Contacts of the strand formed by residues 700 - 703 (chain N) in PDB entry 2PPB
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 700 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642N CYS* 4.4 3.1 - - - -
644N LEU* 4.0 9.9 - - + -
652N LEU* 6.0 0.7 - - + -
653N PHE* 3.3 35.9 - - + -
699N VAL* 1.3 76.3 - - - +
701N LEU* 1.3 66.4 + - - +
702N LEU* 4.3 8.7 - - + -
715N ALA* 3.1 3.8 - - - -
716N PHE* 3.0 28.8 + - - +
718N PRO* 3.5 20.6 - - + +
747N VAL* 3.6 21.5 - - + -
748N HIS 3.1 11.0 - - - +
749N VAL* 3.5 15.5 - - + -
750N PRO* 4.3 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 701 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032M PHE* 6.0 2.5 - - + -
1040M LEU* 5.0 7.9 - - + -
1048M THR* 4.6 10.1 - - + -
1052M MET* 6.0 2.0 - - + -
699N VAL* 4.9 0.2 - - + -
700N VAL* 1.3 75.8 - - - +
702N LEU* 1.3 62.4 + - - +
713N ILE* 4.1 19.3 - - + -
714N GLN 3.2 12.1 - - - +
715N ALA* 3.3 26.5 - - + -
747N VAL* 3.1 12.1 - - - +
748N HIS* 2.9 46.0 + - + +
750N PRO* 4.4 8.5 - - + -
759N ALA* 4.0 18.8 - - + -
763N MET* 3.4 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 702 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631N ILE* 5.2 0.4 - - + -
642N CYS* 4.3 26.9 - - + -
644N LEU* 5.1 3.6 - - + -
700N VAL* 4.3 3.1 - - + -
701N LEU* 1.3 84.9 - - - +
703N ASN* 1.3 59.8 + - - +
713N ILE* 2.9 28.4 - - - +
714N GLN 2.8 15.9 + - - +
716N PHE* 4.3 17.7 - - + -
726N ILE* 4.6 20.4 - - + -
728N LEU* 5.1 11.0 - - + -
736N PHE* 3.3 5.6 - - + -
745N MET* 3.4 36.1 - - + -
746N ALA 3.4 10.8 - - - +
747N VAL* 4.0 16.2 - - + -
748N HIS* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 703 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030M GLN* 5.8 0.2 - - - +
1031M ARG 4.6 6.6 - - - +
1036M GLU* 3.2 28.1 + - - +
702N LEU* 1.3 74.3 - - - +
704N ARG* 1.3 93.0 + - - +
707N THR* 2.8 19.8 + - - -
712N GLY 3.8 5.2 + - - -
713N ILE* 4.2 5.8 - - + +
745N MET* 3.0 13.9 - - - +
746N ALA* 2.9 39.3 + - + +
748N HIS* 3.6 27.3 + - + +
----------------------------------------------------------
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