Contacts of the strand formed by residues 443 - 450 (chain B) in PDB entry 3HN3
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 VAL 443 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ARG* 2.9 14.9 + - - -
393B MET* 4.3 16.4 - - - -
403B VAL* 3.6 11.0 - - + +
405B ASP* 3.7 37.0 - - + +
437B ASP* 4.2 6.1 - - + +
440B HIS* 3.1 26.7 + - + +
442B ALA* 1.3 73.7 - - + +
444B VAL* 1.3 59.4 + - - +
445B MET 4.0 7.4 - - - +
446B TRP* 4.1 11.9 - - + -
477B ARG* 2.8 41.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B TRP* 5.5 1.3 - - + -
327B ARG* 4.4 2.0 - - - +
329B VAL* 3.7 27.7 - - + +
336B PHE* 3.8 8.4 - - + -
338B ILE* 4.3 10.3 - - + -
345B PHE* 3.8 33.9 - - + -
402B VAL* 4.0 21.8 - - + -
403B VAL 3.0 14.7 + - - +
441B PRO 4.1 8.1 - - - +
442B ALA 3.2 12.3 + - - +
443B VAL* 1.3 75.4 - - - +
445B MET* 1.3 62.2 + - + +
477B ARG* 4.0 7.1 - - - +
478B PRO* 3.2 24.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B PHE* 4.2 9.4 - - + -
345B PHE* 4.8 0.9 - - + -
403B VAL 3.5 3.2 + - - +
404B ILE* 3.4 26.4 - - + -
405B ASP* 2.9 29.0 + - - +
443B VAL* 3.7 3.1 - - - +
444B VAL* 1.3 84.0 - - + +
446B TRP* 1.3 76.1 + - - +
477B ARG* 4.7 2.2 - - - -
478B PRO* 3.4 27.1 - - + +
479B VAL 4.6 0.2 - - - -
480B THR* 3.9 23.8 - - + -
498B VAL* 3.9 28.0 - - + -
500B CYS* 4.3 1.8 - - - -
537B ILE* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B ILE* 4.8 0.2 - - - -
405B ASP* 3.4 39.7 - - + +
430B MET* 4.5 6.7 - - + -
433B VAL* 3.9 22.2 - - + -
434B VAL* 3.9 37.2 - - + +
437B ASP* 4.0 20.4 - - + -
438B LYS* 4.4 0.9 - - - -
443B VAL* 4.1 5.8 - - + -
445B MET* 1.3 74.8 - - - +
447B SER* 1.3 59.5 + - - +
448B VAL 4.2 0.2 - - - -
470B THR* 4.0 28.7 - - + -
474B ASP* 2.8 35.9 + - + +
477B ARG* 3.5 29.7 - - + +
478B PRO 3.1 16.8 + - - +
479B VAL* 3.4 8.6 - - + -
480B THR* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 447 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B ILE* 3.9 17.3 - - - -
405B ASP 2.9 7.8 + - - +
406B GLU* 2.8 36.9 + - - +
407B CYS* 3.1 26.0 + - - +
430B MET* 4.6 2.8 - - - +
446B TRP* 1.3 74.8 - - - +
448B VAL* 1.3 61.5 + - - +
449B ALA 3.3 12.8 + - - -
480B THR* 3.3 10.5 - - - -
481B PHE* 3.8 6.8 - - - -
482B VAL* 3.9 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 448 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B CYS* 3.0 13.7 - - - -
409B GLY* 4.0 0.3 - - - -
426B HIS* 2.8 28.6 + - - +
430B MET* 4.0 11.2 - - + -
447B SER* 1.3 75.3 - - - +
449B ALA* 1.3 63.8 + - + +
463B LEU* 4.5 9.6 - - + -
466B VAL* 3.7 23.6 - - + +
467B ILE* 3.9 17.7 - - + -
470B THR* 3.5 24.7 - - - +
479B VAL* 3.8 19.3 - - + -
480B THR 3.0 14.7 + - - +
481B PHE* 3.8 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 449 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B GLU* 3.7 6.3 - - - +
407B CYS* 4.9 0.2 - - - -
409B GLY* 3.2 17.7 - - - +
412B LEU* 5.0 2.0 - - + -
426B HIS* 4.7 3.6 - - + -
447B SER* 3.3 11.5 + - - -
448B VAL* 1.3 84.1 - - - +
450B ASN* 1.3 60.3 + - - +
451B GLU 4.3 0.2 - - - -
452B PRO* 4.0 24.2 - - + -
463B LEU* 4.2 11.4 - - + -
481B PHE* 3.8 8.4 - - + +
482B VAL 3.0 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 450 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B ARG* 3.0 18.4 + - - +
385B HIS* 3.3 29.9 + - + +
406B GLU* 3.6 17.5 + - - +
409B GLY 3.0 10.4 + - - +
410B VAL* 3.9 31.5 - - + +
411B GLY 4.0 2.8 + - - -
412B LEU 5.0 0.2 + - - -
449B ALA* 1.3 72.8 - - - +
451B GLU* 1.3 89.9 + - - +
452B PRO 3.3 2.2 - - - -
482B VAL* 3.3 15.6 - - - +
502B ASN* 3.5 7.3 + - - -
540B GLU* 4.2 1.6 + - - -
----------------------------------------------------------
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