Contacts of the helix formed by residues 469 - 490 (chain B) in PDB entry 3RMD
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 GLY 469 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424B ASN* 3.3 13.9 + - - -
426B SER* 4.0 0.4 - - - -
428B GLU* 3.2 11.4 - - - -
429B THR* 3.2 20.0 - - - +
467B ARG 3.7 0.2 + - - -
468B ASP* 1.3 73.1 - - - +
470B VAL* 1.3 58.2 + - - -
472B PRO* 3.0 22.2 - - - +
473B THR* 2.7 28.9 + - - -
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Residues in contact with VAL 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ILE* 4.0 26.0 - - + +
369B ILE* 4.0 27.1 - - + -
373B LEU* 4.3 17.7 - - + -
378B LYS* 5.4 7.0 - - - +
426B SER* 3.3 5.4 + - - +
427B PRO* 6.2 0.2 - - + -
428B GLU* 2.7 28.3 + - + +
468B ASP 5.3 0.9 - - - +
469B GLY* 1.3 69.2 - - - -
471B VAL* 1.3 72.8 + - + +
473B THR* 3.1 5.7 + - - -
474B GLU* 2.9 29.2 + - + +
577B TYR* 5.4 5.2 - - + -
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Residues in contact with VAL 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B TRP* 6.4 0.2 - - + -
369B ILE* 5.9 6.3 - - + -
420B ILE* 4.3 7.9 - - + -
425B ILE 3.9 4.9 - - - +
426B SER* 3.1 16.0 + - - +
427B PRO* 3.8 17.0 - - + -
470B VAL* 1.3 77.5 - - + +
472B PRO* 1.3 75.1 - - + +
474B GLU* 3.3 5.8 + - + +
475B ILE* 3.2 21.4 + - - +
566B LEU* 4.3 18.3 - - + +
570B LEU* 4.0 34.5 - - + -
575B PHE* 6.0 1.3 - - + -
577B TYR* 4.6 17.9 - - + -
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Residues in contact with PRO 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B ILE* 3.9 22.7 - - + +
421B ARG* 4.3 10.7 - - + +
424B ASN* 3.6 18.2 - - - +
425B ILE 3.2 23.1 - - - +
426B SER* 3.5 3.8 - - - -
468B ASP* 5.5 2.0 - - - +
469B GLY* 3.0 33.9 - - - +
470B VAL 3.4 0.4 - - - -
471B VAL* 1.3 87.8 - - + +
473B THR* 1.3 55.9 + - - +
475B ILE* 2.8 27.6 - - + +
476B THR* 2.8 15.2 + - - -
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Residues in contact with THR 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B ASP* 3.6 22.5 + - - +
469B GLY 2.7 21.1 + - - -
470B VAL* 3.1 6.1 + - - -
472B PRO* 1.3 77.1 - - - +
474B GLU* 1.3 72.4 + - - +
476B THR* 3.3 22.8 + - - -
477B LYS* 3.3 16.3 + - + +
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Residues in contact with GLU 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B TRP* 4.3 10.9 - - + -
368B ILE* 4.3 14.6 - - - +
369B ILE* 3.8 29.2 - - + -
372B SER* 2.7 38.3 + - - -
373B LEU* 5.8 0.9 - - + +
470B VAL* 2.9 30.6 + - + +
471B VAL* 3.9 4.7 - - + +
473B THR* 1.3 76.9 - - - +
475B ILE* 1.3 64.2 + - - +
477B LYS* 3.5 21.7 + - - +
478B VAL* 3.5 21.8 + - - +
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Residues in contact with ILE 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B TRP* 4.4 11.1 - - + -
417B PRO* 4.1 17.7 - - + +
420B ILE* 4.6 9.0 - - + -
421B ARG* 4.0 14.6 - - - -
471B VAL 3.2 12.6 + - - +
472B PRO* 2.8 30.5 - - + +
474B GLU* 1.3 72.3 - - - +
476B THR* 1.3 64.6 + - - +
478B VAL* 3.1 3.2 + - + -
479B PHE* 2.9 33.8 + - + +
563B ILE* 3.3 42.8 - - + -
566B LEU* 3.8 26.0 - - + -
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Residues in contact with THR 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B ARG* 3.5 36.4 + - - +
472B PRO 2.8 18.9 + - - -
473B THR* 3.3 13.2 + - - -
475B ILE* 1.3 79.3 - - - +
477B LYS* 1.3 63.2 + - - +
479B PHE* 3.1 9.6 + - + +
480B ASN* 3.0 41.7 + - - +
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Residues in contact with LYS 477 (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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350B TYR* 5.7 1.3 - - - -
372B SER* 2.8 24.7 + - - +
473B THR* 3.3 16.2 + - + +
474B GLU* 3.7 30.1 + - - +
475B ILE 3.2 0.6 - - - -
476B THR* 1.3 73.7 - - - +
478B VAL* 1.3 57.2 + - + +
479B PHE 2.7 14.6 + - - -
480B ASN* 2.9 22.5 + - - +
481B GLN* 3.0 33.7 + - + +
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Residues in contact with VAL 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B TYR* 3.6 22.2 - - + +
365B TRP* 3.9 20.4 - - + -
368B ILE* 5.1 3.6 - - + -
474B GLU* 3.5 12.5 + - - +
475B ILE 3.1 8.3 + - - +
477B LYS* 1.3 78.9 - - + +
479B PHE* 1.3 59.8 + - - +
481B GLN* 4.1 2.5 - - - +
482B ARG* 3.4 0.7 + - - +
559B ARG* 2.7 68.1 - - + +
562B LEU* 3.9 18.6 - - + -
563B ILE* 3.6 15.3 - - + +
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Residues in contact with PHE 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B THR* 5.6 3.6 - - + -
414B SER* 3.1 29.2 - - - -
417B PRO* 4.0 10.3 - - + -
418B SER* 4.7 5.4 - - - -
421B ARG* 3.7 37.0 - - - -
475B ILE* 2.9 21.0 + - + +
476B THR* 3.2 13.2 - - + +
477B LYS 2.7 4.4 + - - -
478B VAL* 1.3 71.5 - - - +
480B ASN* 1.3 69.4 + - - +
482B ARG* 2.8 16.8 + - - +
483B LYS* 3.3 11.8 + - - +
563B ILE* 3.4 45.8 - - + -
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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
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476B THR* 3.0 33.7 + - - +
477B LYS* 2.9 11.0 + - - +
479B PHE* 1.3 73.9 - - - +
481B GLN* 1.3 56.6 + - + +
483B LYS* 2.6 42.3 + - + +
484B GLU* 2.9 14.6 + - - +
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Residues in contact with GLN 481 (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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350B TYR* 3.2 23.4 + - - -
477B LYS* 3.0 41.0 + - - +
480B ASN* 1.3 78.7 - - + +
482B ARG* 1.3 61.3 + - - +
484B GLU* 3.8 19.9 + - - +
485B HIS* 2.9 36.9 + - + -
559B ARG* 2.5 50.6 + - - +
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Residues in contact with ARG 482 (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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478B VAL 3.4 4.4 + - - +
479B PHE* 2.8 14.6 + - - +
480B ASN 2.8 2.0 + - - -
481B GLN* 1.3 71.2 - - - +
483B LYS* 1.3 71.0 + - + +
485B HIS 3.5 0.9 + - - -
486B LYS* 3.0 49.1 + - + +
556B GLN* 3.9 33.6 + - + +
557B ILE* 6.3 0.4 - - - +
559B ARG* 3.5 15.4 - - + +
560B LYS* 3.0 47.1 - - - +
563B ILE* 4.7 10.0 - - + +
564B ASN* 5.0 0.6 - - - +
907B DTP 3.4 28.6 + - - -
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Residues in contact with LYS 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B PHE 3.3 8.5 + - - +
480B ASN* 2.6 25.6 + - - +
482B ARG* 1.3 71.2 - - - +
484B GLU* 1.3 65.9 + - - +
486B LYS* 2.7 8.3 + - - +
487B GLY* 2.7 23.2 + - - -
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Residues in contact with GLU 484 (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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480B ASN* 2.9 9.1 + - - +
481B GLN* 3.4 22.1 + - - +
483B LYS* 1.3 82.0 - - - +
485B HIS* 1.3 79.8 + - - +
487B GLY* 3.1 2.4 + - - -
488B TYR* 3.0 62.3 + - + +
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Residues in contact with HIS 485 (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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481B GLN* 2.9 35.4 + - + +
482B ARG 4.3 1.3 - - - +
484B GLU* 1.3 90.3 + - - +
486B LYS* 1.3 59.2 + - - +
488B TYR* 3.7 22.7 - + - -
489B MET* 3.3 17.5 + - - +
519B ARG* 5.9 1.3 - - - -
551B ALA 5.4 0.2 + - - -
552B GLY* 3.1 21.8 - - - +
555B ALA* 3.4 24.7 - - + +
556B GLN* 4.1 5.8 - - - +
559B ARG* 3.4 35.5 + - - -
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Residues in contact with LYS 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B ARG* 3.0 43.5 + - + +
483B LYS* 2.7 10.8 + - - +
485B HIS* 1.3 70.9 - - - +
487B GLY* 1.3 61.3 + - - +
488B TYR 3.0 1.6 - - - -
489B MET* 3.4 5.2 - - + +
490B LEU* 2.8 44.7 + - + +
556B GLN* 3.0 36.4 - - + +
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Residues in contact with GLY 487 (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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483B LYS 2.7 12.8 + - - -
484B GLU* 3.6 5.6 - - - -
486B LYS* 1.3 79.9 - - - +
488B TYR* 1.3 52.7 + - - +
490B LEU* 4.5 4.0 - - - +
491B ALA* 2.7 36.9 + - - +
494B ARG* 4.5 1.4 + - - -
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Residues in contact with TYR 488 (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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484B GLU* 3.0 54.9 + - + +
485B HIS* 3.8 25.6 - + - +
486B LYS 3.0 0.2 - - - -
487B GLY* 1.3 78.3 - - - +
489B MET* 1.3 56.4 + - - +
490B LEU 3.0 0.7 - - - -
491B ALA* 2.6 23.2 + - - +
492B ALA* 2.8 19.7 + - - +
519B ARG* 3.5 64.0 + - + +
520B PHE* 4.5 25.1 - + - -
548B THR 5.5 1.3 - - - +
552B GLY* 5.1 4.0 - - - -
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Residues in contact with MET 489 (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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485B HIS 3.3 8.6 + - - +
486B LYS* 3.4 9.2 - - - +
488B TYR* 1.3 79.3 - - - +
490B LEU* 1.3 78.6 + - - +
492B ALA* 3.6 2.5 + - - +
493B GLN* 3.5 11.4 + - - +
548B THR 4.6 0.4 - - - -
549B GLU* 2.5 69.1 - - - +
552B GLY* 3.7 8.9 - - - -
553B MET* 3.4 50.3 - - + -
556B GLN* 3.2 25.8 - - - +
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Residues in contact with LEU 490 (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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486B LYS* 2.8 27.9 + - + +
487B GLY* 4.0 3.4 - - - +
489B MET* 1.3 87.5 - - - +
491B ALA* 1.3 55.2 + - - +
492B ALA 3.3 0.7 - - - -
493B GLN* 3.2 36.0 + - - +
494B ARG* 2.6 33.5 + - - +
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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