Contacts of the strand formed by residues 498 - 509 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B ALA* 3.2 8.0 - - - +
395B GLN* 2.9 52.0 + - + +
396B ASP* 6.1 2.5 - - + -
488B TRP* 3.7 30.5 - - + -
489B PHE 3.2 11.9 - - - +
490B THR* 3.0 26.7 + - - +
491B LEU* 3.9 5.1 - - - +
497B GLY* 1.3 78.6 - - - +
499B LEU* 1.3 61.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 499 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B PHE* 3.8 19.7 - - + -
393B GLU 3.5 17.5 - - - +
394B ALA* 4.3 4.9 - - + -
438B TRP* 3.9 13.0 - - + -
456B ILE* 4.0 24.7 - - + -
458B LEU* 4.4 7.4 - - + -
472B LEU* 3.8 25.1 - - + -
488B TRP* 3.5 3.7 - - - -
489B PHE* 2.7 45.1 + - - +
491B LEU* 3.8 20.4 - - + +
498B LYS* 1.3 75.1 - - - +
500B HIS* 1.3 58.7 + - - +
501B LEU* 3.9 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 500 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B ILE* 3.4 45.5 + - + +
393B GLU* 2.8 52.1 + - + +
486B ASP* 2.6 30.9 + - - -
487B GLU* 3.4 17.5 - - - -
488B TRP* 3.7 27.1 + + + -
499B LEU* 1.3 70.7 - - - +
501B LEU* 1.3 67.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 501 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B ILE* 4.9 3.8 - - + -
390B HIS 3.4 14.8 - - - +
391B PHE* 3.8 26.9 - - + -
392B ILE* 4.1 0.2 - - - -
454B LEU* 4.7 0.9 - - + -
456B ILE* 3.7 24.7 - - + -
472B LEU* 3.8 18.6 - - + -
474B ILE* 4.1 14.8 - - + -
485B LEU* 3.9 1.4 - - - +
486B ASP* 3.4 3.3 - - - +
487B GLU 3.0 32.0 + - - +
489B PHE* 4.0 14.3 - - + -
499B LEU* 3.8 15.4 + - + -
500B HIS* 1.3 83.3 - - - +
502B ARG* 1.3 59.1 + - - +
503B LEU* 4.1 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 502 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ARG 3.7 0.2 - - - +
390B HIS* 2.8 73.8 + - + -
392B ILE* 3.8 8.1 - - + +
484B LEU* 3.9 22.3 - - + +
485B LEU 3.1 12.8 - - - +
486B ASP* 3.7 28.7 + - + +
501B LEU* 1.3 73.0 - - - +
503B LEU* 1.3 62.4 + - - +
504B GLU* 2.6 40.1 + - + +
525B ASP* 5.0 2.0 + - - -
657B LEU* 4.9 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 503 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B LEU* 4.5 4.7 - - + -
388B ARG 3.6 1.3 - - - +
389B ILE* 4.0 25.1 - - + -
454B LEU* 3.9 30.7 - - + -
474B ILE* 4.5 14.1 - - + -
479B VAL* 3.9 37.7 - - + -
483B ARG 4.6 0.4 - - - -
484B LEU* 3.3 10.2 - - - +
485B LEU* 2.7 50.8 + - + -
489B PHE* 5.2 2.7 - - + -
501B LEU* 4.3 15.5 - - + -
502B ARG* 1.3 82.3 - - - +
504B GLU* 1.3 61.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 504 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B VAL 3.5 3.1 - - - +
387B LEU* 3.6 6.5 - - - +
388B ARG* 2.9 63.3 + - + +
390B HIS* 3.2 22.3 + - + +
483B ARG 3.7 3.6 - - - -
484B LEU* 4.3 5.8 - - + -
502B ARG* 2.6 45.2 + - - +
503B LEU* 1.3 79.2 - - - +
505B TRP* 1.3 59.8 + - - +
506B LEU* 3.7 14.4 + - + +
657B LEU* 3.7 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 505 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B LYS* 4.0 14.3 + - + -
385B GLY* 3.9 27.6 - - - -
386B VAL 4.4 4.7 - - - -
387B LEU* 4.3 15.5 - - + +
446B VAL* 3.7 40.4 - - + -
476B LEU* 5.4 4.5 - - + -
479B VAL* 4.2 11.1 - - + +
480B GLU* 3.5 52.6 - - + +
483B ARG* 2.9 59.2 + - - +
503B LEU 4.3 0.2 - - - -
504B GLU* 1.3 69.2 - - - +
506B LEU* 1.3 62.7 + - - +
507B THR* 3.9 10.0 + - - -
657B LEU* 3.4 21.9 - - - +
658B GLU 4.3 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 506 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B GLY* 3.1 8.7 - - - -
386B VAL* 2.8 56.4 + - + +
388B ARG* 3.6 47.1 - - + +
443B GLU* 4.9 0.2 - - - +
504B GLU* 4.1 19.5 - - + +
505B TRP* 1.3 79.5 + - - +
507B THR* 1.3 61.5 + - - +
508B LEU* 4.3 0.5 - - - +
655B LEU* 4.1 21.3 - - + +
656B HIS* 3.4 11.9 - - - +
657B LEU* 3.9 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 507 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B LYS 4.9 6.5 + - - +
483B ARG* 3.4 25.1 + - - -
505B TRP* 3.9 6.7 + - - +
506B LEU* 1.3 74.7 - - - +
508B LEU* 1.3 78.3 + - - +
509B MET* 3.7 6.6 + - - -
654B VAL 3.2 5.0 - - - +
655B LEU* 3.5 2.7 - - - -
656B HIS* 2.6 39.9 + - - +
658B GLU* 3.7 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 508 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B VAL* 3.9 19.3 - - + -
383B PRO* 3.7 19.1 - - + +
384B LYS 4.2 5.4 + - - +
385B GLY* 3.7 29.8 - - - -
507B THR* 1.3 87.3 - - - +
509B MET* 1.3 62.0 + - - +
510B PRO* 3.7 9.1 - - - +
537B LEU* 4.2 17.3 - - + -
539B ILE* 5.1 2.0 - - + -
653B ARG* 3.9 34.0 + - + +
654B VAL 3.5 3.8 - - - -
655B LEU* 3.8 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 509 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B THR* 4.3 7.4 - - - +
508B LEU* 1.3 77.4 - - - +
510B PRO* 1.3 65.6 - - + +
511B ASN* 3.0 48.1 + - - +
513B SER* 4.0 2.5 - - - +
514B ASN* 3.4 26.2 - - + +
629B MET* 3.9 1.6 - - - +
653B ARG* 3.3 9.7 - - - -
654B VAL* 2.7 44.3 + - + +
656B HIS* 3.7 31.4 - - + -
658B GLU* 5.4 6.1 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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