Contacts of the helix formed by residues 340 - 349 (chain B) in PDB entry 3IML
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 ARG 340 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 3.3 46.7 + - - +
117B ASP* 3.5 30.4 + - - -
309B ALA* 3.4 21.1 - - + +
310B GLU* 3.6 33.0 + - - +
338B ASP* 2.8 38.0 + - - +
339B LEU* 1.3 79.4 - - - +
341B PRO* 1.4 75.0 - - + +
342B LYS 3.5 0.4 - - - -
343B GLY* 2.9 5.2 + - - +
344B ILE* 2.9 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B GLN* 3.9 24.2 - - - +
120B ALA* 3.8 31.2 - - + +
271B PRO 5.0 0.6 - - - +
272B SER* 4.9 10.3 - - - +
274B VAL* 3.9 21.5 - - + -
277B SER* 4.7 4.8 + - - +
304B TYR* 4.2 2.7 - - + -
309B ALA 3.2 16.6 - - - +
339B LEU 3.6 2.6 - - - +
340B ARG* 1.4 81.9 - - + +
342B LYS* 1.3 61.9 + - + +
344B ILE* 3.1 24.1 + - + +
345B ILE* 3.3 18.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TYR* 5.8 6.5 - - - -
115B ASN* 3.4 54.4 - - - +
116B LEU* 3.8 19.1 + - + +
118B GLN* 3.6 36.2 + - + +
340B ARG* 3.5 1.0 - - - +
341B PRO* 1.3 77.6 - - + +
343B GLY* 1.3 63.5 + - - +
345B ILE* 3.7 24.7 - - + +
346B GLN* 3.3 22.2 + - - +
351B LEU* 6.1 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 4.0 11.1 + - - +
338B ASP* 3.5 35.1 - - - +
340B ARG* 2.9 14.2 + - - +
342B LYS* 1.3 78.9 - - - +
344B ILE* 1.3 56.1 + - - +
346B GLN* 3.3 6.8 + - - +
347B MET* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B VAL* 5.5 0.4 - - + -
277B SER* 3.4 46.7 - - - +
278B ALA* 4.1 4.5 - - + -
281B ALA* 3.8 17.3 - - + -
304B TYR* 3.6 12.1 - - + +
338B ASP 3.4 15.3 - - - +
339B LEU* 3.5 23.1 - - + +
340B ARG 2.9 16.1 + - - +
341B PRO* 3.1 6.7 + - + +
343B GLY* 1.3 72.5 - - - +
345B ILE* 1.3 67.5 + - - +
347B MET* 3.6 5.3 - - + +
348B LEU* 3.0 41.7 + - + +
350B LEU* 4.1 2.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ARG* 6.1 0.9 - - - +
271B PRO* 3.5 42.6 - - + +
272B SER* 4.1 11.7 - - - +
277B SER* 5.2 0.4 - - - -
341B PRO 3.3 12.6 + - - +
342B LYS* 3.7 29.2 - - + +
344B ILE* 1.3 77.7 - - - +
346B GLN* 1.3 54.9 + - - +
349B ASP* 2.7 31.6 + - - -
350B LEU* 3.2 20.5 + - + +
351B LEU* 3.8 38.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 4.1 30.5 - - + +
338B ASP* 5.5 1.0 + - - +
342B LYS 3.3 11.8 + - - +
343B GLY 3.7 8.1 + - - +
344B ILE 3.2 0.4 - - - -
345B ILE* 1.3 81.8 - - - +
347B MET* 1.3 61.0 + - - +
348B LEU 3.6 0.2 + - - -
349B ASP* 3.7 8.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ALA* 4.3 21.1 - - + -
284B TYR* 3.8 42.0 + - + +
285B VAL* 5.6 0.2 - - + -
337B PHE* 3.9 20.6 - - + -
338B ASP* 3.7 35.0 - - + +
339B LEU* 5.2 1.1 - - + -
343B GLY 2.9 16.0 + - - +
344B ILE* 3.2 9.1 + - + +
346B GLN* 1.3 79.8 - - - +
348B LEU* 1.3 62.2 - - + +
349B ASP 3.5 0.6 + - - -
372B SER* 5.6 0.2 - - - -
378B LYS* 4.3 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B TYR* 4.3 12.6 - - + -
281B ALA* 4.0 24.2 - - + +
284B TYR* 3.8 25.8 - - + -
344B ILE* 3.0 32.4 + - + +
347B MET* 1.3 79.7 - - + +
349B ASP* 1.3 72.9 - - - +
350B LEU* 3.4 16.8 + - + +
352B ARG* 3.2 3.6 + - - -
372B SER* 2.7 61.3 + - - +
373B TRP* 3.6 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B ILE 2.7 17.4 + - - -
346B GLN* 3.7 6.8 + - - +
347B MET 3.5 2.6 - - - -
348B LEU* 1.3 72.7 - - - +
350B LEU* 1.3 55.8 + - - +
351B LEU* 3.4 5.9 + - - +
352B ARG* 2.7 63.2 + - - +
372B SER* 5.6 0.4 - - - -
----------------------------------------------------------
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