Contacts of the strand formed by residues 278 - 284 (chain F) in PDB entry 1PZN
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 ALA 278 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F ILE* 4.5 5.8 - - + -
128F ILE* 4.2 13.7 - - + -
129F GLU 3.3 26.9 - - - +
130F THR* 3.6 10.4 - - + +
132F ALA 4.1 0.2 - - - -
233F LYS 2.9 15.6 + - - +
234F LEU* 3.3 15.6 - - + +
235F LEU 2.8 25.5 + - - -
277F ILE* 1.3 74.9 - - - +
279F VAL* 1.3 59.0 + - - +
280F PHE 4.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 279 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128F ILE* 5.4 1.0 - - - +
129F GLU 4.7 0.2 + - - -
132F ALA 3.0 14.4 + - - +
133F ILE* 3.3 20.5 - - + -
134F THR* 2.7 34.8 + - - +
235F LEU* 3.3 23.8 - - + +
268F LEU* 4.1 29.4 - - + +
271F LEU* 5.4 1.6 - - + -
272F ALA* 3.8 26.7 - - + +
277F ILE* 4.4 3.1 - - + -
278F ALA* 1.3 74.1 - - - +
280F PHE* 1.3 56.6 + - - +
281F VAL* 4.0 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 280 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128F ILE* 4.1 18.2 - - + -
134F THR* 3.4 20.6 - - + -
136F VAL* 3.5 37.7 - - + -
144F LYS 4.0 3.1 - - - -
147F LEU* 3.8 27.4 - - + -
148F ALA* 3.9 34.3 - - + -
151F LEU* 3.8 20.4 - - + -
234F LEU* 4.2 17.5 - - + -
235F LEU 2.8 11.4 + - - +
236F ILE* 3.2 12.4 - - + -
237F VAL 2.9 24.6 + - - +
278F ALA 3.9 0.8 + - - -
279F VAL* 1.3 71.6 - - - +
281F VAL* 1.3 64.5 + - - +
282F THR* 4.2 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 281 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F ILE* 4.1 11.7 - - + -
134F THR 2.9 16.5 + - - +
135F GLU* 3.4 19.9 - - + -
136F VAL* 2.9 28.5 + - - +
237F VAL* 3.3 25.6 - - + +
240F LEU* 3.8 27.8 - - + -
268F LEU* 4.2 11.4 - - + -
279F VAL* 4.0 18.6 - - + -
280F PHE* 1.3 81.2 - - - +
282F THR* 1.3 62.4 + - - +
306F ALA* 4.7 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 282 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F VAL* 3.3 23.8 - - + -
144F LYS* 3.8 33.7 - - + +
148F ALA* 5.1 0.7 - - + -
237F VAL 3.1 4.6 + - - +
238F ASP* 2.4 49.7 + - + +
239F SER* 3.3 8.1 + - - -
240F LEU* 3.0 31.4 + - - +
241F THR 4.0 0.3 + - - -
280F PHE* 4.2 7.6 - - + -
281F VAL* 1.3 75.5 - - - +
283F ASN* 1.3 61.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 283 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135F GLU* 3.3 28.5 - - + +
136F VAL 3.0 6.8 + - - +
137F PHE* 3.0 30.7 - - + +
138F GLY 3.3 2.8 + - - -
144F LYS* 3.5 3.3 - - - +
239F SER* 4.4 0.4 - - - -
240F LEU* 5.7 1.1 - - + -
241F THR* 2.5 43.4 + - + +
245F ARG* 3.7 7.5 - - - +
282F THR* 1.3 77.0 - - - +
284F GLN* 1.3 75.0 + - - +
285F VAL* 5.5 2.9 - - - +
304F ILE 3.4 21.5 - - - +
305F LEU* 4.0 0.7 - - - -
312F ARG* 4.8 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 284 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138F GLY 3.5 9.4 - - - +
140F PHE* 3.1 45.0 - - - +
144F LYS* 3.6 12.1 - - - +
174F GLU* 3.7 23.9 + - - +
239F SER* 4.5 6.8 + - - +
241F THR* 4.1 2.2 + - - -
245F ARG* 3.1 23.5 + - - +
282F THR 4.3 0.2 - - - -
283F ASN* 1.3 87.1 + - - +
285F VAL* 1.3 64.7 + - - +
286F GLN* 4.2 6.5 - - + +
----------------------------------------------------------
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