Contacts of the strand formed by residues 771 - 775 (chain B) 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 VAL 771 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B MET* 3.4 16.8 - - + +
186B ILE* 4.6 10.1 - - + -
207B ILE* 4.2 22.4 - - + -
246B PHE* 3.6 31.9 - - + -
758B TYR* 3.6 7.1 - - - -
759B VAL* 3.0 30.5 + - + -
760B ASN* 2.8 29.9 + - - +
761B ASP 4.3 2.7 - - - -
762B PHE* 4.1 6.7 - - + -
770B LYS* 1.3 75.8 - - - +
772B TYR* 1.3 68.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 772 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PRO* 5.3 8.7 - - + +
125B GLN* 3.5 21.1 + - - -
183B ALA* 4.1 12.8 - - + -
184B MET 2.9 7.8 + - - +
185B ARG* 3.6 38.0 + - - +
186B ILE* 2.9 29.6 + - - +
273B GLU* 4.1 32.3 + - + +
756B GLY* 5.1 2.5 - - - -
757B SER* 3.4 9.0 - - - -
758B TYR* 3.4 35.9 - - + -
770B LYS* 3.7 29.1 - - + +
771B VAL* 1.3 79.7 - - - +
773B VAL* 1.4 60.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 773 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ARG* 5.0 0.2 - - - -
186B ILE* 3.3 25.4 - - + +
188B MET* 4.2 15.0 - - + -
200B PRO* 5.4 0.4 - - + +
203B VAL* 4.2 10.5 - - + -
204B ILE* 4.0 18.8 - - + -
207B ILE* 4.1 20.0 - - + -
752B ALA* 3.6 25.1 - - + +
756B GLY* 3.2 1.2 - - - -
757B SER* 2.9 40.7 + - - +
759B VAL* 4.3 8.2 - - + +
771B VAL* 5.7 0.2 - - + -
772B TYR* 1.4 74.5 - - - +
774B MET* 1.3 63.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 774 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A GLY* 5.5 0.9 - - - -
222A THR 3.8 18.8 - - - +
223A PRO* 5.1 0.4 - - - -
185B ARG* 3.7 24.9 - - - +
186B ILE 3.0 8.6 + - - +
187B TRP* 3.2 15.9 - - + -
188B MET* 2.8 27.6 + - - -
752B ALA 3.3 7.9 - - - -
753B ALA 3.5 9.0 - - - +
754B TRP 3.7 20.2 - - - +
755B GLY 4.0 9.4 - - - +
756B GLY* 3.8 14.1 - - - -
773B VAL* 1.3 78.2 - - - +
775B SER* 1.3 72.8 + - - +
780B ARG* 3.6 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 775 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B TRP* 3.6 8.7 - - - -
188B MET* 3.6 11.9 + - - +
753B ALA* 2.9 25.1 + - - +
774B MET* 1.3 75.8 - - - +
776B GLU* 1.3 79.1 + - - +
777B ALA 3.4 0.3 + - - -
779B TYR* 3.6 9.4 - - - +
780B ARG* 2.8 26.2 + - - -
789B TRP* 3.2 33.7 - - - -
----------------------------------------------------------
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