Contacts of the strand formed by residues 705 - 712 (chain B) in PDB entry 3BBT
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 GLY 705 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701B SER* 3.4 2.8 - - - -
702B GLY 3.0 29.9 + - - +
703B ALA 3.7 0.6 - - - -
704B PHE* 1.3 82.1 - - - +
706B THR* 1.3 65.8 + - - -
726B LYS* 4.8 6.6 - - - +
727B ILE 3.3 14.1 - - - -
728B LEU* 4.1 5.1 - - - +
729B ASN* 4.1 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 706 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698B VAL* 3.9 21.8 - - + -
700B GLY 3.9 3.1 - - - -
701B SER* 3.6 19.4 - - - +
705B GLY* 1.3 76.3 + - - -
707B VAL* 1.3 65.9 + - - +
708B TYR* 3.7 30.8 - - + +
725B ILE 3.4 1.9 - - - +
726B LYS* 3.4 3.0 - - - +
727B ILE* 2.8 42.1 + - - +
729B ASN* 5.8 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 707 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B FMM 3.5 45.5 - - + +
698B VAL* 3.9 5.0 - - - +
699B LEU* 3.0 46.2 + - + -
700B GLY 2.8 24.0 + - - +
701B SER* 5.9 0.2 - - - -
705B GLY 6.0 0.2 - - - -
706B THR* 1.3 71.6 - - - +
708B TYR* 1.3 66.0 + - - +
724B ALA* 4.6 1.8 - - + -
725B ILE 3.4 4.3 - - - +
726B LYS* 3.6 33.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 708 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695B ARG* 3.3 52.3 + - + -
697B LYS* 3.5 15.0 - - - +
698B VAL* 3.6 22.8 - - + +
699B LEU* 4.0 3.6 - - - -
706B THR* 3.7 28.9 - - + +
707B VAL* 1.3 76.6 - - - +
709B LYS* 1.3 64.0 + - - +
710B GLY 3.4 0.3 + - - -
724B ALA* 3.4 5.7 - - - +
725B ILE* 2.7 50.9 + - + +
727B ILE* 3.6 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 709 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695B ARG* 3.8 1.0 - - - -
696B VAL* 2.9 41.6 + - + +
697B LYS* 2.9 24.6 + - + +
699B LEU* 3.6 34.0 - - + +
708B TYR* 1.3 69.8 - - - +
710B GLY* 1.3 61.3 + - - +
723B VAL 4.1 2.7 - - - -
724B ALA* 4.9 0.2 - - - +
773B LEU* 3.8 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 710 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694B LYS 3.3 11.4 - - - -
695B ARG* 4.2 1.1 - - - -
696B VAL* 3.8 4.2 - - - +
708B TYR 3.4 2.2 + - - -
709B LYS* 1.3 78.5 - - - +
711B ILE* 1.3 69.3 + - - +
722B PRO* 3.9 2.4 - - - +
723B VAL* 2.9 37.0 + - - +
725B ILE* 3.8 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 711 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692B GLU 3.8 0.9 - - - +
693B LEU* 3.6 4.2 - - - +
694B LYS* 2.8 66.2 + - + +
695B ARG 5.5 0.2 - - - +
696B VAL* 4.8 11.7 - - + -
710B GLY* 1.3 78.4 - - - +
712B TRP* 1.3 60.2 + - - +
713B VAL* 4.2 5.5 + - + +
720B LYS* 4.6 26.0 - - + +
721B ILE 3.5 4.7 - - - +
722B PRO* 4.1 7.4 - - + -
723B VAL* 4.4 2.0 - - - -
725B ILE* 4.8 0.4 - - - +
718D THR* 4.9 12.3 - - - +
719D VAL* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 712 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686B ARG* 3.8 38.1 - - - -
688B LEU* 3.6 40.9 - - + +
692B GLU* 3.5 24.3 + - + -
693B LEU* 4.1 10.8 - - + -
711B ILE* 1.3 74.3 - - - +
713B VAL* 1.3 71.1 + - - +
714B PRO* 3.5 34.9 - - + +
719B VAL* 6.0 0.4 - - + -
720B LYS* 3.4 23.6 - - - -
721B ILE* 3.0 51.2 + - + +
723B VAL* 4.1 9.9 - - + -
759B LEU* 5.2 15.5 - - + -
770B VAL* 6.0 0.4 - - + -
----------------------------------------------------------
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