Contacts of the helix formed by residues 371 - 376 (chain F) in PDB entry 2POZ
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 ILE 371 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345F GLU* 3.8 18.8 - - + +
346F VAL 2.8 11.8 + - - +
347F LEU 3.3 31.6 - - - +
348F GLU* 3.4 31.4 - - - +
370F LEU* 1.3 71.6 - - - +
372F LYS* 1.3 65.2 + - - +
373F ARG* 4.3 8.1 - - + +
374F ASN* 3.0 43.4 + - + +
375F ILE* 3.3 13.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 372 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F ASN* 4.8 0.8 + - - -
11F TYR* 2.9 29.9 + - - -
24F GLU* 2.5 35.3 + - - +
370F LEU* 3.3 16.0 + - + +
371F ILE* 1.3 71.7 - - - +
373F ARG* 1.3 58.7 + - - +
374F ASN 3.0 0.2 + - - -
375F ILE* 3.1 13.1 + - + +
376F GLU* 2.8 50.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 373 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371F ILE* 3.3 7.7 - - + +
372F LYS* 1.3 79.0 - - - +
374F ASN* 1.3 74.4 + - - +
376F GLU* 4.4 4.2 - - - +
377F PRO* 3.2 27.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 374 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344F VAL* 3.7 20.6 - - + +
345F GLU* 2.8 38.2 + - - +
371F ILE* 3.0 31.3 + - + +
373F ARG* 1.3 101.5 + - - +
375F ILE* 1.3 61.9 + - + +
377F PRO* 3.6 7.6 - - - +
378F TYR* 3.8 10.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 375 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F TYR* 3.2 51.7 - - + +
13F LEU* 4.4 7.9 - - + -
22F LEU* 4.1 14.4 - - + -
346F VAL* 3.9 33.0 - - + +
370F LEU* 4.2 25.6 - - + -
371F ILE 3.3 10.5 + - - +
372F LYS* 3.1 20.8 + - + +
374F ASN* 1.3 78.6 - - + +
376F GLU* 1.3 70.1 + - - +
377F PRO* 3.2 3.1 - - - -
378F TYR* 2.9 20.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 376 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F ASN* 5.3 1.7 - - - +
11F TYR* 3.8 19.5 + - - -
372F LYS* 2.8 34.6 + - + +
373F ARG* 4.4 4.3 - - - +
375F ILE* 1.3 77.9 - - - +
377F PRO* 1.3 65.7 - - + +
378F TYR 3.1 1.4 + - - -
379F LEU* 3.1 36.9 + - - +
----------------------------------------------------------
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