Contacts of the helix formed by residues 313 - 321 (chain B) in PDB entry 3LX9
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 ASP 313 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B ALA 3.0 12.2 + - - +
310B LEU* 3.2 21.3 + - + +
311B LEU 3.4 0.8 - - - -
312B GLN* 1.3 73.0 - - - +
314B LYS* 1.3 58.7 + - - +
315B ASP* 3.2 22.3 + - - +
316B VAL* 3.3 22.7 + - + +
317B ILE* 2.9 30.7 + - - +
387B LEU* 4.4 5.1 - - - +
388B LEU* 3.8 20.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B GLN 2.9 10.0 + - - +
313B ASP* 1.3 73.8 + - - +
315B ASP* 1.3 76.8 + - - +
317B ILE* 3.9 8.2 - - - +
318B ALA* 2.9 30.0 + - - +
391B LYS* 5.1 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ASP* 3.2 9.5 + - - +
314B LYS* 1.3 95.3 - - - +
316B VAL* 1.3 61.4 + - - +
318B ALA* 3.5 8.5 - - - +
319B ILE* 3.3 25.1 + - - +
387B LEU* 3.9 24.8 - - + +
391B LYS* 2.7 45.3 + - - +
416B GLN* 4.5 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B MET* 3.9 31.6 - - + +
288B ALA* 3.7 22.7 - - + +
313B ASP* 3.3 30.3 + - + +
315B ASP* 1.3 75.6 - - - +
317B ILE* 1.3 64.5 + - - +
319B ILE* 3.0 19.2 + - - +
320B ASN* 3.0 10.6 + - + +
387B LEU* 4.6 7.6 - - + -
388B LEU* 3.7 25.8 - - + -
414B LEU* 4.0 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B MET* 3.9 19.7 - - + -
84B ALA* 3.7 32.5 - - + +
86B TYR* 4.6 0.4 - - - +
284B MET* 4.1 11.2 - - + -
294B LEU* 4.7 3.8 - - + -
311B LEU 3.4 25.6 - - - +
312B GLN* 3.8 14.6 - - - +
313B ASP 2.9 20.8 + - - +
314B LYS* 3.9 6.7 - - - +
316B VAL* 1.3 75.6 - - - +
318B ALA* 1.3 52.9 + - - +
320B ASN* 3.1 8.4 + - - +
321B GLN* 2.7 51.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B LYS 2.9 20.7 + - - +
315B ASP* 3.5 10.1 - - - +
317B ILE* 1.3 76.8 - - - +
319B ILE* 1.3 57.6 + - + +
321B GLN* 3.6 6.0 - - - +
322B ASP* 3.0 28.8 + - - +
416B GLN* 6.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ALA* 3.9 23.3 - - + +
289B ILE* 4.6 0.9 - - + +
315B ASP 3.3 5.8 + - - +
316B VAL* 3.0 9.6 + - - +
318B ALA* 1.3 75.0 - - - +
320B ASN* 1.3 63.8 + - - +
322B ASP* 3.2 16.2 + - - +
342B ARG* 2.8 19.8 + - - -
344B LEU* 4.1 15.3 - - + -
350B ALA* 3.7 33.7 - - + -
387B LEU* 3.4 32.1 - - + -
414B LEU* 4.1 15.9 - - + -
415B LEU 5.0 0.2 - - - +
416B GLN* 3.5 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PRO* 3.4 17.2 - - - +
287B TRP 3.1 21.4 + - - -
288B ALA* 3.7 12.0 - - + +
291B ALA 4.0 0.4 - - - -
292B ALA 2.7 31.6 + - - +
294B LEU* 3.3 33.3 - - + +
316B VAL 3.0 9.4 + - - +
317B ILE 3.1 7.6 + - - +
319B ILE* 1.3 76.5 - - - +
321B GLN* 1.3 85.6 + - - +
322B ASP 3.4 2.3 + - - -
342B ARG* 3.3 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B THR* 2.6 42.2 + - + +
40B PRO* 2.9 28.3 + - - +
42B MET* 3.6 29.1 - - - +
317B ILE* 2.7 29.2 + - + +
318B ALA* 3.6 6.3 - - - +
320B ASN* 1.3 94.3 + - - +
322B ASP* 1.3 67.5 + - - +
323B PRO* 3.2 4.9 - - - +
----------------------------------------------------------
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