Contacts of the strand formed by residues 702 - 709 (chain B) in PDB entry 3NR8
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 ILE 702 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B HIS* 3.8 11.2 - - + +
603B PHE* 3.6 30.5 - - + -
694B TRP* 3.7 35.5 + - + +
696B SER* 3.2 30.7 - - - +
700B THR 4.2 1.6 - - - +
701B HIS* 1.3 81.3 - - - +
703B ILE* 1.3 71.2 + - - +
725B PHE* 3.8 12.8 - - + -
726B GLU 3.2 16.4 - - - +
727B VAL* 4.2 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 703 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B LYS* 5.3 1.8 - - - +
694B TRP* 5.7 0.2 - - - -
701B HIS* 6.2 1.6 - - + -
702B ILE* 1.3 80.1 - - - +
704B CYS* 1.3 82.4 + - - +
705B ASN* 4.1 10.8 - - - +
725B PHE* 3.3 5.9 - - - +
726B GLU* 3.0 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 704 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B LYS* 2.6 29.6 + - - -
653B GLU* 3.6 36.0 + - - +
694B TRP* 4.0 14.0 - - + -
702B ILE 4.3 0.2 + - - -
703B ILE* 1.3 81.8 - - - +
705B ASN* 1.3 54.9 + - - +
706B SER 3.2 26.2 - - - -
707B TYR* 4.2 2.2 - - - -
724B THR 3.6 8.1 - - - -
725B PHE* 3.9 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 705 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B LYS* 3.3 24.8 - - - +
454B THR 4.9 0.5 - - - +
455B LEU* 4.1 16.8 - - + +
703B ILE* 4.1 16.1 + - - +
704B CYS* 1.3 76.3 - - - +
706B SER* 1.3 62.3 + - - +
724B THR* 2.8 20.3 + - - +
725B PHE 5.3 1.1 - - - -
726B GLU* 4.4 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 706 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B SER* 2.9 24.7 + - - -
453B LYS* 3.3 13.0 - - - -
455B LEU* 3.9 10.8 - - - -
704B CYS* 3.2 10.8 - - - -
705B ASN* 1.3 80.1 - - - +
707B TYR* 1.3 65.8 + - - +
722B PHE* 3.9 1.8 - - - -
723B GLY* 3.4 2.4 - - - -
724B THR* 2.5 57.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 707 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B LYS* 2.6 31.6 + - + +
652B GLU* 2.7 28.8 + - + -
653B GLU* 3.6 52.5 - - + -
654B GLU 4.8 4.8 - - - +
655B ILE* 4.0 13.2 - - + +
657B PHE* 3.6 23.4 - + - -
690B ASP 4.2 1.7 + - - -
691B ARG* 3.5 11.8 - - - +
692B ILE* 3.2 46.2 + - + -
704B CYS* 4.2 1.8 - - - -
706B SER* 1.3 75.5 - - - +
708B GLY* 1.3 57.6 + - - +
721B VAL* 3.9 11.7 - - + -
722B PHE 3.3 15.7 - - - -
723B GLY* 4.4 2.7 - - - -
725B PHE* 6.1 1.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 708 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B LEU 3.1 14.1 - - - -
452B GLY* 4.0 2.2 - - - -
657B PHE* 3.7 11.5 - - - -
707B TYR* 1.3 75.0 - - - +
709B CYS* 1.3 63.9 + - - +
721B VAL* 3.4 8.7 - - - +
722B PHE* 3.0 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 709 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B GLY* 3.4 3.1 - - - -
451B LEU* 2.8 36.6 + - - +
657B PHE* 3.3 31.6 - - + -
658B PRO* 4.3 12.3 - - - -
660B THR* 4.2 7.9 - - + -
663B TYR* 5.7 1.8 - - - -
708B GLY* 1.3 75.4 - - - +
710B THR* 1.3 69.7 + - - +
719B SER* 4.5 6.5 - - - -
720B PRO 3.2 15.9 - - - +
721B VAL* 3.8 12.8 - - + -
722B PHE* 3.3 11.2 - - - -
----------------------------------------------------------
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