Contacts of the strand formed by residues 488 - 494 (chain B) in PDB entry 2NT0
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 SER 488 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B SER 3.3 13.2 - - - -
43B THR* 4.0 8.3 - - - +
357B TRP* 4.3 3.6 - - - -
460B VAL 5.2 0.2 + - - -
461B LEU* 3.7 4.1 - - - +
462B ASN 2.9 27.1 + - - +
484B SER* 3.8 7.6 + - - -
485B PRO* 2.6 50.4 + - - +
486B GLY 3.3 0.2 - - - -
487B TYR* 1.3 78.5 - - - +
489B ILE* 1.3 65.4 + - - +
490B HIS* 4.2 7.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 489 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B SER* 2.9 41.6 + - - +
357B TRP* 4.5 0.2 - - + -
364B SER* 3.5 33.9 - - - +
419B HIS* 3.8 24.5 - - + +
422B HIS* 3.4 41.9 - - + +
423B PHE* 4.0 1.8 - - + -
459B VAL* 3.9 19.1 - - + -
460B VAL 3.3 13.0 - - - +
461B LEU* 4.1 9.9 - - + -
488B SER* 1.3 75.8 - - - +
490B HIS* 1.3 68.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 490 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ARG* 3.9 16.1 - - + -
40B TYR 3.1 7.0 - - - +
41B GLU* 2.8 39.8 + - + +
422B HIS* 3.8 1.8 - - - -
458B VAL 3.7 0.3 - - - +
459B VAL* 3.3 6.5 - - - +
460B VAL* 2.9 38.1 + - + +
483B ILE 3.1 26.1 + - - -
484B SER* 4.5 3.8 - - - -
485B PRO* 3.5 12.9 - - + +
488B SER* 4.2 6.9 + - - -
489B ILE* 1.3 86.5 - - - +
491B THR* 1.3 62.8 + - - +
492B TYR* 2.7 41.2 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 491 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B SER 3.8 0.5 - - - +
39B ARG* 3.4 4.0 - - - -
40B TYR* 2.9 35.9 + - - +
422B HIS* 2.8 40.6 + - - +
426B PHE* 3.7 28.0 - - + -
457B VAL* 3.5 30.1 - - + -
458B VAL 3.4 4.3 - - - +
459B VAL* 3.9 4.8 - - + +
490B HIS* 1.3 76.3 + - - +
492B TYR* 1.3 65.4 + - - +
493B LEU* 4.1 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 492 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 3.8 28.5 - + - -
38B SER 3.4 3.4 - - - -
39B ARG* 3.3 19.7 + - + -
457B VAL* 3.1 7.6 - - - +
458B VAL* 2.7 46.2 + - + +
460B VAL* 4.2 16.2 - - + -
470B LEU* 5.7 0.6 - - + +
472B ILE* 4.0 13.9 - - + -
480B LEU* 4.0 7.9 - - + -
482B THR* 2.4 46.5 + - + +
483B ILE 4.0 0.9 + - - -
490B HIS* 2.7 42.5 + - + -
491B THR* 1.3 73.5 - - - +
493B LEU* 1.3 62.9 + - - +
494B TRP* 3.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 493 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B PRO* 3.5 9.7 - - + +
37B PHE* 3.3 1.9 - - - -
38B SER* 2.8 46.2 + - - -
40B TYR* 3.8 35.2 - - + -
426B PHE* 3.9 29.2 - - + -
451B HIS* 4.0 26.2 - - + +
456B ALA 3.4 5.6 - - - +
457B VAL* 4.1 7.6 - - + -
491B THR* 4.1 9.6 - - + +
492B TYR* 1.3 80.7 - - - +
494B TRP* 1.3 67.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 494 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B PRO* 3.9 7.9 - - - -
36B THR 3.7 16.2 - - - +
37B PHE* 4.0 2.9 - - + -
56B ILE* 3.8 10.1 - - + -
69B LEU* 4.3 7.4 - - + -
455B SER* 3.5 4.2 - - - -
456B ALA* 2.9 52.6 + - + +
458B VAL* 3.5 32.5 - - + -
472B ILE* 3.8 19.3 - - + -
474B ASP* 2.8 39.3 + - + -
477B VAL* 3.7 15.8 - - + +
480B LEU* 3.6 30.3 - - + -
492B TYR* 3.9 13.7 - - + -
493B LEU* 1.3 84.5 - - - +
495B HIS* 1.3 85.3 + - - +
496B ARG* 4.3 1.1 - - + -
----------------------------------------------------------
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