Contacts of the strand formed by residues 695 - 702 (chain G) in PDB entry 5LS6
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 CYS 695 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638G ILE* 3.6 19.1 - - - -
693G PRO* 3.4 19.5 - - - +
694G ASN* 1.3 91.3 - - - +
696G TYR* 1.3 60.7 + - - +
710G ILE* 4.1 11.4 - - + -
711G PHE 3.4 12.1 - - - +
713G LYS* 3.9 7.2 - - - +
716G ILE* 4.3 0.9 - - - -
722G LEU* 3.5 36.3 - - - -
723G PHE 3.1 13.9 + - - +
724G PHE* 3.3 20.2 - - + +
725G ASP 4.1 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 696 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574G TYR* 5.7 1.0 + - - -
634G LYS* 6.0 0.7 - - - -
635G ASN* 2.6 35.9 + - - +
695G CYS* 1.3 72.4 - - - +
697G ALA* 1.3 74.6 + - - +
698G LYS* 4.4 18.7 + - + +
710G ILE* 3.6 7.4 - - - +
711G PHE* 3.1 58.5 + + + +
712G ALA 4.1 9.4 - - - -
713G LYS* 4.0 31.0 - - + -
724G PHE* 4.4 4.7 - - - -
725G ASP 5.6 1.1 - - - +
728G TYR* 3.8 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 697 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696G TYR* 1.3 77.8 - - - +
698G LYS* 1.3 60.8 + - - +
699G VAL* 4.4 0.9 + - - +
708G ILE* 3.9 5.4 - - + -
709G GLY 3.2 8.5 - - - +
710G ILE* 3.2 33.4 - - + -
728G TYR* 2.7 43.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 698 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574G TYR* 3.4 39.6 + - - -
577G VAL* 3.7 40.4 - - + +
696G TYR* 4.4 20.1 + - + +
697G ALA* 1.3 74.7 - - - +
699G VAL* 1.3 63.0 + - - +
700G MET* 3.9 19.3 + - + +
708G ILE* 4.0 0.3 - - - -
709G GLY* 3.0 27.5 + - - +
711G PHE* 4.0 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 699 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577G VAL* 3.3 18.0 - - - +
668G ASN 4.5 5.8 - - - +
669G LEU* 3.8 40.4 - - + +
697G ALA 5.4 0.4 - - - +
698G LYS* 1.3 76.3 - - - +
700G MET* 1.3 62.0 + - - +
706G HIS* 4.0 20.6 - - + -
707G ARG 3.9 9.2 - - - +
708G ILE* 4.2 22.7 - - + +
728G TYR* 5.3 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 700 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574G TYR* 5.0 4.7 - - + -
577G VAL* 3.4 31.9 - - + +
578G ARG 4.0 7.6 - - - +
579G GLU* 4.3 6.7 - - + +
603G ASN* 3.8 20.6 - - - +
606G ILE* 3.9 23.3 - - + -
698G LYS* 4.0 33.4 - - + +
699G VAL* 1.3 83.1 - - - +
701G MET* 1.3 63.4 + - - +
702G VAL* 3.7 14.3 + - + +
706G HIS* 3.6 5.3 - - - -
707G ARG 3.2 28.1 + - - +
711G PHE* 4.1 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 701 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520G TYR* 3.9 13.2 - - + -
541G ASN* 5.2 5.4 - - + +
544G GLU* 4.6 5.6 - - - +
576G ALA 5.5 0.2 - - - +
577G VAL 3.1 8.6 + - - +
578G ARG* 3.3 41.9 - - + +
579G GLU 3.2 24.6 + - - +
700G MET* 1.3 69.3 - - - +
702G VAL* 1.3 61.4 + - - +
703G ASN 4.6 1.3 - - - +
704G GLY* 3.4 47.6 - - - +
705G ASP 3.6 2.9 - - - +
706G HIS* 3.3 42.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 702 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579G GLU* 3.6 27.8 - - + +
606G ILE* 4.2 16.4 - - + -
607G GLN* 3.8 41.7 - - + +
700G MET 3.8 12.1 - - - +
701G MET* 1.3 81.1 - - - +
703G ASN* 1.3 76.8 + - - +
704G GLY 3.4 0.4 - - - -
705G ASP* 2.7 27.7 + - - +
707G ARG* 4.1 16.3 + - + +
----------------------------------------------------------
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