Contacts of the strand formed by residues 420 - 430 (chain B) in PDB entry 1NSC
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 ASP 420 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PRO* 3.8 1.7 - - - +
83B ARG* 2.9 60.1 + - - -
84B LEU 3.1 7.5 + - - +
85B SER* 3.0 12.8 - - - +
86B CYS* 2.7 27.9 + - - -
355B ARG* 3.0 15.0 + - - +
413B GLU* 3.4 22.2 - - + +
414B ILE 3.6 5.8 - - - +
415B LYS* 3.0 24.4 + - - +
419B CYS* 1.3 72.8 - - - +
421B VAL* 1.3 55.7 + - - +
422B PRO* 3.5 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ALA* 4.2 15.0 - - + -
209A TYR* 3.5 27.4 - - + +
86B CYS* 3.5 25.8 - - + -
413B GLU* 3.2 5.7 - - - -
414B ILE* 2.9 49.8 + - + +
416B ASP* 4.3 1.8 - - + -
420B ASP* 1.3 71.6 - - - +
422B PRO* 1.3 71.1 - - + +
423B CYS* 3.6 4.9 + - - -
446B CYS* 4.1 13.0 - - + -
447B LEU* 3.7 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B SER* 4.3 6.5 - - - +
86B CYS 5.0 0.4 - - - +
91B PHE* 3.8 7.9 - - + -
352B VAL* 3.7 17.9 - - + -
353B HIS 3.4 26.5 - - - +
354B GLN* 4.5 10.1 - - + -
363B TRP* 5.4 0.4 - - + -
412B PHE 3.8 4.5 - - - +
413B GLU* 4.2 5.1 - - + +
420B ASP 3.5 9.9 - - - +
421B VAL* 1.3 82.9 - - - +
423B CYS* 1.3 61.1 + - - +
446B CYS* 3.5 1.9 - - - -
447B LEU* 2.9 60.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 423 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B PHE* 4.0 2.7 - - - -
352B VAL* 3.7 4.6 - - - +
411B GLY* 3.3 5.0 - - - -
412B PHE* 2.9 53.2 + - + +
414B ILE* 3.7 22.7 - - - -
421B VAL* 3.9 9.0 - - - -
422B PRO* 1.3 75.7 - - - +
424B ILE* 1.3 64.9 + - - +
444B ILE* 4.4 0.2 - - + -
445B TYR 3.3 5.4 - - - +
446B CYS* 2.0 47.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 424 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B PHE* 3.9 8.7 - - + -
350B GLY 4.1 15.5 - - - -
351B PHE 4.2 0.4 - - - +
352B VAL* 4.0 13.0 - - + -
363B TRP* 4.1 21.1 - - + +
364B TYR 4.2 2.5 - - - -
365B SER* 3.8 21.5 - - - +
378B LEU* 3.8 24.2 - - + -
399B MET* 4.4 9.4 - - + -
409B SER* 4.5 0.9 - - - -
410B PHE 3.2 10.3 - - - +
411B GLY* 4.6 1.1 - - - -
412B PHE* 4.3 2.5 - - - -
423B CYS* 1.3 76.4 - - - +
425B GLY* 1.3 73.5 + - - +
426B ILE* 4.2 11.7 - - + +
443B ALA 4.0 0.2 - - - +
444B ILE* 3.6 2.4 - - - +
445B TYR* 2.8 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 425 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B SER* 3.3 6.8 - - - -
410B PHE* 2.9 59.8 + - - -
412B PHE* 4.1 3.7 - - - -
424B ILE* 1.3 73.3 - - - +
426B ILE* 1.3 63.5 + - - +
443B ALA 3.2 9.2 - - - -
444B ILE* 4.4 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 426 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B MET* 4.0 34.3 - - + -
399B MET* 3.8 43.7 - - + -
400B VAL* 4.3 13.5 - - + -
406B GLY* 4.5 2.5 - - - -
408B TYR 3.7 3.4 - - - +
409B SER* 4.3 2.2 - - - -
410B PHE* 4.1 3.1 - - - -
424B ILE* 4.2 9.4 - - + +
425B GLY* 1.3 79.3 - - - +
427B GLU* 1.3 72.9 + - - +
428B MET* 3.6 13.3 + - + +
442B THR* 3.3 6.3 - - - +
443B ALA* 2.8 44.5 + - + +
445B TYR* 4.1 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ARG* 2.8 50.3 + - - +
116B GLU 2.9 17.9 + - - -
117B PRO* 3.5 28.1 - - + +
407B TRP* 2.8 30.8 + - - +
408B TYR* 2.7 40.0 + - + +
410B PHE* 4.6 3.0 - - + -
425B GLY 4.3 0.4 - - - -
426B ILE* 1.3 73.5 - - - +
428B MET* 1.3 60.0 + - - +
429B VAL* 3.5 12.6 - - + -
440B ALA* 3.7 7.2 - - + -
441B ALA 3.6 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 4.6 4.9 - - - -
400B VAL* 3.8 15.3 - - + -
404B GLU* 3.8 9.9 - - + +
405B PRO* 3.5 28.5 - - + +
426B ILE* 3.8 16.8 - - + +
427B GLU* 1.3 75.6 - - - +
429B VAL* 1.3 64.0 + - - +
430B HIS* 3.6 5.4 + - - -
440B ALA* 3.4 0.7 - - - -
441B ALA* 2.8 35.1 + - - +
443B ALA* 3.9 23.3 - - - -
457B THR* 3.8 32.1 - - - +
459B THR* 3.8 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ARG* 3.7 8.3 - - - +
405B PRO* 3.1 27.9 - - - +
407B TRP* 3.5 35.2 + - + -
427B GLU* 3.5 37.5 + - + +
428B MET* 1.3 71.9 - - - +
430B HIS* 1.3 66.9 + - - +
431B ASP* 3.5 5.4 + - - +
438B HIS* 3.6 34.8 - - + +
439B SER 3.3 11.0 - - - +
440B ALA* 3.9 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B SER* 4.7 0.6 + - - -
100B HIS* 3.7 18.7 + + + +
405B PRO* 5.5 1.4 - - - +
428B MET 4.2 3.1 - - - -
429B VAL* 1.3 71.5 + - - +
431B ASP* 1.3 59.6 + - - +
437B TRP* 3.6 35.7 - + + -
438B HIS* 3.7 8.0 + - - -
439B SER 2.8 30.2 + - - +
440B ALA* 4.0 1.6 - - - -
441B ALA* 3.9 15.2 + - + +
459B THR* 3.5 39.7 + - + +
461B VAL* 3.6 25.3 + - + +
463B MET* 3.6 22.5 - - - +
----------------------------------------------------------
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