Contacts of the helix formed by residues 321 - 329 (chain F) in PDB entry 4IGM
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 321 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F LYS* 3.5 28.7 - - + -
3F ILE* 3.8 18.8 - - + +
317F ASN 3.1 5.5 + - - +
319F LEU 3.3 2.2 - - - -
320F LYS* 1.3 82.1 - - + +
322F GLY* 1.3 68.3 + - - +
323F ASN 3.4 1.8 - - - -
324F ALA* 3.0 17.6 + - - +
325F LEU* 3.2 22.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 322 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317F ASN 2.8 19.4 + - - -
318F LYS* 3.8 10.3 - - - -
321F ALA* 1.3 73.3 - - - +
323F ASN* 1.3 62.8 + - - +
324F ALA 3.2 0.9 + - - -
325F LEU* 3.4 17.6 + - - +
326F ALA* 3.4 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 323 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263F TYR* 3.7 4.9 - - + -
283F LYS 2.7 25.1 + - - -
284F ASP* 2.8 34.8 + - - +
286F VAL 2.8 27.6 + - - +
287F ILE* 4.3 9.0 - - + -
318F LYS* 2.7 42.0 + - - +
319F LEU* 3.9 1.0 - - - +
322F GLY* 1.3 72.9 - - - -
324F ALA* 1.3 55.8 + - - +
326F ALA* 3.4 7.3 - - - +
327F PHE* 3.1 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 324 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F ILE* 3.9 29.6 - - + +
5F ILE* 4.7 6.7 - - + -
287F ILE* 3.5 30.6 - - + +
318F LYS 4.4 0.6 + - - -
319F LEU 5.9 0.2 - - - +
320F LYS 5.4 0.9 - - - +
321F ALA* 3.0 13.6 + - - +
323F ASN* 1.3 75.7 - - - +
325F LEU* 1.3 60.1 + - - +
327F PHE* 3.6 1.4 + - - +
328F LEU* 3.1 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 325 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F ILE* 3.7 24.5 - - + -
321F ALA* 3.2 23.8 + - + +
322F GLY* 3.4 9.4 + - - +
324F ALA* 1.3 75.2 - - - +
326F ALA* 1.3 55.3 + - - +
328F LEU* 4.8 1.8 - - + -
329F GLY* 2.8 13.3 + - - -
330F LEU* 2.8 68.2 + - + +
331F GLU 4.4 8.3 - - - +
332F ARG* 4.1 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 326 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219F LYS* 3.7 14.1 - - - -
263F TYR* 3.9 15.3 - - + +
284F ASP 5.7 0.9 - - - +
322F GLY 3.4 8.9 + - - +
323F ASN* 3.4 14.6 - - - +
325F LEU* 1.3 77.5 - - - +
327F PHE* 1.3 64.5 + - - +
329F GLY* 3.0 14.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 327 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F ILE* 3.9 16.2 - - + -
114F LEU* 5.4 2.5 - - + -
170F SER* 2.5 45.4 + - - -
171F LEU 3.6 16.2 - - - -
172F PHE* 4.4 6.7 - - + -
219F LYS* 3.3 26.0 - - + +
220F VAL 3.8 3.4 - - - -
221F CYS* 3.5 37.7 - - + -
263F TYR* 3.9 27.5 + + + -
287F ILE* 3.7 22.0 - - + -
323F ASN 3.1 13.8 + - - +
324F ALA 3.7 2.5 - - - +
325F LEU 3.5 0.2 - - - -
326F ALA* 1.3 78.7 - - - +
328F LEU* 1.3 77.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 328 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F ILE* 5.3 6.7 - - + -
5F ILE* 3.9 19.1 - - + -
70F VAL* 6.1 0.9 - - + -
72F ALA* 5.1 0.7 - - + -
112F VAL* 4.3 15.3 - - + -
114F LEU* 4.0 22.7 - - + -
139F PRO* 3.7 30.2 - - + +
168F LYS 5.4 2.6 - - - +
170F SER* 3.7 9.9 - - - +
219F LYS* 5.7 0.4 - - - -
324F ALA* 3.1 24.8 + - + +
325F LEU* 4.3 2.5 - - + +
327F PHE* 1.3 101.6 - - + +
329F GLY* 1.3 62.9 + - - +
330F LEU* 3.5 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 329 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219F LYS* 5.3 3.8 - - - +
325F LEU 2.8 9.8 + - - -
326F ALA* 3.0 11.0 + - - -
327F PHE 3.3 0.4 + - - -
328F LEU* 1.3 80.5 - - - +
330F LEU* 1.3 62.6 + - - +
331F GLU* 5.7 0.7 - - - +
----------------------------------------------------------
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