Contacts of the helix formed by residues 321 - 329 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E LYS* 3.6 25.1 - - + -
3E ILE* 4.1 18.2 - - + -
317E ASN* 2.9 6.8 + - + +
318E LYS 3.4 1.0 + - - -
319E LEU 3.5 0.2 - - - -
320E LYS* 1.3 80.1 - - + +
322E GLY* 1.3 72.5 + - - +
323E ASN 3.4 2.0 - - - -
324E ALA* 3.1 7.9 + - - +
325E LEU* 3.1 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 322 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317E ASN 2.9 17.5 + - - -
318E LYS* 3.6 11.7 - - - -
321E ALA* 1.3 75.3 - - - +
323E ASN* 1.3 62.7 + - - +
325E LEU* 3.4 10.6 - - - +
326E ALA* 3.1 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 323 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263E TYR* 3.6 6.0 - - + -
283E LYS 3.1 20.8 + - - -
284E ASP* 2.9 35.3 + - - +
286E VAL 2.6 31.0 + - - +
287E ILE* 4.0 9.0 - - + -
318E LYS* 2.9 35.7 + - - +
319E LEU 3.6 0.8 - - - +
322E GLY* 1.3 68.6 - - - -
324E ALA* 1.3 60.6 + - - +
326E ALA* 3.4 6.6 + - - +
327E PHE* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 324 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E ILE* 3.5 32.3 - - + +
5E ILE* 4.4 7.9 - - + -
287E ILE* 3.4 28.8 - - + +
318E LYS 4.6 0.4 + - - -
320E LYS 5.9 0.2 - - - -
321E ALA* 3.1 9.2 + - - +
323E ASN* 1.3 75.7 - - - +
325E LEU* 1.3 57.5 + - - +
327E PHE* 2.9 7.3 + - - +
328E LEU* 2.8 40.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 325 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E ILE* 3.7 22.4 - - + -
321E ALA* 3.1 20.1 + - + +
322E GLY* 3.4 10.5 - - - +
324E ALA* 1.3 76.1 - - - +
326E ALA* 1.3 58.3 + - - +
328E LEU* 3.7 1.7 - - - -
329E GLY* 3.0 7.4 + - - -
330E LEU* 2.8 66.2 + - + +
331E GLU 4.6 6.1 - - - +
332E ARG* 3.6 37.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 326 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219E LYS* 3.4 17.9 - - - -
263E TYR* 4.1 11.4 - - + +
284E ASP 6.1 0.2 - - - +
322E GLY 3.1 11.4 + - - +
323E ASN* 3.8 10.8 - - - +
324E ALA 3.2 0.2 - - - -
325E LEU* 1.3 79.1 - - - +
327E PHE* 1.3 62.1 + - - +
329E GLY* 3.4 9.8 + - - -
330E LEU 5.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 327 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E ILE* 4.1 15.3 - - + -
114E LEU* 5.5 2.7 - - + -
170E SER* 2.8 42.3 + - - -
171E LEU 3.5 21.3 - - - -
172E PHE* 4.3 7.4 - - + -
219E LYS* 3.7 19.7 - - + +
220E VAL 3.8 4.7 - - - -
221E CYS* 3.6 30.5 - - + -
263E TYR* 3.9 30.2 + + + -
287E ILE* 3.8 20.2 - - + -
323E ASN 2.9 17.9 + - - +
324E ALA 2.9 2.4 + - - +
326E ALA* 1.3 76.8 - - - +
328E LEU* 1.3 82.2 + - + +
329E GLY 3.1 5.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 328 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E ILE* 5.7 4.7 - - + -
5E ILE* 3.7 23.3 - - + -
70E VAL* 6.1 1.8 - - + -
72E ALA* 5.0 0.7 - - + -
112E VAL* 3.9 22.9 - - + -
114E LEU* 4.1 15.0 - - + -
139E PRO* 3.6 36.6 - - + +
168E LYS 5.7 0.9 - - - +
170E SER* 4.4 9.8 + - - -
324E ALA* 2.8 22.8 + - + +
325E LEU* 4.1 1.3 - - + +
327E PHE* 1.3 94.4 - - + +
329E GLY* 1.3 62.8 + - - +
330E LEU* 3.4 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 329 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168E LYS* 6.0 3.4 - - - -
219E LYS* 6.1 1.6 - - - -
325E LEU 3.0 6.5 + - - -
326E ALA* 3.4 7.5 + - - -
327E PHE 3.1 6.5 + - - -
328E LEU* 1.3 77.7 - - - +
330E LEU* 1.3 60.5 + - - +
----------------------------------------------------------
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