Contacts of the helix formed by residues 278 - 292 (chain E) in PDB entry 1H4L
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 278 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E GLN* 2.6 47.3 + - + +
275E ILE 4.6 2.2 - - - -
276E ASN 3.4 1.0 - - - -
277E ALA* 1.3 75.2 - - + +
279E PRO* 1.4 56.3 - - - +
280E HIS* 3.0 24.4 + - - +
281E TYR* 2.7 36.8 + - - +
282E PHE* 2.9 9.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 279 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B GLY 5.4 7.4 - - - +
275E ILE 5.3 0.4 - - - +
276E ASN 5.0 4.0 - - - +
277E ALA 3.7 7.4 - - - +
278E ASP* 1.4 85.8 - - - +
280E HIS* 1.3 62.9 + - - +
282E PHE* 3.3 12.3 + - + +
283E THR* 3.0 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 280 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278E ASP* 3.0 12.9 + - - +
279E PRO* 1.3 78.1 - - - +
281E TYR* 1.3 65.0 + - - +
283E THR* 3.2 12.2 + - + +
284E GLN* 3.1 57.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 281 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206E MET* 3.7 18.6 - - + +
209E ARG* 4.0 11.2 + - - -
271E LYS* 3.7 31.3 - - + +
274E GLN* 3.3 28.5 - - + +
275E ILE* 3.2 39.7 - - + -
278E ASP* 2.7 36.3 + - + +
280E HIS* 1.3 72.9 - - - +
282E PHE* 1.3 61.4 + - - +
284E GLN* 3.1 20.6 + - + +
285E VAL* 3.0 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 282 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ILE* 3.9 29.6 - - + -
154B PRO* 5.0 10.1 - - + -
199E ALA* 3.9 28.9 - - + -
202E VAL* 3.9 28.9 - - + -
275E ILE* 3.4 40.1 + - + +
278E ASP 2.9 7.5 + - - +
279E PRO* 3.6 13.0 - - + +
281E TYR* 1.3 77.6 - - - +
283E THR* 1.3 58.3 + - - +
285E VAL* 3.3 1.4 + - - +
286E PHE* 2.8 47.3 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 283 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279E PRO 3.0 13.7 + - - -
280E HIS* 3.6 14.6 - - + +
282E PHE* 1.3 78.3 - - - +
284E GLN* 1.3 60.1 + - + +
286E PHE* 3.7 14.3 - - + +
287E SER* 2.7 37.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 284 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280E HIS* 3.1 48.1 + - + +
281E TYR* 3.1 23.0 + - + +
283E THR* 1.3 75.0 - - + +
285E VAL* 1.3 67.7 + - + +
287E SER* 3.2 5.9 + - - -
288E ASP* 2.9 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 285 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202E VAL* 3.8 11.4 - - + -
205E TYR* 3.7 25.6 - - + -
206E MET* 4.0 19.1 - - + -
209E ARG* 3.8 13.2 - - - +
275E ILE* 4.0 13.7 - - + -
281E TYR* 3.0 47.6 + - + +
282E PHE 3.7 4.5 - - - +
284E GLN* 1.3 74.6 - - + +
286E PHE* 1.3 64.8 + - - +
288E ASP* 3.1 11.3 + - - +
289E LEU* 3.0 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 286 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E LEU* 3.6 32.5 - - + -
198E PRO* 5.8 1.3 - - + -
202E VAL* 3.6 33.1 - - + +
282E PHE* 2.8 30.8 + + + +
283E THR* 3.7 15.3 - - + +
285E VAL* 1.3 77.1 - - - +
287E SER* 1.3 66.6 + - - +
289E LEU* 3.5 3.4 + - - +
290E LYS* 3.1 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 287 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283E THR* 2.7 27.6 + - - -
284E GLN* 3.5 7.2 - - - -
285E VAL 3.1 0.2 - - - -
286E PHE* 1.3 76.5 - - - +
288E ASP* 1.3 68.4 + - - +
290E LYS* 2.8 28.6 + - - +
291E ASN* 3.0 19.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 288 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205E TYR* 3.5 15.3 - - - +
209E ARG* 2.7 24.3 + - - +
284E GLN* 2.9 24.2 + - - +
285E VAL 3.6 3.8 - - - +
287E SER* 1.3 75.5 + - - +
289E LEU* 1.3 66.3 + - - +
291E ASN* 3.0 21.4 + - - +
292E GLU* 3.0 18.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 289 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E LEU* 3.7 35.4 - - + +
154E CYS* 3.3 31.0 - - + +
155E LEU* 3.6 14.1 - - - +
201E VAL* 4.0 15.0 - - + -
202E VAL* 4.3 10.1 - - + -
205E TYR* 3.5 49.5 - - + -
285E VAL 3.0 8.4 + - - +
286E PHE* 3.7 10.1 - - - +
288E ASP* 1.3 76.1 - - - +
290E LYS* 1.3 64.1 + - - +
292E GLU* 3.1 19.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 290 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E LEU* 5.0 5.4 - - + +
154E CYS* 3.9 9.2 - - - -
286E PHE* 3.1 33.7 + - + +
287E SER* 2.8 20.0 + - - +
289E LEU* 1.3 81.9 - - - +
291E ASN* 1.3 61.0 + - - +
292E GLU 3.4 0.3 + - - -
293E SER* 3.7 15.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 291 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161E ARG* 5.7 2.4 + - - -
287E SER* 3.0 29.5 + - - -
288E ASP* 3.0 14.4 + - - +
290E LYS* 1.3 74.8 - - - +
292E GLU* 1.3 60.5 + - - +
293E SER* 3.0 15.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 292 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E CYS 3.6 10.5 - - - +
157E GLU* 3.5 13.7 - - - +
158E PHE* 3.0 53.3 + - + -
161E ARG* 4.6 26.5 + - - +
205E TYR* 2.5 28.8 + - + -
288E ASP* 3.0 14.5 + - - +
289E LEU* 3.1 18.2 + - + +
291E ASN* 1.3 76.7 - - - +
293E SER* 1.3 65.8 + - - +
----------------------------------------------------------
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