Contacts of the helix formed by residues 274 - 279 (chain C) in PDB entry 3UDB
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 HIS 274 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C GLU* 3.4 30.1 - - + -
252C HIS* 3.0 33.2 + + - -
253C LEU* 3.6 30.3 + - + -
256C ARG* 5.5 0.4 - - + -
266C ILE* 4.6 9.9 - - + -
270C GLU 3.2 8.1 + - - +
271C ILE* 3.1 17.9 + - - +
272C ARG 3.5 0.2 - - - -
273C ASN* 1.3 78.4 - - - +
275C GLU* 1.3 83.0 + - + +
276C TRP* 3.0 19.7 + - + +
277C PHE* 2.8 17.5 + - + +
278C LEU* 3.0 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 275 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C GLU* 3.4 27.1 - - + +
273C ASN 3.6 2.6 + - - -
274C HIS* 1.3 80.3 + - + +
276C TRP* 1.3 61.0 + - - +
278C LEU* 3.4 17.9 + - + +
279C LYS* 3.4 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 276 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C GLU* 2.7 41.5 + - + -
117C ALA* 4.3 1.6 - - + -
118C ARG* 3.0 87.8 + - + +
121C PHE* 3.8 24.2 - + - -
207C LEU* 3.7 23.3 - - + -
211C LEU* 5.2 0.7 - - + -
247C SER* 3.7 2.9 - - - -
249C GLU* 4.1 11.8 - - + +
250C CYS* 3.2 38.8 - - + +
253C LEU* 3.6 22.4 - - + -
274C HIS* 3.0 21.1 + - + +
275C GLU* 1.3 77.2 - - - +
277C PHE* 1.3 62.6 + - - +
279C LYS* 3.8 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 277 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C ARG* 4.9 0.7 - - - +
121C PHE* 4.0 14.1 - + - -
122C GLN* 2.9 52.9 + - + +
125C ILE* 3.7 33.0 - - + -
253C LEU* 5.3 1.3 - - + +
271C ILE* 3.1 35.0 - - + +
272C ARG* 3.7 25.1 - - + -
274C HIS* 2.8 8.9 + - + +
276C TRP* 1.3 87.6 - - + +
278C LEU* 1.3 56.8 + - - +
279C LYS 3.4 0.2 - - - -
281C LEU* 3.6 27.4 - - + +
286C MET* 3.6 27.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 278 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ARG 3.4 21.3 - - - +
273C ASN* 3.4 32.1 - - - +
274C HIS 3.0 14.9 + - - +
275C GLU* 3.4 11.0 + - + +
276C TRP 3.3 0.2 - - - -
277C PHE* 1.3 77.4 - - - +
279C LYS* 1.3 64.2 + - - +
280C ASN 3.1 1.4 + - - -
281C LEU* 3.1 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 279 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C ASP* 4.1 6.9 + - - -
118C ARG* 3.2 47.2 - - - +
122C GLN* 3.2 13.2 + - - -
275C GLU 3.4 9.4 + - - +
276C TRP* 3.8 3.4 - - - +
277C PHE 3.4 0.2 - - - -
278C LEU* 1.3 73.5 - - - +
280C ASN* 1.3 93.3 + - - +
281C LEU 3.1 1.0 + - - -
----------------------------------------------------------
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