Contacts of the helix formed by residues 479 - 498 (chain B) in PDB entry 1N4M
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 ASP 479 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475B LYS 3.6 12.9 + - - +
476B LEU* 2.8 17.3 + - - +
477B LEU 3.3 0.4 - - - -
478B ASN* 1.3 76.2 - - - +
480B ASN* 1.3 65.4 + - - +
481B ILE* 3.0 23.2 + - - +
482B PHE* 3.0 20.9 + - + +
483B HIS* 3.1 16.7 + - - -
426D PHE* 3.1 23.7 - - + +
427D ASP* 3.1 24.2 + - - +
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Residues in contact with ASN 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A ASN* 4.0 19.2 + - - +
481A ILE* 5.6 8.5 - - + -
522A ASN* 5.9 0.6 - - - +
418B ARG* 3.1 46.1 - - - +
478B ASN 3.2 7.7 + - - +
479B ASP* 1.3 72.2 + - - +
481B ILE* 1.3 66.3 + - + +
483B HIS* 3.2 1.9 + - - +
484B MET* 2.7 51.3 + - - +
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Residues in contact with ILE 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A ASN* 5.6 9.4 - - + +
479B ASP* 3.0 11.1 + - - +
480B ASN* 1.3 89.1 - - + +
482B PHE* 1.3 59.0 + - - +
484B MET* 3.6 5.8 - - + -
485B SER* 2.6 43.0 + - - +
523B LEU* 4.4 6.1 - - + -
527B ASP* 3.4 46.0 - - + +
530B LYS* 5.3 1.1 - - - +
426D PHE* 4.3 9.9 - - + -
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Residues in contact with PHE 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B MET* 4.5 6.3 - - + -
460B MET* 3.9 20.2 - - + -
461B LEU* 6.5 0.4 - - + -
476B LEU* 3.5 46.4 - - + -
477B LEU* 4.5 8.5 - - + -
479B ASP* 3.0 18.8 + - + +
481B ILE* 1.3 77.3 - - - +
483B HIS* 1.3 81.3 + + - +
485B SER* 3.4 0.7 - - - -
486B LEU* 2.7 64.0 + - + +
531B VAL* 4.9 2.9 - - + -
422D ILE* 3.8 19.3 - - + -
426D PHE* 3.5 38.6 - + + -
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Residues in contact with HIS 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B ILE* 4.0 13.7 - - + -
418B ARG* 3.2 39.2 + - - +
453B TYR* 2.7 30.8 + - - +
457B MET* 4.0 20.3 - - + +
477B LEU* 2.5 41.3 + - + -
479B ASP 3.1 22.5 + - - -
480B ASN 3.5 4.9 - - - +
482B PHE* 1.3 93.7 - + - +
484B MET* 1.3 58.6 + - - +
486B LEU* 3.4 1.9 + - - +
487B LEU* 2.8 33.9 + - - +
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Residues in contact with MET 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B ARG* 3.5 32.3 - - + -
422B ILE* 3.5 29.8 - - + -
480B ASN* 2.7 41.6 + - - +
481B ILE* 3.6 9.0 - - + +
483B HIS* 1.3 74.9 - - - +
485B SER* 1.3 57.8 + - - +
487B LEU* 3.7 14.2 - - + +
488B ALA* 2.8 31.0 + - - +
521B LEU* 3.9 23.0 - - + +
523B LEU* 3.9 15.7 - - + +
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Residues in contact with SER 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B ILE* 2.6 36.0 + - - +
482B PHE 3.4 3.1 - - - -
484B MET* 1.3 72.0 - - - +
486B LEU* 1.3 66.9 + - - +
488B ALA* 3.2 2.8 + - - +
489B CYS* 2.9 24.1 + - - +
523B LEU* 3.8 12.1 - - - +
527B ASP 3.3 30.1 + - - -
528B PHE* 3.9 6.6 + - - +
531B VAL* 3.8 18.4 - - - +
426D PHE* 4.2 5.1 - - - -
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Residues in contact with LEU 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B TYR* 3.3 31.6 - - + +
456B VAL* 3.7 28.7 - - + -
457B MET* 3.6 27.8 - - + -
460B MET* 3.9 15.5 - - + -
482B PHE* 2.7 42.0 + - + +
483B HIS 3.6 3.6 - - - +
485B SER* 1.3 72.8 - - - +
487B LEU* 1.3 63.7 + - - +
489B CYS* 3.1 3.6 + - - +
490B ALA* 3.1 21.8 + - - +
531B VAL* 3.8 13.3 - - + +
535B PHE* 3.8 13.1 - - + -
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Residues in contact with LEU 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B VAL* 5.2 4.7 - - + -
422B ILE* 3.9 21.8 - - + -
446B TYR* 4.3 15.0 - - + +
449B GLY 4.8 0.2 - - - +
450B VAL* 4.6 11.2 - - + -
453B TYR* 3.7 41.7 - - + -
483B HIS 2.8 23.1 + - - +
484B MET* 3.7 14.1 - - + +
486B LEU* 1.3 72.9 - - - +
488B ALA* 1.3 63.4 + - - +
489B CYS 3.2 0.2 + - - -
490B ALA* 3.3 2.8 + - - +
491B LEU* 3.1 48.7 + - + +
521B LEU* 4.1 8.1 - - + -
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Residues in contact with ALA 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B MET 2.8 21.9 + - - +
485B SER 3.6 2.5 - - - +
487B LEU* 1.3 73.0 - - - +
489B CYS* 1.3 58.2 + - - +
491B LEU* 3.5 0.8 + - - -
492B GLU* 2.9 27.2 + - - +
517B ILE* 3.6 16.0 - - + +
518B LEU* 4.6 3.1 - - + -
521B LEU* 3.3 25.1 - - + -
523B LEU* 3.6 19.7 - - + -
528B PHE* 3.8 10.9 - - + -
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Residues in contact with CYS 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B SER 2.9 12.6 + - - +
486B LEU 3.1 9.2 + - - +
488B ALA* 1.3 75.1 - - - +
490B ALA* 1.3 60.2 + - - +
492B GLU* 3.0 4.9 + - - +
493B VAL* 2.9 31.0 + - - +
528B PHE* 3.6 15.5 - - + -
531B VAL* 3.9 17.9 - - + -
532B ILE* 4.6 5.4 - - - -
535B PHE* 3.5 39.5 - - + -
550B LEU* 3.8 20.4 - - - -
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Residues in contact with ALA 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B GLY* 3.2 26.0 - - - +
452B LEU* 3.5 16.7 - - + +
453B TYR* 3.7 10.3 - - + +
486B LEU 3.1 12.4 + - - +
487B LEU 3.8 6.5 - - - +
489B CYS* 1.3 74.6 - - - +
491B LEU* 1.3 58.5 + - - +
493B VAL* 3.0 5.5 + - - +
494B VAL* 2.9 31.8 + - - +
535B PHE* 3.7 17.2 - - + -
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Residues in contact with LEU 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B PHE* 4.0 22.2 - - + -
445B ARG 4.1 4.0 - - - +
446B TYR* 3.7 41.7 - - + +
449B GLY* 3.6 23.8 - - - -
487B LEU* 3.1 44.1 + - + +
488B ALA 3.7 5.2 - - - +
490B ALA* 1.3 79.0 - - - +
492B GLU* 1.3 52.0 + - - +
494B VAL* 3.4 4.7 - - + +
495B MET* 2.5 42.6 + - - +
517B ILE* 3.9 17.5 - - + -
521B LEU* 4.8 3.1 - - + -
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Residues in contact with GLU 492 (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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488B ALA 2.9 15.6 + - - +
489B CYS* 3.0 15.0 + - - +
491B LEU* 1.3 75.1 - - - +
493B VAL* 1.3 61.4 + - - +
495B MET* 4.4 8.2 - - - +
496B ALA* 2.8 39.0 + - - +
512B LEU 5.4 0.9 - - - +
513B SER 4.7 2.8 - - - +
514B PHE* 3.6 25.8 + - + +
517B ILE* 3.3 25.7 - - + +
528B PHE* 4.5 6.5 - - + -
549B HIS* 2.7 36.7 + - + +
550B LEU* 4.2 11.7 - - + -
553B CYS* 4.4 5.8 - - - -
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Residues in contact with VAL 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B LEU* 6.1 4.0 - - + -
452B LEU* 3.5 14.8 - - + -
489B CYS 2.9 19.3 + - - +
490B ALA 3.3 6.1 - - - +
492B GLU* 1.3 75.1 - - - +
494B VAL* 1.3 53.4 + - - +
496B ALA* 3.6 0.9 - - - +
497B THR* 2.6 41.2 + - - -
535B PHE* 3.5 29.8 - - + -
542B LEU* 4.0 12.1 - - + -
546B MET* 3.4 30.9 - - + +
550B LEU* 4.3 14.8 - - + -
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Residues in contact with VAL 494 (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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389B LEU* 5.5 4.0 - - + -
445B ARG* 3.7 27.8 - - + +
448B LEU* 4.1 13.5 - - + -
449B GLY* 3.6 25.6 - - - +
452B LEU* 4.3 9.0 - - + -
490B ALA 2.9 15.7 + - - +
491B LEU* 3.4 8.5 - - + +
493B VAL* 1.3 75.2 - - + +
495B MET* 1.3 66.7 + - - +
497B THR* 2.8 25.9 - - + +
498B TYR* 3.0 33.0 + - + -
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Residues in contact with MET 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B PHE* 3.6 23.8 - - + -
430B PHE* 3.7 18.4 - - + -
445B ARG* 4.8 13.2 - - - +
491B LEU* 2.5 32.5 + - - +
492B GLU* 4.0 13.0 - - - +
494B VAL* 1.3 73.7 - - - +
496B ALA* 1.3 58.6 + - - +
498B TYR* 3.1 8.9 + - - +
499B SER* 2.9 22.9 + - - -
512B LEU* 3.4 43.7 - - + +
516B TRP* 3.4 28.5 - - + -
517B ILE* 4.7 4.3 - - + -
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Residues in contact with ALA 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B GLU* 2.8 21.4 + - - +
493B VAL 3.7 2.2 - - - +
495B MET* 1.3 73.9 - - - +
497B THR* 1.3 54.7 + - - +
498B TYR 2.9 4.7 - - - -
499B SER* 2.6 36.2 + - - -
500B ARG* 4.1 3.5 + - - +
546B MET* 3.8 10.1 - - + -
549B HIS* 3.4 36.3 - - + +
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Residues in contact with THR 497 (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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382B ILE* 5.0 17.2 + - - +
386B MET* 5.3 11.1 - - + +
493B VAL* 2.6 23.5 + - + -
494B VAL* 2.8 28.9 + - + +
496B ALA* 1.3 72.0 - - - +
498B TYR* 1.3 83.3 + - + +
499B SER 3.4 0.8 + - - -
500B ARG* 4.4 10.8 + - - +
546B MET* 4.3 8.7 - - - +
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Residues in contact with TYR 498 (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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386B MET* 3.4 35.9 - - + +
445B ARG* 3.3 48.9 - - - +
448B LEU* 3.8 26.2 - - + +
494B VAL* 3.0 25.8 + - + +
495B MET* 3.2 6.7 - - - +
496B ALA 2.9 1.0 - - - -
497B THR* 1.3 90.7 - - + +
499B SER* 1.3 57.2 + - - +
500B ARG 2.7 10.3 + - - +
501B SER* 3.1 34.3 + - - -
502B THR* 3.6 12.0 + - - +
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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