Contacts of the strand formed by residues 545 - 554 (chain D) in PDB entry 1P8J
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 545 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470D ALA* 4.3 3.4 - - - -
471D VAL* 2.7 45.9 + - - +
508D PRO* 3.5 8.7 - - - -
543D PRO 3.4 0.4 + - - -
544D ALA* 1.3 74.5 - - - +
546D GLU* 1.3 59.5 + - - -
547D TRP* 3.7 1.0 + - - -
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Residues in contact with GLU 546 (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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468D ARG* 2.8 52.1 + - - +
469D LYS* 3.3 13.4 + - - +
470D ALA* 4.2 6.5 + - + +
506D ILE* 4.2 0.7 - - - +
507D SER 4.1 1.9 - - - +
508D PRO* 3.4 24.8 - - - +
545D GLY* 1.3 71.2 - - - -
547D TRP* 1.3 71.0 + - - +
548D VAL* 4.1 6.6 - - + +
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Residues in contact with TRP 547 (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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454D ILE* 5.7 2.0 - - + -
467D VAL 3.7 0.5 - - - +
468D ARG* 3.3 4.0 - - - -
469D LYS* 2.8 36.9 + - + +
471D VAL* 3.5 28.9 - - + +
484D LEU* 3.9 27.8 - - + -
487D VAL* 4.2 15.9 - - + -
505D LEU* 3.7 40.2 - - + -
506D ILE 3.5 16.2 - - - -
507D SER* 3.7 21.1 - - - -
508D PRO* 3.2 23.1 - - + +
535D THR* 5.8 1.1 - - + -
538D SER* 4.5 3.6 - - - -
543D PRO* 2.9 23.8 + - + +
545D GLY 3.9 0.2 - - - -
546D GLU* 1.3 71.5 - - - +
548D VAL* 1.3 65.1 + - - +
566D PHE* 5.8 4.9 - - + -
568D LEU* 3.8 21.0 - - + +
570D LEU* 4.1 10.1 - - + +
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Residues in contact with VAL 548 (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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466D GLU* 3.7 28.7 - - + +
467D VAL 3.2 4.3 - - - +
468D ARG* 3.8 37.5 - - + +
504D HIS 3.7 0.5 - - - +
505D LEU* 3.4 8.0 - - - +
506D ILE* 2.8 57.5 + - + +
546D GLU* 4.1 10.3 - - + +
547D TRP* 1.3 82.0 - - - +
549D LEU* 1.3 65.9 + - - +
550D GLU* 4.2 10.3 - - + +
566D PHE* 5.6 0.4 - - - -
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Residues in contact with LEU 549 (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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465D LEU* 3.8 1.3 - - + +
466D GLU* 3.3 6.2 - - - +
467D VAL* 2.8 42.4 + - + +
491D LEU* 3.8 21.8 - - + -
503D ILE* 3.8 19.5 - - + -
504D HIS 3.4 13.2 - - - +
505D LEU* 4.5 4.0 - - + -
515D LEU* 4.2 13.9 - - + -
547D TRP 4.3 0.2 - - - -
548D VAL* 1.3 73.0 - - - +
550D GLU* 1.3 60.9 + - - +
551D ILE* 4.1 13.7 - - + -
563D LEU* 3.9 20.9 - - + -
566D PHE* 3.7 44.8 - - + -
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Residues in contact with GLU 550 (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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464D ARG* 4.7 14.8 + - - +
465D LEU 3.6 4.7 - - - +
466D GLU* 4.6 15.3 - - + +
502D ALA 3.6 1.4 - - - +
503D ILE* 3.2 8.5 - - - +
504D HIS* 2.7 48.6 + - + +
506D ILE* 3.8 17.9 - - + +
512D ARG* 2.8 41.0 + - - -
548D VAL* 4.2 12.6 - - + +
549D LEU* 1.3 78.1 - - - +
551D ILE* 1.3 63.1 + - - +
552D GLU* 6.0 2.0 - - + -
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Residues in contact with ILE 551 (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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461D ILE* 3.7 26.7 - - + +
464D ARG* 3.4 2.7 - - - +
465D LEU* 2.8 52.0 + - + +
491D LEU* 4.8 3.8 - - + -
493D LEU* 4.4 12.3 - - + -
501D LEU* 3.8 18.6 - - + -
502D ALA 3.5 2.7 - - - -
503D ILE* 4.1 21.5 - - + -
549D LEU* 4.1 12.1 - - + -
550D GLU* 1.3 79.3 - - - +
552D GLU* 1.3 64.4 + - - +
563D LEU* 3.9 40.8 - - + -
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Residues in contact with GLU 552 (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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461D ILE* 5.5 0.7 - - - -
463D LYS 3.6 8.1 - - - +
464D ARG* 4.2 21.9 + - + -
501D LEU* 3.5 9.3 - - - -
502D ALA* 3.0 56.1 + - + +
504D HIS* 4.3 13.6 - - - +
512D ARG* 5.4 3.7 + - - -
550D GLU* 5.7 2.0 - - + -
551D ILE* 1.3 77.1 - - - +
553D ASN* 1.3 62.7 + - - +
554D THR* 3.4 13.9 + - + +
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Residues in contact with ASN 553 (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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461D ILE* 5.6 0.4 - - - +
462D GLY 4.1 4.1 + - - +
463D LYS* 2.7 61.4 + - + +
495D TYR* 3.2 18.8 + - - +
500D ASP* 3.7 8.0 - - - +
501D LEU* 4.9 0.9 - - - -
552D GLU* 1.3 71.7 - - - +
554D THR* 1.3 55.5 + - - +
555D SER* 2.8 26.1 + - - -
557D ALA 2.9 28.5 + - - -
558D ASN* 4.7 0.2 - - - +
559D ASN* 2.9 33.5 + - - +
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Residues in contact with THR 554 (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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463D LYS* 4.6 1.8 - - - +
500D ASP* 2.7 31.1 + - - +
502D ALA* 3.5 32.5 - - + +
518D ALA* 3.6 21.6 - - + +
552D GLU* 4.0 14.1 - - + +
553D ASN* 1.3 71.8 - - - +
555D SER* 1.3 58.5 + - - +
556D GLU* 5.8 0.3 - - - +
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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