Contacts of the helix formed by residues 337 - 347 (chain B) in PDB entry 3LUE
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 TYR 337 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B MET* 5.5 0.3 - - - +
18B LYS* 3.9 21.1 - - + +
26B ALA* 5.6 4.0 - - + -
27B PRO* 4.0 33.4 - - + -
30B VAL* 3.4 23.1 - - + +
334B GLU* 2.8 4.7 + - + +
336B LYS* 1.3 120.5 + - + +
338B SER* 1.3 61.5 + - - -
339B VAL* 3.4 2.5 - - - -
340B TRP* 3.1 14.6 + - + -
341B ILE* 3.1 32.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LEU 3.9 2.4 - - - +
141B SER* 3.6 30.3 + - - +
144B ALA* 4.1 7.0 - - - +
300B SER* 5.0 1.7 - - - -
332B PRO* 5.2 5.5 - - - +
334B GLU 3.7 12.2 + - - -
335B ARG* 4.0 18.9 - - - +
336B LYS 3.7 1.8 + - - -
337B TYR* 1.3 72.7 - - - +
339B VAL* 1.3 64.5 + - - +
340B TRP 3.1 0.2 + - - -
341B ILE* 3.1 3.7 + - - +
342B GLY* 3.0 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ASP* 3.4 34.3 - - - +
106B THR* 4.0 8.7 - - + -
137B GLN* 3.4 45.1 - - + +
140B LEU* 3.3 23.0 - - + +
141B SER* 3.2 23.1 - - - +
154B ASP* 4.4 2.0 - - - +
301B GLY* 5.0 13.2 - - - +
335B ARG 5.4 1.1 - - - +
336B LYS 5.4 0.4 + - - -
337B TYR 3.4 1.2 - - - -
338B SER* 1.3 73.6 - - - +
340B TRP* 1.3 63.2 + - - +
342B GLY 3.5 0.2 + - - -
343B GLY 3.4 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 3.2 36.2 + - + +
11B ASP* 4.1 11.7 + - + +
18B LYS* 3.3 43.7 - - + -
19B ALA 3.7 0.6 - - - -
20B GLY* 3.4 33.5 - - - +
21B PHE 3.8 11.2 - - - -
24B ASP* 3.2 28.9 - - + -
25B ASP 3.8 1.6 - - - -
26B ALA* 3.4 24.2 - - - -
27B PRO* 3.4 26.7 - - + -
337B TYR* 3.1 10.2 + - - +
339B VAL* 1.3 80.8 - - - +
341B ILE* 1.3 62.6 + - + +
343B GLY* 3.3 0.7 + - - -
344B SER* 3.0 38.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ASP 4.4 8.3 - - - +
25B ASP* 3.2 29.8 - - - +
26B ALA* 4.8 1.1 - - + -
27B PRO* 5.1 1.1 - - + -
144B ALA* 4.0 7.4 - - + -
337B TYR* 3.1 43.5 + - + +
338B SER* 4.3 3.1 - - - +
340B TRP* 1.3 86.3 - - + +
342B GLY* 1.3 61.3 + - - +
343B GLY 3.3 0.2 - - - -
344B SER* 4.0 2.9 - - - -
345B ILE* 3.2 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LEU* 3.1 33.1 - - - +
143B TYR* 4.6 6.5 - - - +
144B ALA* 3.4 13.8 - - - +
338B SER 3.0 10.5 + - - -
341B ILE* 1.3 79.1 - - - +
343B GLY* 1.3 54.6 + - - +
345B ILE* 3.8 3.9 - - - +
346B LEU* 3.2 27.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
9B VAL* 3.8 14.4 - - - -
104B LEU* 4.1 6.7 - - - +
140B LEU* 3.6 21.6 - - - +
339B VAL 3.4 5.9 + - - -
340B TRP 3.3 5.2 + - - -
342B GLY* 1.3 74.3 - - - +
344B SER* 1.3 59.1 + - - +
346B LEU* 3.3 3.5 + - - -
347B ALA* 2.8 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 3.4 14.8 - - - +
22B ALA* 3.7 5.1 - - - +
23B GLY* 3.1 10.9 + - - -
24B ASP 2.7 41.2 + - - -
340B TRP* 3.0 32.4 + - - -
341B ILE 3.9 5.4 - - - -
343B GLY* 1.3 74.0 - - - +
345B ILE* 1.3 50.4 + - - +
348B SER* 2.8 24.4 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
143B TYR* 4.0 26.9 - - + +
144B ALA* 4.0 27.1 - - + +
341B ILE* 3.2 28.5 + - + +
342B GLY* 3.8 4.7 - - - +
343B GLY 3.2 1.2 - - - -
344B SER* 1.3 72.0 - - - +
346B LEU* 1.3 69.8 - - - +
348B SER* 2.6 20.6 + - - -
349B LEU* 3.2 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU* 3.5 21.8 - - + -
133B TYR* 5.1 4.3 - - + -
135B ALA* 5.3 4.9 - - + -
140B LEU* 5.7 4.3 - - + -
143B TYR* 4.7 23.3 - - + -
342B GLY 3.2 16.1 + - - +
343B GLY* 3.6 4.3 - - - +
345B ILE* 1.3 81.8 - - + +
347B ALA* 1.3 56.0 + - - +
348B SER 2.8 7.8 + - - -
349B LEU* 3.0 28.5 + - + +
351B THR* 6.0 2.7 - - + -
352B PHE* 3.3 52.7 - - + +
355B MET* 4.8 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ALA* 5.8 0.3 - - - -
7B ALA* 3.9 23.4 + - + +
9B VAL* 4.8 2.2 - - + -
22B ALA* 3.6 21.6 - - + +
104B LEU* 4.4 13.2 - - + -
343B GLY 2.8 21.1 + - - +
346B LEU* 1.3 69.9 - - - +
348B SER* 1.3 56.6 + - - +
349B LEU 4.7 0.7 - - - +
352B PHE* 3.7 18.3 - - + +
356B TRP* 4.1 13.4 - - + -
----------------------------------------------------------
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