Contacts of the strand formed by residues 443 - 448 (chain B) in PDB entry 6J94
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
----------------------------------------------------------
128B PHE* 3.9 29.2 - - + -
129B PHE* 4.6 9.4 - - + -
132B LEU* 5.1 3.1 - - + -
177B LEU* 5.9 1.6 - - - +
441B PRO* 3.2 20.5 - - - +
442B PRO* 1.3 95.5 - - + +
444B LEU* 1.3 68.4 + - - +
445B ILE* 3.7 14.4 + - + +
466B PHE* 3.5 37.5 - - + -
467B ILE 3.2 12.6 - - - +
468B SER* 4.4 8.7 - - - -
469B VAL 4.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LEU* 3.9 33.4 - - + -
177B LEU* 6.2 0.2 - - - -
441B PRO* 3.9 13.2 - - + -
443B VAL* 1.3 79.1 - - - +
445B ILE* 1.3 63.1 + - - +
446B ARG* 3.9 10.0 + - - +
465B ILE 3.7 1.2 - - - +
466B PHE 3.7 0.3 - - - -
467B ILE* 2.8 52.2 + - + +
469B VAL* 3.7 21.8 - - + -
507B LEU* 4.4 7.9 - - + +
510B GLY* 4.7 9.6 - - - -
601B HEM 3.6 44.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B PHE* 6.0 0.7 - - + -
174B LYS* 3.8 22.7 - - - +
176B ILE* 4.4 14.6 - - + +
177B LEU* 3.9 45.0 - - + +
289B VAL* 4.4 10.8 - - + -
443B VAL* 3.7 13.9 - - + +
444B LEU* 1.3 72.8 - - - +
446B ARG* 1.3 89.5 + - - +
464B ASP* 6.0 1.3 - - + +
465B ILE 3.4 7.2 - - - +
466B PHE* 3.4 44.6 - - + -
601B HEM 5.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ILE* 4.0 27.8 + - + +
165B LEU* 3.3 29.5 + - - +
172B TYR* 4.4 15.3 - - + +
173B SER 3.2 19.7 - - - +
174B LYS* 3.5 8.0 - - - +
175B GLY* 4.6 3.0 - - - -
444B LEU* 4.2 7.0 - - - +
445B ILE* 1.3 95.4 + - - +
447B ARG* 1.3 62.1 + - - +
464B ASP* 3.8 2.6 - - - +
465B ILE* 2.9 39.8 + - + +
467B ILE* 4.5 10.5 - - + -
511B GLY 5.0 2.4 + - - -
514B ARG* 3.7 31.3 - - - +
601B HEM 2.8 42.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 447 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A PRO* 6.3 1.6 - - - +
172B TYR* 3.3 7.3 - - - -
173B SER* 2.9 36.8 + - - +
175B GLY* 3.7 28.1 - - - -
176B ILE* 3.8 18.4 - - - +
179B GLU* 2.8 37.6 + - - -
446B ARG* 1.3 75.9 - - - +
448B SER* 1.3 77.0 + - - +
449B ILE* 3.4 4.5 + - + +
462B GLY* 3.9 20.6 - - - -
463B GLU 3.2 10.1 - - - +
464B ASP* 2.9 28.8 + - - +
465B ILE* 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 448 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ALA 3.4 7.8 + - - -
172B TYR* 3.6 20.7 + - - -
447B ARG* 1.3 78.7 - - - +
449B ILE* 1.3 59.3 + - - +
450B ASP 2.3 31.7 + - - -
451B ASN 4.8 0.2 - - - -
459B ILE* 4.0 12.0 - - - +
460B LYS 3.3 19.3 + - - -
461B ARG* 3.8 1.4 - - - +
462B GLY* 2.9 21.6 + - - -
463B GLU* 3.1 17.1 + - - -
465B ILE* 4.8 0.2 - - - -
----------------------------------------------------------
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