Contacts of the strand formed by residues 487 - 495 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484E LEU* 3.7 35.4 - - + -
485E GLU 4.4 3.8 - - - +
486E HIS* 1.3 80.7 - - - +
488E GLN* 1.3 65.7 + - - +
489E ALA 4.2 0.2 + - - -
505E LEU* 3.9 28.5 - - + -
533E PHE 3.8 0.5 - - - +
534E MET* 3.2 4.6 - - - +
535E THR* 2.8 50.0 + - + +
538E SER* 4.7 4.5 - - - -
547E TRP* 4.1 9.2 - - + -
568E LEU* 4.0 16.2 - - + -
569E VAL 3.6 2.5 - - - -
570E LEU* 4.0 9.6 - - + -
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Residues in contact with GLN 488 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310E ASN* 5.5 2.2 + - - +
311E SER* 6.1 0.6 - - - +
312E ILE* 4.2 16.4 - - + +
487E VAL* 1.3 78.4 - - - +
489E ALA* 1.3 60.0 - - - +
490E ARG* 3.5 28.0 + - + +
532E ALA* 3.6 27.2 + - + +
533E PHE 3.3 5.6 - - - +
534E MET* 4.4 14.2 - - + +
567E THR 3.6 0.9 - - - +
568E LEU* 3.5 7.4 - - - +
569E VAL* 2.9 52.9 + - + +
571E TYR* 4.1 21.6 + - + -
269H LEU* 5.2 0.2 - - - +
272H GLU* 5.2 5.1 + - - +
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Residues in contact with ALA 489 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487E VAL 4.2 0.2 - - - -
488E GLN* 1.3 71.1 - - - +
490E ARG* 1.3 60.7 + - - +
491E LEU* 3.4 6.3 + - + +
505E LEU* 4.1 14.1 - - + +
515E LEU* 3.3 32.5 - - + +
531E TRP 3.3 2.6 - - - +
533E PHE* 2.8 34.9 + - - +
549E LEU* 5.0 0.7 - - + -
566E PHE* 4.0 19.5 - - + -
567E THR 3.8 3.8 - - - -
568E LEU* 4.7 0.9 - - - -
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Residues in contact with ARG 490 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488E GLN* 3.5 26.1 + - + +
489E ALA* 1.3 69.4 - - - +
491E LEU* 1.3 60.8 + - - +
530E ASP* 2.9 53.0 + - - +
531E TRP 3.3 7.2 - - - +
532E ALA* 4.0 21.4 - - + +
565E LYS* 3.6 5.7 + - - +
566E PHE* 3.3 5.9 - - - -
567E THR* 2.8 46.0 + - - +
569E VAL* 4.1 15.9 - - + +
268H ARG* 4.1 16.3 - - - +
269H LEU* 3.6 31.2 - - - +
272H GLU* 4.0 18.4 + - - -
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Residues in contact with LEU 491 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489E ALA 3.8 9.6 - - - +
490E ARG* 1.3 75.0 - - - +
492E THR* 1.3 63.4 + - - +
493E LEU* 4.1 10.1 - - + -
503E ILE* 3.9 33.4 - - + -
515E LEU* 4.8 2.0 - - + -
528E PHE* 3.8 8.2 - - + +
530E ASP 3.1 2.1 + - - -
531E TRP 3.0 29.4 + - - +
533E PHE* 3.7 28.7 - - + -
549E LEU* 3.8 21.1 - - + -
551E ILE* 4.9 2.5 - - + -
563E LEU* 4.3 8.1 - - + -
565E LYS 3.5 2.9 - - - +
566E PHE* 3.5 38.6 - - + -
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Residues in contact with THR 492 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491E LEU* 1.3 70.9 - - - +
493E LEU* 1.3 64.2 + - - +
528E PHE 3.2 11.2 - - - +
529E ASN* 4.0 16.8 + - - +
530E ASP* 2.9 19.4 + - - +
563E LEU* 3.7 0.9 - - - +
564E THR* 2.9 39.3 + - - +
565E LYS* 3.1 43.2 + - + +
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Residues in contact with LEU 493 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461E ILE* 4.3 13.5 - - + -
491E LEU* 4.7 6.7 - - + -
492E THR* 1.3 77.2 - - - +
494E SER* 1.3 75.1 + - - +
495E TYR* 4.1 3.4 - - + -
501E LEU* 4.0 26.7 - - + -
503E ILE* 4.3 14.8 - - + -
526E ASP 4.4 1.7 - - - +
527E GLY* 3.4 5.9 - - - -
528E PHE* 2.9 58.3 + - + +
551E ILE* 4.4 11.7 - - + -
562E THR 3.1 14.6 - - - +
563E LEU* 3.8 14.4 - - + -
564E THR* 4.3 2.0 - - - +
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Residues in contact with SER 494 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461E ILE* 4.2 0.3 - - - +
493E LEU* 1.3 76.5 - - - +
495E TYR* 1.3 63.4 + - - +
525E ALA 5.7 2.5 - - - -
526E ASP 5.3 2.5 - - - -
527E GLY* 4.5 3.4 - - - +
561E GLY* 2.9 6.4 - - - -
562E THR* 2.8 49.3 + - - +
564E THR* 5.3 2.0 - - - +
560G TYR* 4.2 11.4 - - - -
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Residues in contact with TYR 495 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461E ILE* 3.8 21.8 - - + -
462E GLY 3.2 10.2 + - - -
493E LEU* 4.1 5.0 - - + +
494E SER* 1.3 74.5 - - - +
496E ASN* 1.3 68.7 + - - +
497E ARG 3.4 26.5 - - - +
498E ARG* 4.8 5.1 + - - +
500E ASP* 4.6 2.9 - - + -
501E LEU* 3.5 45.1 - - + -
524E SER 4.3 1.0 - - - +
525E ALA* 3.4 24.5 + - - +
527E GLY* 4.4 6.3 + - - -
553E ASN* 3.2 27.4 + - - +
559E ASN* 3.2 32.3 - - + +
560E TYR* 3.3 27.6 - - - -
561E GLY* 3.7 6.3 - - - -
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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