Contacts of the strand formed by residues 483 - 495 (chain B) in PDB entry 4OMD
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 ARG 483 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395B HIS* 4.3 18.8 + - - -
399B GLN* 4.6 13.3 - - - +
441B TRP* 5.7 2.8 - - - -
444B VAL* 5.2 7.1 - - - +
481B ILE* 3.6 2.2 - - - +
482B THR* 1.3 81.6 - - - +
484B LEU* 1.3 64.6 + - - +
485B GLU* 4.6 1.7 - - - +
540B ASP* 2.9 42.8 + - - +
541B GLU 3.8 2.0 - - - -
572B GLY* 3.3 2.3 - - - -
573B THR* 2.8 48.6 + - - +
574B ALA 4.9 4.3 - - - +
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Residues in contact with LEU 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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481B ILE* 4.0 3.1 - - + +
482B THR 4.0 0.4 - - - -
483B ARG* 1.3 73.6 - - - +
485B GLU* 1.3 69.8 + - - +
486B HIS 3.7 9.6 - - - +
487B ALA* 4.0 17.0 - - + -
538B SER* 3.6 38.1 - - - +
539B TRP* 3.7 2.1 + - - -
540B ASP* 2.6 30.0 + - - +
541B GLU* 2.9 22.0 + - + +
543B PRO* 4.1 13.0 - - + -
547B TRP* 4.4 13.2 - - + -
570B LEU* 3.8 29.8 - - + -
571B TYR 3.3 17.5 - - - +
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Residues in contact with GLU 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ARG* 3.0 45.6 + - - +
395B HIS* 3.0 34.6 + - + +
444B VAL* 4.7 0.2 - - - +
447B GLN* 4.5 4.0 + - - +
483B ARG 4.6 1.8 - - - +
484B LEU* 1.3 87.0 - - - +
486B HIS* 1.3 71.8 + - - +
487B ALA 4.0 0.2 + - - -
535B THR 4.4 4.2 - - - +
536B THR* 4.9 0.2 - - - -
538B SER 4.6 0.2 - - - -
539B TRP* 3.6 45.5 + - + -
571B TYR* 2.8 14.9 + - - +
572B GLY* 3.9 15.6 + - - -
573B THR* 3.9 9.2 + - - +
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Residues in contact with HIS 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ILE* 3.4 59.1 + - + +
390B TRP* 4.3 12.1 - + - -
391B ARG* 5.2 2.5 - - + -
394B GLN* 2.7 30.6 + - - -
447B GLN* 5.3 1.2 + - - -
484B LEU* 3.7 2.4 - - - +
485B GLU* 1.3 93.0 + - + +
487B ALA* 1.3 61.1 + - - +
534B MET* 4.1 18.8 - - + -
535B THR 4.0 5.4 - - - -
536B THR* 4.7 4.5 - - + -
539B TRP* 3.6 23.2 - + - -
571B TYR* 3.2 37.9 + - + +
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Residues in contact with ALA 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B LEU* 4.0 20.6 - - + -
486B HIS* 1.3 77.9 - - - +
488B GLN* 1.3 63.5 + - - +
505B LEU* 5.4 2.2 - - + +
533B PHE 3.9 0.3 - - - +
534B MET* 3.4 3.3 - - - +
535B THR* 3.0 49.8 + - + +
547B TRP* 4.6 9.2 - - + -
568B LEU* 5.4 2.7 - - + -
569B VAL 3.4 9.0 - - - +
570B LEU* 4.4 10.8 - - + -
571B TYR* 5.0 0.2 - - - -
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Residues in contact with GLN 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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272A GLU* 5.2 3.5 + - - +
310B ASN* 5.3 2.4 + - - +
311B SER* 5.9 1.2 - - - +
312B ILE* 4.2 15.7 - - + +
449B LYS* 5.5 0.2 - - - -
487B ALA* 1.3 78.6 - - - +
489B ALA* 1.3 60.7 + - - +
490B ARG* 3.8 18.3 + - + +
505B LEU* 5.4 0.9 - - - -
532B ALA* 3.9 28.9 + - + +
533B PHE 3.2 7.2 - - - +
534B MET* 4.2 15.0 - - + +
568B LEU* 3.5 8.9 - - - +
569B VAL* 2.9 46.3 + - + +
571B TYR* 3.3 34.8 + - + -
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Residues in contact with ALA 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B GLN* 1.3 73.6 - - - +
490B ARG* 1.3 63.1 + - - +
491B LEU* 3.3 8.9 + - + +
505B LEU* 4.1 13.7 - - + +
515B LEU* 3.7 28.9 - - + -
531B TRP 3.4 0.5 - - - +
533B PHE* 2.8 33.1 + - - +
549B LEU* 5.1 0.2 - - + -
566B PHE* 4.0 21.1 - - + -
567B THR 3.6 5.2 - - - -
568B LEU* 4.8 0.4 - - + -
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Residues in contact with ARG 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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268A ARG* 3.2 29.8 - - - +
269A LEU* 3.9 36.2 - - - +
272A GLU* 4.5 11.1 + - - -
488B GLN* 3.8 17.3 + - + +
489B ALA* 1.3 69.9 - - - +
491B LEU* 1.3 59.7 + - - +
530B ASP* 3.1 46.5 + - - +
531B TRP 3.3 7.9 - - - +
532B ALA* 3.6 26.8 - - + +
565B LYS* 3.4 6.9 + - - +
566B PHE* 3.4 4.7 - - - -
567B THR* 2.8 46.0 + - - +
569B VAL* 4.0 14.4 - - + -
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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
----------------------------------------------------------
489B ALA* 3.7 12.8 - - + +
490B ARG* 1.3 75.2 - - - +
492B THR* 1.3 63.2 + - - +
493B LEU* 4.1 10.1 - - + -
503B ILE* 3.7 43.1 - - + -
515B LEU* 4.9 1.6 - - + -
528B PHE* 3.8 7.9 - - + +
530B ASP 3.1 2.6 + - - -
531B TRP 3.0 30.7 + - - +
533B PHE* 4.0 17.5 - - + -
549B LEU* 3.7 19.3 - - + -
551B ILE* 4.9 2.5 - - + -
563B LEU* 4.4 7.4 - - + -
565B LYS 3.3 2.7 - - - +
566B PHE* 3.4 39.7 - - + -
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Residues in contact with THR 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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491B LEU* 1.3 70.0 - - - +
493B LEU* 1.3 63.0 + - - +
528B PHE 3.1 13.0 - - - +
529B ASN* 4.1 11.9 - - - +
530B ASP* 2.9 18.3 + - - +
563B LEU* 3.7 1.6 - - - +
564B THR* 2.8 37.7 + - - +
565B LYS* 2.8 47.9 + - - +
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Residues in contact with LEU 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B ILE* 4.3 13.9 - - + -
491B LEU* 4.8 6.7 - - + -
492B THR* 1.3 77.8 - - - +
494B SER* 1.3 73.7 + - - +
495B TYR* 4.1 2.2 - - + -
501B LEU* 4.0 24.5 - - + -
503B ILE* 4.3 23.3 - - + -
526B ASP 4.4 1.6 - - - +
527B GLY* 3.5 4.0 - - - -
528B PHE* 2.9 56.2 + - + +
551B ILE* 4.4 5.6 - - + -
562B THR 3.2 14.6 - - - +
563B LEU* 3.9 19.3 - - + -
564B THR* 4.7 2.2 - - - -
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Residues in contact with SER 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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461B ILE* 4.0 0.7 - - - +
493B LEU* 1.3 77.2 - - - +
495B TYR* 1.3 66.3 + - - +
525B ALA 5.7 1.1 - - - -
526B ASP 5.5 0.9 - - - -
527B GLY* 4.5 3.8 - - - +
561B GLY* 3.0 22.9 - - - -
562B THR* 2.9 30.0 + - - +
564B THR* 5.5 2.0 - - - +
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Residues in contact with TYR 495 (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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461B ILE* 3.7 27.6 - - + -
462B GLY 3.6 7.4 + - - -
493B LEU* 4.1 3.5 - - + +
494B SER* 1.3 79.3 - - - +
496B ASN* 1.3 62.0 + - - +
497B ARG 3.3 34.3 - - - +
498B ARG* 4.7 4.7 + - - +
500B ASP* 4.6 2.9 - - + -
501B LEU* 3.5 38.7 - - + +
524B SER 4.3 0.9 - - - +
525B ALA* 3.4 24.9 + - - +
527B GLY* 4.4 7.6 + - - +
553B ASN* 3.5 21.9 - - - +
559B ASN* 3.0 36.4 - - + +
560B TYR* 3.3 29.6 - - - -
561B GLY* 3.6 2.9 - - - -
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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