Contacts of the strand formed by residues 498 - 509 (chain A) in PDB entry 4NPJ
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 LYS 498 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394A ALA* 3.1 8.6 - - - +
395A GLN* 3.0 56.4 + - + +
396A ASP* 5.7 2.0 - - + +
488A TRP* 3.8 25.4 - - + -
489A PHE 3.2 7.6 - - - +
490A THR* 3.6 32.3 - - + +
491A LEU* 4.1 3.7 - - - +
497A GLY* 1.3 79.5 - - - +
499A LEU* 1.3 60.7 + - - +
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Residues in contact with LEU 499 (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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391A PHE* 3.7 22.9 - - + -
393A GLU 3.5 17.5 - - - +
394A ALA* 4.1 4.7 - - + -
438A TRP* 4.0 15.5 - - + -
456A ILE* 3.9 28.7 - - + -
458A LEU* 4.5 5.2 - - + -
472A LEU* 4.1 11.2 - - + -
487A GLU 3.7 1.4 - - - +
488A TRP* 3.4 3.6 - - - -
489A PHE* 2.8 36.6 + - - +
491A LEU* 4.1 19.9 - - + +
498A LYS* 1.3 74.3 - - - +
500A HIS* 1.3 62.2 + - - +
501A LEU* 3.8 30.1 + - + -
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Residues in contact with HIS 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A ILE* 3.3 47.2 + - + +
393A GLU* 2.6 41.2 + - + +
486A ASP* 3.3 33.2 + - - -
487A GLU* 3.3 19.8 + - - -
488A TRP* 3.7 39.9 + + + -
499A LEU* 1.3 72.7 - - - +
501A LEU* 1.3 64.2 + - - +
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Residues in contact with LEU 501 (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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389A ILE* 4.9 5.4 - - + -
390A HIS 3.5 15.7 - - - +
391A PHE* 3.8 26.5 - - + -
392A ILE* 3.9 4.0 - - - -
454A LEU* 4.8 9.9 - - + -
456A ILE* 3.4 28.5 - - + -
472A LEU* 4.0 18.2 - - + -
474A ILE* 5.5 2.5 - - + -
485A LEU* 4.4 1.0 - - - +
486A ASP* 3.4 2.1 + - - -
487A GLU 3.0 35.4 + - - +
489A PHE* 4.4 16.1 - - + -
499A LEU* 3.8 12.5 + - + -
500A HIS* 1.3 83.3 + - - +
502A ARG* 1.3 61.0 - - - +
503A LEU* 4.2 15.0 - - + -
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Residues in contact with ARG 502 (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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388A ARG 3.7 0.2 - - - +
390A HIS* 2.8 66.5 + - + -
392A ILE* 3.8 8.2 - - + +
484A LEU* 4.3 22.4 - - + +
485A LEU 3.2 12.8 - - - +
486A ASP* 3.3 26.7 + - + +
501A LEU* 1.3 75.1 - - - +
503A LEU* 1.3 61.1 + - - +
504A GLU* 4.1 16.9 + - - -
525A ASP* 5.4 5.9 + - - -
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Residues in contact with LEU 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A LEU* 4.3 12.3 - - + -
388A ARG 3.5 1.3 - - - +
389A ILE* 3.5 37.2 - - + -
454A LEU* 4.1 22.0 - - + -
474A ILE* 4.8 7.6 - - + -
479A VAL* 4.0 30.6 - - + +
483A ARG 3.8 1.0 - - - +
484A LEU* 3.3 8.2 - - - +
485A LEU* 2.9 52.4 + - + -
489A PHE* 5.4 4.0 - - + -
501A LEU* 4.5 18.6 - - + -
502A ARG* 1.3 78.1 - - - +
504A GLU* 1.3 62.1 + - - +
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Residues in contact with GLU 504 (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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386A VAL 3.5 2.3 - - - +
387A LEU* 3.5 5.6 - - - -
388A ARG* 2.8 65.8 + - + +
390A HIS* 3.0 33.8 + - + +
483A ARG 3.7 4.3 - - - +
484A LEU* 3.7 16.4 - - + -
502A ARG* 4.1 16.0 + - + -
503A LEU* 1.3 76.1 - - - +
505A TRP* 1.3 59.8 + - - +
506A LEU* 3.7 15.1 + - + +
525A ASP* 4.9 3.1 - - - +
657A LEU* 4.6 11.2 - - + +
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Residues in contact with TRP 505 (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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384A LYS* 3.8 34.1 - - + -
385A GLY* 4.1 6.5 - - - -
386A VAL 3.8 4.0 - - - -
387A LEU* 4.5 16.1 - - + +
446A VAL* 3.6 48.2 - - + -
476A LEU* 5.6 4.0 - - + -
479A VAL* 4.3 13.9 - - + +
480A GLU* 3.6 48.5 - - + +
483A ARG* 2.9 58.6 + - - +
503A LEU 4.1 0.6 - - - -
504A GLU* 1.3 69.6 - - - +
506A LEU* 1.3 65.1 + - - +
507A THR* 3.6 12.9 + - + +
656A HIS 4.1 1.9 - - - +
657A LEU* 3.6 17.2 - - - +
658A GLU 5.1 0.2 + - - -
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Residues in contact with LEU 506 (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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385A GLY* 3.3 5.2 - - - -
386A VAL* 2.7 56.6 + - + +
388A ARG* 3.5 45.5 - - + +
504A GLU* 4.2 20.9 - - + +
505A TRP* 1.3 75.5 + - - +
507A THR* 1.3 62.6 + - - +
508A LEU* 4.5 0.3 - - - +
655A LEU* 4.2 20.4 - - + +
656A HIS 3.3 11.2 - - - +
657A LEU* 3.5 34.1 - - + +
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Residues in contact with THR 507 (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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384A LYS 4.5 9.6 - - - +
385A GLY* 4.7 0.9 - - - -
483A ARG* 3.4 26.5 + - - +
505A TRP* 3.6 15.5 + - + +
506A LEU* 1.3 75.1 - - - +
508A LEU* 1.3 68.6 + - - +
509A MET* 3.7 0.9 + - - +
654A VAL 3.3 4.7 - - - +
655A LEU* 3.5 1.9 - - - -
656A HIS* 2.7 37.3 + - - +
658A GLU* 2.8 29.6 + - - +
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Residues in contact with LEU 508 (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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382A VAL* 4.7 5.4 - - + -
383A PRO* 3.8 19.7 - - + +
384A LYS 4.8 2.1 + - - +
385A GLY* 3.9 23.6 - - - +
507A THR* 1.3 80.3 - - - +
509A MET* 1.3 62.1 + - - +
510A PRO* 4.2 3.5 - - - +
537A LEU* 4.2 20.0 - - + -
539A ILE* 4.6 11.7 - - + -
653A ARG* 3.8 35.1 + - + +
654A VAL 3.7 4.0 - - - -
655A LEU* 3.7 20.4 - - + -
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Residues in contact with MET 509 (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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507A THR* 4.6 1.1 - - - +
508A LEU* 1.3 76.1 - - - +
510A PRO* 1.3 64.3 - - + +
511A ASN* 3.2 30.3 + - - +
513A SER* 4.0 20.0 - - - +
514A ASN* 4.2 17.0 - - - +
629A MET* 4.2 0.5 - - - +
653A ARG* 3.2 9.1 - - - -
654A VAL* 2.9 35.3 + - + +
656A HIS* 3.4 49.6 - - + +
658A GLU* 5.4 2.7 - - - +
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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