.5 + - - +
449B GLN* 5.0 0.2 - - - -
450B VAL* 4.0 25.3 - - + +
453B ALA* 4.1 9.5 - - + +
454B VAL 6.0 0.2 - - - -
455B THR* 3.6 28.9 - - + -
478B TRP* 3.2 17.8 - - + -
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Residues in contact with GLY 447 (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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443B ASN 3.9 5.4 - - - -
444B ARG* 2.9 9.2 + - - -
446B LEU* 1.3 76.3 - - - +
448B GLU* 1.3 65.6 + - - +
449B GLN 3.8 0.2 - - - -
451B SER* 3.9 24.5 + - - -
478B TRP* 4.2 12.6 - - - -
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Residues in contact with GLU 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B ARG* 3.5 38.4 + - + +
445B ILE* 3.5 15.7 - - - +
447B GLY* 1.3 84.2 - - - +
449B GLN* 1.3 74.7 + - - +
451B SER* 4.4 5.6 + - - -
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Residues in contact with GLN 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU* 3.7 23.7 - - + +
120B ARG* 3.1 27.4 + - - +
391B LEU* 4.0 21.1 - - + -
395B GLU* 4.6 3.8 - - - +
445B ILE* 2.7 37.6 + - + +
448B GLU* 1.3 86.5 + - - +
450B VAL* 1.3 62.9 + - + +
451B SER 3.7 1.1 + - - -
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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
------------------------------------------------------------
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