Contacts of the strand formed by residues 487 - 495 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484A LEU* 3.8 36.1 - - + -
485A GLU 4.4 3.8 - - - +
486A HIS* 1.3 80.5 - - - +
488A GLN* 1.3 65.6 + - - +
489A ALA 4.3 0.3 + - - -
505A LEU* 3.9 21.1 - - + -
533A PHE 3.8 0.3 - - - +
534A MET* 3.2 4.0 - - - +
535A THR* 2.9 55.0 + - + +
538A SER* 4.8 4.0 - - - -
547A TRP* 4.1 9.4 - - + -
568A LEU* 4.0 16.4 - - + -
569A VAL 3.6 2.7 - - - -
570A LEU* 4.1 7.9 - - + -
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Residues in contact with GLN 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A ASN 5.5 1.6 + - - -
311A SER* 6.1 1.2 - - - +
312A ILE* 4.2 17.0 - - + +
487A VAL* 1.3 78.6 - - - +
489A ALA* 1.3 60.1 + - - +
490A ARG* 3.5 23.2 + - + -
532A ALA* 3.7 24.8 + - + +
533A PHE 3.2 5.2 - - - +
534A MET* 4.4 14.1 - - + +
567A THR 3.7 0.7 - - - +
568A LEU* 3.5 7.3 - - - +
569A VAL* 2.9 51.7 + - + +
571A TYR* 4.1 22.2 + - + -
4069A SO4 3.5 22.3 + - - -
269B LEU* 5.1 0.9 - - - +
272B GLU* 5.3 0.2 - - - +
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Residues in contact with ALA 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487A VAL* 4.2 0.4 - - - +
488A GLN* 1.3 72.8 - - - +
490A ARG* 1.3 60.9 + - - +
491A LEU* 3.4 6.8 + - + +
505A LEU* 4.1 14.4 - - + -
515A LEU* 3.4 32.8 - - + -
531A TRP 3.3 3.3 - - - +
533A PHE* 2.7 34.3 + - - +
549A LEU* 4.9 0.4 - - + -
566A PHE* 4.0 20.4 - - + -
567A THR 3.8 2.9 - - - -
568A LEU* 4.7 0.7 - - - -
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Residues in contact with ARG 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488A GLN* 3.5 19.6 + - + +
489A ALA* 1.3 68.8 - - - +
491A LEU* 1.3 61.5 + - - +
492A THR* 5.5 0.2 - - - -
530A ASP* 2.9 52.0 + - - +
531A TRP 3.3 7.0 - - - +
532A ALA* 4.0 15.5 - - + +
565A LYS* 3.5 4.6 - - - +
566A PHE* 3.3 5.9 + - - -
567A THR* 2.8 47.2 + - - +
569A VAL* 4.1 15.4 - - + +
4069A SO4 2.5 47.0 + - - -
268B ARG* 3.9 7.7 - - - +
269B LEU* 3.5 34.5 - - - +
272B GLU* 4.2 2.6 + - - -
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Residues in contact with LEU 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489A ALA 3.8 9.6 - - - +
490A ARG* 1.3 73.7 - - - +
492A THR* 1.3 62.3 + - - +
493A LEU* 4.1 7.9 - - + -
503A ILE* 3.9 33.7 - - + -
515A LEU* 4.8 1.6 - - + -
528A PHE* 3.8 8.9 - - + +
530A ASP 3.1 2.1 + - - -
531A TRP 3.0 28.7 + - - +
533A PHE* 3.7 27.4 - - + -
549A LEU* 3.8 21.8 - - + -
551A ILE* 4.7 6.3 - - + -
563A LEU* 4.3 8.1 - - + -
565A LYS 3.4 2.7 - - - +
566A PHE* 3.5 39.0 - - + -
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Residues in contact with THR 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491A LEU* 1.3 72.9 - - - +
493A LEU* 1.3 65.0 + - - +
528A PHE 3.2 11.4 - - - +
529A ASN* 4.3 11.9 - - + +
530A ASP* 2.8 25.3 + - - +
563A LEU* 3.7 2.1 - - - +
564A THR* 2.9 43.3 + - - +
565A LYS* 3.0 35.4 + - + -
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Residues in contact with LEU 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461A ILE* 4.3 6.1 - - + -
491A LEU* 4.7 6.1 - - + -
492A THR* 1.3 78.1 - - - +
494A SER* 1.3 75.1 + - - +
495A TYR* 4.1 3.4 - - + -
501A LEU* 4.0 29.4 - - + -
503A ILE* 4.3 14.8 - - + -
526A ASP 4.4 1.6 - - - +
527A GLY* 3.4 6.2 - - - -
528A PHE* 3.0 59.2 + - + +
529A ASN* 5.5 0.3 + - - -
551A ILE* 4.3 18.2 - - + -
562A THR 3.1 14.1 - - - +
563A LEU* 3.9 13.2 - - + -
564A THR* 4.5 2.2 - - - -
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Residues in contact with SER 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461A ILE* 4.2 0.5 - - - +
493A LEU* 1.3 76.7 - - - +
495A TYR* 1.3 64.0 + - - +
525A ALA 5.6 2.7 - - - -
526A ASP 5.3 1.8 - - - -
527A GLY* 4.5 2.9 - - - -
561A GLY* 2.9 3.8 - - - -
562A THR* 2.8 41.2 + - - +
564A THR* 5.4 2.3 - - - +
4014A SO4 3.1 29.7 + - - -
560C TYR* 4.7 3.3 - - - -
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Residues in contact with TYR 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461A ILE* 3.7 29.6 - - + -
462A GLY 3.2 9.1 + - - -
493A LEU* 4.1 5.2 - - + +
494A SER* 1.3 74.0 - - - +
496A ASN* 1.3 69.2 + - - +
497A ARG 3.4 26.5 - - - +
498A ARG* 4.8 5.6 - - - +
500A ASP* 4.6 3.1 - - + -
501A LEU* 3.5 39.5 - - + -
524A SER 4.3 1.0 - - - +
525A ALA* 3.3 23.3 + - - +
527A GLY* 4.4 6.7 + - - +
553A ASN* 3.2 23.1 - - + +
559A ASN* 3.1 36.3 - - + +
560A TYR* 3.2 28.3 - - - -
561A GLY* 3.6 6.7 - - - -
4014A SO4 4.4 3.8 + - - -
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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