Contacts of the strand formed by residues 482 - 497 (chain A) in PDB entry 5C58
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 482 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465A LYS* 3.6 6.6 + - - +
466A ALA* 2.9 32.1 + - - +
481A ALA* 1.3 75.4 - - - +
483A ASN* 1.3 70.5 + - - +
515A ARG 3.5 12.1 - - - -
516A GLY* 4.6 2.9 - - - -
593A ILE* 4.1 9.4 - - - +
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Residues in contact with ASN 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A TYR* 3.1 27.6 + - + +
464A ASP 3.2 16.2 - - - +
465A LYS* 4.4 8.1 - - + +
482A GLY* 1.3 78.3 + - - +
484A ARG* 1.3 61.0 + - - +
485A SER 4.2 0.2 - - - -
513A ARG 3.6 2.1 - - - +
514A LEU* 3.2 4.9 - - - +
515A ARG* 2.9 72.8 + - - +
516A GLY* 5.4 0.4 - - - -
593A ILE* 3.8 7.2 - - - +
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Residues in contact with ARG 484 (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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170A TYR 4.4 14.6 + - - -
171A GLY* 5.5 3.2 - - - -
183A ASN* 6.3 0.4 - - - -
220A GLY* 5.5 4.6 - - - -
462A TYR* 3.9 25.4 + - - +
464A ASP* 3.1 45.3 + - + +
483A ASN* 1.3 74.1 - - - +
485A SER* 1.3 61.4 + - - +
486A VAL* 5.0 4.9 - - - +
512A TYR* 4.1 19.9 - - + +
513A ARG 3.4 2.7 - - - -
514A LEU* 3.7 8.1 - - + -
589A ARG* 5.2 2.0 - - - +
590A PRO* 3.3 45.8 + - - +
591A PRO 3.1 21.1 - - - -
592A ALA* 3.9 18.8 - - - +
593A ILE* 3.6 19.7 - - + +
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Residues in contact with SER 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A PHE* 3.6 19.8 - - - -
462A TYR 3.3 8.1 - - - -
463A TYR* 3.5 31.7 - - - +
483A ASN* 4.2 0.8 + - - -
484A ARG* 1.3 77.0 - - - +
486A VAL* 1.3 62.6 + - - +
512A TYR* 3.1 5.5 - - - +
513A ARG* 2.8 47.9 + - - +
515A ARG* 5.6 1.0 + - - -
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Residues in contact with VAL 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ALA* 4.4 8.5 - - + -
220A GLY* 5.5 0.9 - - - +
460A GLU 3.9 1.0 - - - +
461A PHE* 3.7 20.7 - - - -
462A TYR* 3.3 49.8 + - + +
484A ARG* 5.0 7.9 - - - +
485A SER* 1.3 81.1 - - - +
487A ALA* 1.3 60.9 + - - +
488A SER* 3.9 14.7 + - - +
510A ASP* 4.5 6.7 - - + -
511A ARG 3.2 24.2 - - - +
512A TYR* 3.6 13.5 - - + -
588A TRP* 5.4 0.2 - - + -
590A PRO* 5.3 5.6 - - + -
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Residues in contact with ALA 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A GLU 3.7 4.7 - - - +
461A PHE* 4.0 19.4 - - + -
486A VAL* 1.3 71.6 - - - +
488A SER* 1.3 59.8 + - - +
509A TYR* 3.6 2.6 - - - +
510A ASP* 3.4 2.6 - - - -
511A ARG* 2.7 52.2 + - + +
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Residues in contact with SER 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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216A MET 6.1 0.4 - - - -
219A ALA* 3.2 26.6 - - - +
459A LEU* 3.3 8.2 - - - +
460A GLU* 2.8 43.7 + - - +
486A VAL* 4.1 3.5 + - - +
487A ALA* 1.3 77.1 + - - +
489A LEU* 1.3 62.7 + - - +
490A PHE* 5.7 3.1 - - - -
508A ARG* 4.7 7.4 - - - -
509A TYR 3.3 5.4 - - - -
510A ASP* 3.2 21.0 + - - -
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Residues in contact with LEU 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A GLY* 3.4 21.3 - - - +
459A LEU* 4.1 18.8 - - + +
488A SER* 1.3 77.4 - - - +
490A PHE* 1.3 63.9 + - - +
507A LEU* 4.3 2.3 - - - +
508A ARG* 3.6 1.1 - - - +
509A TYR* 2.9 48.3 + - + +
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Residues in contact with PHE 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A GLY 4.2 13.9 - - - +
215A GLY 3.8 20.6 - - - +
216A MET* 4.0 23.6 - - + -
440A GLN* 3.8 22.2 - - + -
456A ASN* 3.6 35.7 - - - -
457A TYR* 3.7 1.9 - - - +
458A GLY* 3.0 59.4 + - - +
459A LEU* 4.0 6.5 - - - -
460A GLU* 5.5 0.9 - - + -
488A SER* 5.7 3.1 - - - -
489A LEU* 1.3 82.6 - - - +
491A ALA* 1.3 67.7 + - - +
492A ASN* 4.3 4.5 - - + -
507A LEU* 3.4 12.1 - - - +
508A ARG* 3.9 18.4 - - + -
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Residues in contact with ALA 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A ASN 3.8 7.0 - - - -
457A TYR* 4.2 12.3 - - + +
490A PHE* 1.3 80.5 - - - +
492A ASN* 1.3 59.3 + - - +
493A LEU 4.4 0.2 + - - -
505A GLY 4.5 0.3 - - - +
506A GLY* 3.5 2.3 - - - -
507A LEU* 3.1 35.9 + - + +
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Residues in contact with ASN 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A GLY 3.3 28.6 + - - +
215A GLY* 4.2 5.3 - - - -
454A ARG 3.9 0.9 - - - +
455A ALA* 3.8 1.9 - - - +
456A ASN* 2.8 59.6 + - - +
490A PHE* 4.3 4.1 - - + -
491A ALA* 1.3 76.2 - - - +
493A LEU* 1.3 61.3 + - - +
494A THR* 5.5 1.5 + - - -
504A GLU* 4.7 16.9 + - + +
505A GLY 4.3 0.7 - - - -
506A GLY* 3.5 21.8 - - - +
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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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445A PHE* 4.6 7.0 - - + -
453A PHE* 4.1 30.3 - - + -
454A ARG 3.6 20.2 - - - +
455A ALA* 3.9 13.2 - - + +
492A ASN* 1.3 76.0 - - - +
494A THR* 1.3 75.5 + - - +
495A TYR* 5.9 0.7 - - + -
503A LEU 3.7 2.2 - - - +
504A GLU* 3.3 2.8 - - - +
505A GLY 2.8 38.5 + - - +
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Residues in contact with THR 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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452A ASP 3.8 0.2 - - - +
453A PHE* 3.2 9.5 - - - +
454A ARG* 2.9 73.3 + - + +
492A ASN* 5.5 1.4 + - - -
493A LEU* 1.3 78.1 - - - +
495A TYR* 1.3 71.3 + - - +
496A ASP* 5.4 4.7 - - + -
502A THR* 5.9 3.4 - - - -
503A LEU 3.7 3.4 - - - +
504A GLU* 3.6 29.6 + - + +
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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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451A HIS* 3.0 42.5 + - + -
452A ASP 3.6 4.3 - - - -
453A PHE* 3.3 46.0 - + + -
493A LEU* 5.9 0.9 - - + -
494A THR* 1.3 79.0 - - - +
496A ASP* 1.3 64.1 + - - +
497A TYR* 3.3 35.5 - - + +
501A LEU* 3.5 12.5 - - + +
502A THR* 3.2 5.7 - - - -
503A LEU* 2.7 67.8 + - + +
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Residues in contact with ASP 496 (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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450A GLY 2.8 14.9 - - - +
452A ASP* 3.0 31.5 + - + +
494A THR* 5.4 5.8 - - + -
495A TYR* 1.3 77.0 - - - +
497A TYR* 1.3 59.1 + - - +
498A ASP 3.7 0.2 + - - -
499A GLY* 3.2 30.6 + - - -
501A LEU 3.2 4.5 - - - -
502A THR* 3.4 24.7 - - - +
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Residues in contact with TYR 497 (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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449A PRO 5.4 0.9 - - - -
450A GLY* 3.3 4.9 - - - -
451A HIS* 3.2 40.6 - + - -
495A TYR* 3.3 26.7 - - + +
496A ASP* 1.3 70.2 - - - +
498A ASP* 1.3 88.8 + - + +
499A GLY 2.8 11.4 + - - -
500A TRP* 3.2 36.3 + + - -
501A LEU* 2.8 34.9 + - + -
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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
------------------------------------------------------------
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