Contacts of the helix formed by residues 269 - 282 (chain A) in PDB entry 3L4U
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 THR 269 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A GLY 3.3 5.4 - - - -
230A SER* 3.8 3.1 - - - -
267A GLY 3.3 0.4 - - - -
268A ASN* 1.3 89.0 - - + +
270A PRO* 1.4 75.0 - - - +
271A GLU* 3.6 8.5 + - - +
272A GLN* 3.0 38.4 + - - +
273A VAL* 3.2 13.5 + - - +
657A HIS 5.3 1.1 - - - -
660A TYR* 3.5 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A LEU* 3.5 18.4 - - + +
223A LEU* 4.1 11.2 - - + -
228A GLY 3.6 10.1 - - - +
230A SER* 3.4 18.1 - - - +
269A THR* 1.4 85.8 - - - +
271A GLU* 1.3 62.5 + - - +
273A VAL* 3.1 13.2 + - - +
274A VAL* 3.2 10.9 + - - +
656A LEU* 4.2 17.0 - - + +
657A HIS* 3.4 37.5 - - + +
660A TYR* 3.8 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A THR* 3.2 8.5 + - - +
270A PRO* 1.3 78.5 - - - +
272A GLN* 1.3 58.4 + - + +
274A VAL* 3.3 6.2 + - - +
275A GLN* 2.9 40.5 + - - +
649A ASP* 3.4 11.5 - - - +
650A THR* 2.5 49.9 + - - +
653A ARG* 3.4 26.2 + - - +
657A HIS* 2.8 37.2 + - + +
658A GLU* 4.8 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A GLY* 3.8 10.2 - - - -
268A ASN* 2.8 41.0 + - - +
269A THR* 3.0 26.8 + - - +
271A GLU* 1.3 76.8 - - + +
273A VAL* 1.3 58.3 + - - +
275A GLN* 3.3 20.3 + - - +
276A GLU* 2.9 36.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A PHE* 3.9 15.3 - - + -
221A LEU* 4.0 8.5 - - + -
230A SER* 3.4 47.8 - - - +
231A PHE* 3.7 7.2 - - - +
232A GLY* 3.6 27.6 - - - +
265A PHE* 4.5 6.1 - - + +
266A LEU 4.3 1.8 - - - -
267A GLY* 3.8 10.1 - - - +
269A THR 3.8 2.9 - - - +
270A PRO 3.1 7.3 + - - +
272A GLN* 1.3 75.4 - - - +
274A VAL* 1.3 66.9 + - - +
276A GLU* 3.2 8.8 + - - +
277A TYR* 2.9 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A PHE* 4.9 3.6 - - + -
221A LEU* 3.7 17.5 - - + -
270A PRO 3.2 12.7 + - - +
271A GLU* 3.3 8.3 + - - +
273A VAL* 1.3 76.9 - - - +
275A GLN* 1.3 57.6 + - - +
277A TYR* 3.2 6.6 + - - +
278A LEU* 2.9 41.4 + - + +
561A ASN 4.3 2.0 - - - +
562A LEU* 3.7 37.2 - - + +
648A GLY 3.4 17.5 - - - +
650A THR* 4.2 17.7 - - + +
657A HIS* 4.2 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A GLU* 2.9 25.9 + - - +
272A GLN* 3.6 27.2 - - - +
273A VAL 3.3 0.2 - - - -
274A VAL* 1.3 75.7 - - - +
276A GLU* 1.3 59.2 + - - +
278A LEU* 3.8 0.9 - - - +
279A GLU* 2.9 29.3 + - - +
283A ARG* 5.1 0.7 + - - -
647A ARG* 3.3 40.5 - - - +
648A GLY* 3.7 17.7 - - - +
649A ASP* 2.8 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A THR* 4.4 8.0 + - - +
95A ASN* 3.4 35.7 + - + +
96A ARG* 4.7 10.4 + - - +
265A PHE* 3.7 27.5 - - + -
266A LEU 3.8 17.9 - - - +
267A GLY* 5.4 0.2 - - - -
272A GLN* 2.9 21.8 + - + +
273A VAL* 3.2 6.9 + - - +
275A GLN* 1.3 74.2 - - - +
277A TYR* 1.3 65.4 + - - +
279A GLU* 3.4 10.6 + - - +
280A LEU* 3.3 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLN* 4.1 5.9 + - - -
218A THR 5.8 0.2 + - - -
219A PHE* 3.6 47.3 + + + +
234A PHE* 3.7 30.3 - + + -
265A PHE* 3.8 23.5 - + + -
273A VAL 2.9 12.4 + - - +
274A VAL 3.5 5.6 - - - +
276A GLU* 1.3 75.9 - - - +
278A LEU* 1.3 71.6 + - + +
280A LEU* 3.1 5.9 + - + +
281A ILE* 3.0 51.2 + - + +
530A ALA* 3.5 29.3 - - - +
531A GLY 4.5 0.3 + - - -
562A LEU 3.6 25.4 - - - -
563A PHE* 4.0 12.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A HIS* 5.1 0.2 + - - -
274A VAL* 2.9 26.6 + - + +
275A GLN 4.1 2.2 - - - +
277A TYR* 1.3 86.0 - - + +
279A GLU* 1.3 61.7 + - - +
281A ILE* 3.6 23.1 - - + -
282A GLY* 2.9 34.2 + - - +
283A ARG* 3.4 19.7 + - + +
284A PRO* 4.0 11.2 - - + -
561A ASN 5.0 0.9 - - - +
562A LEU 4.3 0.4 - - - +
563A PHE 4.0 0.2 - - - +
564A GLY* 3.5 35.9 - - - +
648A GLY* 3.4 33.2 - - - +
649A ASP 4.9 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A THR* 6.2 0.2 - - + -
96A ARG* 3.9 20.1 + - - +
115A HIS* 4.3 9.5 + - - -
275A GLN 2.9 19.3 + - - +
276A GLU* 3.6 12.1 - - - +
278A LEU* 1.3 76.5 - - - +
280A LEU* 1.3 63.7 + - - +
283A ARG* 2.9 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLN* 4.6 1.3 - - - +
96A ARG* 3.9 24.7 - - - +
115A HIS* 3.3 18.2 - - - -
116A VAL* 3.6 30.3 - - + +
234A PHE* 4.2 11.2 - - + -
263A TYR* 3.5 57.0 - - + -
265A PHE* 3.7 24.2 - - + -
276A GLU 3.3 2.9 + - - +
277A TYR* 3.1 10.2 + - + +
279A GLU* 1.3 81.3 - - - +
281A ILE* 1.3 60.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A HIS* 3.5 31.8 - - + +
115A HIS* 3.6 7.9 - - - +
116A VAL* 4.1 10.3 - - + -
234A PHE* 4.0 20.6 - - + -
236A MET* 4.7 0.7 - - + -
277A TYR* 3.0 39.7 + - + +
278A LEU* 3.6 20.2 - - + -
280A LEU* 1.3 75.4 - - + +
282A GLY* 1.3 73.2 + - - +
530A ALA* 3.9 24.9 - - + -
531A GLY* 3.8 23.6 - - - +
534A LYS* 5.4 0.7 - - - +
563A PHE 4.5 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A HIS* 3.5 25.7 - - - -
278A LEU* 2.9 15.5 + - - +
280A LEU 3.4 2.0 - - - -
281A ILE* 1.3 95.1 - - - +
283A ARG* 1.3 66.2 + - - -
284A PRO* 3.9 1.0 - - - +
531A GLY* 4.9 2.1 - - - -
533A GLY* 5.9 0.2 - - - -
534A LYS* 4.8 12.4 + - - +
564A GLY 5.2 1.6 - - - +
----------------------------------------------------------
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