Contacts of the strand formed by residues 767 - 770 (chain C) in PDB entry 5NC5
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 ARG 767 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLN* 3.8 4.9 + - - +
67A GLN* 3.5 32.2 + - - +
818A ARG* 6.0 1.1 - - - +
821A GLY 5.4 5.3 + - - -
822A LEU* 5.7 4.9 - - - +
159C ALA 3.9 9.4 + - - -
160C ALA* 3.6 40.1 + - + +
164C ASP* 3.5 37.6 + - - +
181C GLN* 2.8 26.6 + - - -
763C ILE* 3.6 2.8 - - - +
764C ASP 2.9 32.9 + - - +
765C ARG 3.2 3.6 - - - +
766C GLY* 1.3 82.5 - - - +
768C VAL* 1.3 70.2 + - - +
769C LYS* 3.3 8.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 768 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASP 3.5 26.5 - - - +
63A GLN* 3.3 33.8 + - + +
64A VAL* 4.9 7.2 - - + -
67A GLN* 3.2 28.9 + - - +
181C GLN* 4.4 2.3 + - - +
761C ASP* 3.4 37.7 - - + +
762C PHE 3.4 6.1 - - - +
763C ILE* 4.0 12.3 - - + -
767C ARG* 1.3 78.1 + - - +
769C LYS* 1.3 65.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 769 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C ASP* 3.5 30.7 + - - +
160C ALA* 3.8 14.7 - - - +
181C GLN* 3.5 29.8 - - - +
182C TYR* 3.6 22.4 - - + +
761C ASP* 3.4 7.7 - - - +
762C PHE* 3.0 40.9 + - + +
764C ASP* 3.0 47.1 + - + +
765C ARG* 4.0 5.7 - - - +
767C ARG* 3.6 12.9 - - - +
768C VAL* 1.3 79.2 - - - +
770C LYS* 1.3 64.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 770 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLN* 5.9 1.2 + - - -
117A LEU* 6.2 1.6 - - - +
181C GLN* 5.5 1.8 - - - +
182C TYR 4.5 1.6 + - - -
183C ALA* 3.2 7.5 - - + -
184C MET 2.9 22.9 + - - -
273C GLU* 3.4 32.2 + - - +
758C TYR* 3.9 29.3 + - + +
760C ASN 3.9 4.0 - - - -
761C ASP* 4.3 4.2 + - - +
762C PHE* 3.3 5.5 - - - -
769C LYS* 1.3 79.2 - - - +
771C VAL* 1.3 62.8 + - - +
772C TYR* 3.3 37.2 - - + +
----------------------------------------------------------
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