Contacts of the strand formed by residues 487 - 495 (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 VAL 487 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484D LEU* 3.8 36.8 - - + -
485D GLU 4.4 4.0 - - - +
486D HIS* 1.3 80.5 - - - +
488D GLN* 1.3 65.3 + - - +
505D LEU* 3.9 28.3 - - + -
533D PHE 3.7 0.3 - - - +
534D MET* 3.2 5.0 - - - +
535D THR* 2.9 48.0 + - + +
538D SER* 4.8 4.3 - - - -
547D TRP* 4.2 7.0 - - + -
568D LEU* 3.9 16.6 - - + -
569D VAL 3.6 3.1 - - - -
570D LEU* 4.0 9.2 - - + -
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Residues in contact with GLN 488 (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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269C LEU* 5.0 1.0 - - - +
272C GLU* 5.1 0.7 + - - +
310D ASN 5.6 1.8 + - - -
311D SER* 6.2 1.0 - - - +
312D ILE* 4.2 17.0 - - + +
487D VAL* 1.3 79.0 - - - +
489D ALA* 1.3 59.0 + - - +
490D ARG* 3.4 22.4 + - + -
532D ALA* 3.8 21.7 + - + +
533D PHE 3.2 6.5 - - - +
534D MET* 4.4 13.8 - - + +
567D THR 3.6 0.5 - - - +
568D LEU* 3.5 7.4 - - - +
569D VAL* 2.9 52.1 + - + +
571D TYR* 4.1 21.6 + - + -
4012D SO4 3.3 21.2 + - - -
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Residues in contact with ALA 489 (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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487D VAL* 4.2 0.4 - - - +
488D GLN* 1.3 71.2 - - - +
490D ARG* 1.3 61.4 + - - +
491D LEU* 3.4 7.3 + - + +
505D LEU* 4.1 13.9 - - + -
515D LEU* 3.4 32.1 - - + -
531D TRP 3.3 2.9 - - - +
533D PHE* 2.8 33.9 + - - +
549D LEU* 5.0 0.7 - - + -
566D PHE* 4.0 20.0 - - + -
567D THR 3.8 3.6 - - - -
568D LEU* 4.8 0.2 - - - -
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Residues in contact with ARG 490 (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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268C ARG* 4.0 7.7 - - - +
269C LEU* 3.4 39.9 - - - +
272C GLU* 4.2 2.0 + - - -
488D GLN* 3.4 18.0 + - + +
489D ALA* 1.3 68.6 - - - +
491D LEU* 1.3 62.9 + - - +
530D ASP* 2.9 55.3 + - - +
531D TRP 3.3 6.1 - - - +
532D ALA* 3.9 15.2 - - + +
565D LYS* 3.5 4.4 - - - +
566D PHE* 3.3 5.5 + - - -
567D THR* 2.8 47.0 + - - +
569D VAL* 4.1 11.0 - - + -
4012D SO4 2.5 47.6 + - - -
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Residues in contact with LEU 491 (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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489D ALA 3.8 9.0 - - - +
490D ARG* 1.3 76.1 - - - +
492D THR* 1.3 61.5 + - - +
493D LEU* 4.1 8.3 - - + -
503D ILE* 3.9 33.0 - - + -
515D LEU* 4.8 1.3 - - + -
528D PHE* 3.9 8.4 - - + +
530D ASP 3.1 2.5 + - - -
531D TRP 3.0 30.3 + - - +
533D PHE* 3.6 29.4 - - + -
549D LEU* 3.8 21.1 - - + -
551D ILE* 4.8 5.4 - - + -
563D LEU* 4.3 9.0 - - + -
565D LYS 3.4 2.5 - - - +
566D PHE* 3.5 38.4 - - + -
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Residues in contact with THR 492 (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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491D LEU* 1.3 70.7 - - - +
493D LEU* 1.3 63.6 + - - +
528D PHE 3.2 10.8 - - - +
529D ASN* 4.4 10.3 - - + +
530D ASP* 2.9 24.8 + - - +
563D LEU* 3.7 1.3 - - - +
564D THR* 2.9 39.5 + - - +
565D LYS* 3.1 39.7 + - + +
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Residues in contact with LEU 493 (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* 4.3 10.3 - - + -
491D LEU* 4.1 6.5 - - + -
492D THR* 1.3 77.8 - - - +
494D SER* 1.3 74.4 + - - +
495D TYR* 4.1 3.6 - - + -
501D LEU* 4.0 28.7 - - + -
503D ILE* 4.4 8.7 - - + -
526D ASP 4.4 1.6 - - - +
527D GLY* 3.4 6.9 - - - -
528D PHE* 2.9 60.1 + - + +
529D ASN* 5.3 0.9 - - - +
551D ILE* 4.4 16.6 - - + -
562D THR 3.1 14.8 - - - +
563D LEU* 3.9 13.0 - - + -
564D THR* 4.4 2.2 - - - +
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Residues in contact with SER 494 (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* 4.2 0.5 - - - +
493D LEU* 1.3 77.2 - - - +
495D TYR* 1.3 64.4 + - - +
525D ALA 5.6 1.1 - - - -
526D ASP 5.4 1.8 - - - -
527D GLY* 4.5 2.9 - - - +
561D GLY* 2.9 5.6 - - - -
562D THR* 2.8 50.3 + - - +
564D THR* 5.6 2.4 - - - +
801J DKA 4.1 14.8 - - - +
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Residues in contact with TYR 495 (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 26.2 - - + -
462D GLY 3.1 17.9 + - - -
493D LEU* 4.1 5.6 - - + +
494D SER* 1.3 73.6 - - - +
496D ASN* 1.3 68.0 + - - +
497D ARG 3.4 26.7 - - - +
498D ARG* 4.8 5.1 + - - +
500D ASP* 4.7 2.9 - - + -
501D LEU* 3.5 40.6 - - + +
524D SER 4.3 1.0 - - - +
525D ALA* 3.4 24.0 + - - +
527D GLY* 4.5 7.0 + - - -
553D ASN* 3.2 15.3 - - + +
559D ASN* 3.1 36.5 - - + +
560D TYR* 3.3 26.7 - - - -
561D GLY* 3.6 7.2 - - - -
801J DKA 3.6 7.5 - - - +
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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
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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