Contacts of the strand formed by residues 705 - 712 (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 ASP 705 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288G ARG* 3.1 13.7 + - - -
289G CYS* 6.0 0.2 - - - +
296G LEU* 3.9 17.1 - - + +
297G HIS* 3.1 33.1 + - - -
519G ASN* 5.1 2.2 - - - +
700G MET 3.7 0.2 - - - +
701G MET* 3.6 3.0 - - - +
702G VAL* 2.7 41.2 + - - +
703G ASN* 3.2 10.9 - - - +
704G GLY* 1.3 78.4 - - - +
706G HIS* 1.3 60.0 - - - +
707G ARG* 3.8 19.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 706 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119G ASN* 4.6 4.7 + - - -
517G VAL* 3.4 22.4 - - + +
518G TYR 3.6 24.0 - - - -
519G ASN* 3.1 27.8 + - - -
520G TYR 4.1 0.9 - - - -
541G ASN* 4.8 1.9 + - - -
645G ILE* 5.4 3.1 - - - +
669G LEU* 3.6 40.2 - - + +
670G ASN* 3.3 9.7 + - + +
699G VAL* 4.0 14.4 - - + -
700G MET 3.6 3.1 - - - -
701G MET* 3.3 40.8 - - + +
705G ASP* 1.3 74.6 - - - +
707G ARG* 1.3 64.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 707 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G GLN 4.2 4.2 + - - -
118G GLN* 3.9 29.5 - - - +
119G ASN* 4.9 6.6 - - - +
296G LEU* 6.5 0.7 - - - -
606G ILE* 3.3 42.8 + - + +
607G GLN* 3.6 19.8 + - - +
609G GLY* 6.0 0.6 - - - -
640G GLU* 2.9 42.2 + - - +
669G LEU* 4.1 1.7 - - - +
699G VAL* 4.1 2.9 - - - +
700G MET* 3.2 29.3 + - - +
702G VAL* 4.1 20.6 + - + +
705G ASP* 4.2 20.3 + - + +
706G HIS* 1.3 80.8 - - - +
708G ILE* 1.3 64.1 + - - +
709G GLY 3.6 1.2 + - - -
627I ILE* 6.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 708 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119G ASN* 5.3 1.0 - - - +
606G ILE* 5.2 0.4 - - - -
640G GLU* 2.9 28.4 + - - +
641G TYR* 2.9 43.9 + - + +
667G PHE* 4.1 24.7 - - + +
668G ASN 3.9 21.5 - - - +
669G LEU* 3.8 19.7 - - + -
675G VAL* 4.4 8.5 - - + -
697G ALA* 3.9 22.7 - - + -
698G LYS 4.0 4.9 - - - +
699G VAL* 4.2 11.7 - - + +
707G ARG* 1.3 71.6 - - - +
709G GLY* 1.3 62.0 + - - +
710G ILE* 3.9 1.3 - - + -
728G TYR* 4.3 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 709 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606G ILE* 4.5 7.6 - - - -
637G PHE* 4.4 7.4 - - - -
639G SER 3.9 3.8 - - - -
697G ALA* 3.2 15.2 - - - +
698G LYS 3.0 18.8 + - - -
707G ARG 3.6 1.6 + - - -
708G ILE* 1.3 73.2 - - - +
710G ILE* 1.3 62.8 + - - -
711G PHE* 3.2 30.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 710 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637G PHE* 4.0 1.4 - - - -
638G ILE* 3.0 31.5 + - + +
639G SER 2.7 24.7 + - - +
641G TYR* 3.7 39.9 - - + +
684G ILE* 4.1 29.8 - - + -
695G CYS* 4.1 18.2 - - + -
696G TYR 3.6 9.9 - - - +
697G ALA* 3.2 23.6 - - + -
708G ILE* 3.9 2.5 - - + -
709G GLY* 1.3 71.9 - - - -
711G PHE* 1.3 61.8 + - - +
724G PHE* 4.4 18.6 - - + -
728G TYR* 4.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 711 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579G GLU* 5.7 1.6 - - - -
606G ILE* 4.9 2.2 - - + -
635G ASN 3.6 14.8 - - - +
636G GLU 3.1 19.3 - - - +
637G PHE* 3.4 38.4 - + + -
638G ILE* 4.0 7.0 - - - -
695G CYS* 3.4 5.5 - - - +
696G TYR* 3.1 62.2 + + + +
698G LYS* 4.0 22.0 - - + -
700G MET* 4.1 22.7 - - - -
709G GLY* 3.2 27.6 - - - -
710G ILE* 1.3 71.9 - - - +
712G ALA* 1.3 61.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 712 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632G VAL* 4.5 5.4 - - + -
633G GLN 3.9 16.4 - - - +
634G LYS* 3.8 1.6 - - - +
635G ASN* 2.8 32.1 + - - +
636G GLU 3.4 6.3 + - - +
638G ILE* 4.0 8.7 - - + +
694G ASN 3.7 4.7 - - - -
695G CYS* 4.3 0.4 - - - +
696G TYR* 4.1 2.2 - - - -
711G PHE* 1.3 75.2 - - - +
713G LYS* 1.3 59.6 + - - +
714G ARG 3.3 19.3 - - - +
716G ILE* 3.9 20.0 - - + -
----------------------------------------------------------
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