Contacts of the strand formed by residues 608 - 616 (chain B) in PDB entry 1NA8
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 LEU 608 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B PHE* 4.7 7.2 - - + -
562B SER* 3.8 26.2 - - - +
563B ALA 3.7 13.2 - - - +
564B VAL* 4.6 6.5 - - + -
570B VAL* 4.5 10.5 - - + -
596B LEU* 4.2 16.2 - - + -
598B LEU* 4.6 8.3 - - + -
606B VAL* 4.8 1.1 - - + -
607B ARG* 1.3 75.4 - - - +
609B ARG* 1.3 79.0 + - - +
610B TYR* 3.8 8.7 - - + +
626B ASP* 3.2 8.4 - - - +
627B VAL* 2.8 52.3 + - + +
630B PHE* 4.0 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 609 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562B SER* 3.2 3.3 - - - -
563B ALA* 2.9 42.2 + - + +
608B LEU* 1.3 79.6 - - - +
610B TYR* 1.3 67.5 + - - +
611B LYS* 5.2 14.2 - - + +
624B MET* 5.6 14.5 - - + +
625B GLY* 3.3 11.2 + - - +
626B ASP* 2.8 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 610 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B VAL* 3.3 44.1 + - + -
518B TYR* 3.5 21.7 - + + -
560B PHE* 3.7 22.7 - + + -
561B GLN 3.1 12.8 - - - +
608B LEU* 4.1 5.8 - - + -
609B ARG* 1.3 77.5 - - - +
611B LYS* 1.3 65.7 + - - +
612B LEU* 3.9 28.3 - - + -
623B GLU* 4.2 2.6 - - - +
624B MET* 3.2 19.1 + - - +
625B GLY* 2.9 60.2 + - - -
626B ASP 4.2 2.9 - - - -
627B VAL* 4.2 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 611 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B VAL 3.5 3.3 - - - +
560B PHE* 4.8 0.4 - - - -
561B GLN* 2.8 54.4 + - + +
563B ALA* 6.3 3.4 - - - -
609B ARG* 5.2 13.2 - - + +
610B TYR* 1.3 79.4 - - - +
612B LEU* 1.3 60.0 + - - +
613B THR* 4.2 6.0 + - + +
622B ASN* 5.2 8.3 - - - +
623B GLU 3.4 6.1 - - - +
624B MET* 4.5 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 612 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B TYR* 3.7 28.3 - - + -
523B PHE* 4.2 7.4 - - + -
525B ILE* 3.3 35.9 - - + -
558B ILE* 4.4 7.2 - - + -
559B VAL 3.4 14.6 - - - +
560B PHE* 4.2 10.5 - - + +
610B TYR* 3.9 17.2 - - + -
611B LYS* 1.3 72.3 - - - +
613B THR* 1.3 69.3 + - - +
614B PHE* 3.7 30.5 - - + -
621B TYR 3.8 0.9 - - - +
623B GLU* 2.8 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 613 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B ASN 3.3 2.7 + - - +
558B ILE* 3.3 0.3 - - - -
559B VAL* 2.9 53.3 + - - +
561B GLN* 5.6 4.0 + - - +
611B LYS* 5.0 5.8 - - + +
612B LEU* 1.3 83.9 - - - +
614B PHE* 1.3 68.9 + - - +
621B TYR 3.2 11.0 - - - +
622B ASN* 3.7 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 614 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B TYR* 3.5 22.9 - + - -
521B HIS* 4.5 3.1 - + - -
523B PHE* 3.7 23.1 - + + -
555B ILE* 3.8 22.4 - - + -
556B ARG 3.7 7.0 - - - +
557B ASN* 3.5 10.7 + - - -
558B ILE* 3.9 8.1 - - + -
612B LEU* 3.7 31.9 - - + -
613B THR* 1.3 82.9 - - - +
615B THR* 1.3 71.4 + - - +
616B MET* 4.0 17.7 - - + -
621B TYR* 2.9 63.4 + + + +
623B GLU* 4.1 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 615 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554B PRO 3.8 0.9 - - - +
555B ILE* 3.5 5.0 - - - -
556B ARG* 2.9 37.3 + - - +
557B ASN* 3.1 32.5 + - + +
614B PHE* 1.3 85.7 - - - +
616B MET* 1.3 64.4 + - - +
617B GLY 3.9 11.7 + - - -
619B GLN 3.3 7.2 - - - -
620B THR* 3.9 23.8 - - + -
621B TYR* 4.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 616 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B HIS* 3.8 32.1 - - + +
523B PHE* 5.5 0.2 - - - -
551B ALA* 3.7 30.3 - - + -
552B PRO* 5.7 0.4 - - + -
553B GLN* 3.4 30.1 - - + +
554B PRO 4.0 5.8 - - - -
555B ILE* 4.1 16.4 - - + -
614B PHE* 4.0 21.5 - - + -
615B THR* 1.3 76.7 - - - +
617B GLY* 1.3 59.7 + - - +
618B ASP 3.3 0.2 + - - -
619B GLN* 2.8 41.5 + - - +
621B TYR* 3.8 20.6 - - + -
----------------------------------------------------------
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