Contacts of the strand formed by residues 717 - 723 (chain C) in PDB entry 5UH8
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 LYS 717 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618C LEU* 3.6 11.9 - - + +
620C ARG* 3.3 32.0 + - - +
621C SER* 5.1 0.2 - - - -
622C GLU* 3.4 37.3 + - + +
716C GLY* 1.3 81.3 - - - +
718C ASN* 1.3 63.5 + - - +
719C LEU* 3.6 22.3 + - + +
745C ASP 4.5 1.8 + - - -
746C VAL* 2.8 56.7 + - + +
747C LEU* 4.5 4.0 - - + -
1029C TYR* 3.1 10.4 - - - -
1030C ILE* 3.0 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 718 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622C GLU* 3.6 20.3 + - - +
623C ALA 2.6 26.9 + - - -
624C PRO* 3.4 4.0 - - - +
625C LEU* 2.5 55.0 + - + +
717C LYS* 1.3 74.8 - - - +
719C LEU* 1.3 65.4 + - - +
740C ARG* 5.3 1.7 + - - -
914C ASP* 4.3 2.8 - - - +
1027C TYR* 4.1 12.4 - - + +
1028C MET 4.0 4.6 - - - -
1029C TYR* 3.7 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 719 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717C LYS* 3.6 25.6 - - + +
718C ASN* 1.3 80.9 - - - +
720C LEU* 1.3 61.6 + - - +
721C VAL* 3.4 1.2 + - - +
737C LEU* 5.0 1.6 - - + -
740C ARG* 5.0 0.9 - - - +
741C LEU* 4.3 17.9 - - + -
746C VAL* 4.3 14.1 - - + -
747C LEU* 4.5 11.2 - - + -
914C ASP* 3.5 17.3 - - + +
915C ILE* 3.9 27.8 - - + -
1027C TYR* 3.1 12.6 - - - -
1028C MET 3.1 37.0 + - - +
1030C ILE* 3.7 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 720 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719C LEU* 1.3 69.5 - - - +
721C VAL* 1.3 59.3 + - - +
907C LEU* 4.8 6.1 - - + -
911C THR* 4.6 16.6 - - - +
912C PRO 3.8 9.4 - - - +
913C VAL* 3.6 30.6 - - + +
914C ASP* 2.7 48.5 + - - +
915C ILE* 3.0 7.3 + - - -
938C TRP* 4.7 5.4 - - + -
1025C VAL* 3.8 22.2 - - + -
1026C GLY* 3.4 16.8 - - - +
1027C TYR* 3.7 34.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 721 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719C LEU 3.4 3.9 + - - +
720C LEU* 1.3 75.8 - - - +
722C ALA* 1.3 70.1 + - - +
723C ILE* 4.1 14.8 - - + -
913C VAL* 4.6 0.8 - - - +
915C ILE* 3.3 25.4 - - + +
917C LEU* 3.8 31.2 - - + -
934C THR* 3.7 29.6 - - + +
1025C VAL* 3.6 9.4 - - - +
1026C GLY 2.6 38.7 + - - +
1027C TYR 4.5 0.2 - - - +
1028C MET* 4.6 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 722 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721C VAL* 1.3 76.6 - - - +
723C ILE* 1.3 62.5 + - - +
724C MET* 3.2 8.8 + - + -
905C PRO* 5.6 0.7 - - + -
913C VAL* 4.1 19.5 - - + -
915C ILE 3.0 10.1 + - - +
916C ILE* 3.7 12.8 - - + +
917C LEU 3.3 20.1 + - - -
1010C LEU* 4.0 26.7 - - + -
1023C VAL* 4.5 2.0 - - + -
1024C THR 3.6 5.6 - - - -
1025C VAL* 4.4 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 723 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721C VAL* 4.1 24.7 - - + -
722C ALA* 1.3 72.1 - - - +
724C MET* 1.3 62.6 + - - +
917C LEU* 4.0 15.3 - - + +
918C ASN 5.1 0.4 - - - -
919C THR* 3.2 30.8 + - + +
922C VAL* 5.0 6.5 - - + -
931C ILE* 4.4 19.1 - - + -
934C THR* 5.0 4.5 - - + +
1023C VAL* 3.5 3.3 - - - +
1024C THR* 3.0 41.4 + - + +
1028C MET* 5.1 1.8 - - + -
730D THR* 3.2 19.0 + - + +
731D VAL* 4.2 22.7 - - + +
----------------------------------------------------------
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