Contacts of the helix formed by residues 277 - 288 (chain E) in PDB entry 3Q3G
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 SER 277 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244E GLU* 5.1 0.9 + - - -
274E ALA 4.6 1.6 + - - -
276E ARG* 1.4 80.0 - - - +
278E GLU* 1.3 62.8 + - - +
279E LYS* 4.0 8.3 + - - +
280E SER* 2.6 45.6 + - - -
281E ARG* 3.2 18.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 278 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277E SER* 1.3 73.7 - - - +
279E LYS* 1.4 62.0 + - - +
281E ARG* 3.2 36.9 + - - +
282E GLN* 3.2 31.9 + - - +
285E ASN* 5.8 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 279 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A SER* 6.0 3.4 - - - -
244E GLU* 4.6 5.6 - - - +
277E SER* 3.4 8.0 - - - +
278E GLU* 1.4 77.1 - - - +
280E SER* 1.4 60.8 + - - +
282E GLN* 3.3 25.2 + - - +
283E GLU* 3.6 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 280 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244E GLU* 3.7 24.1 + - - -
274E ALA 3.2 21.7 + - - -
275E PHE* 3.3 23.7 - - - -
277E SER* 2.6 43.1 + - - -
279E LYS* 1.4 74.1 - - - +
281E ARG* 1.4 63.3 + - - +
283E GLU* 3.1 20.1 + - - +
284E LEU 3.4 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 281 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E PHE 3.4 14.0 + - - +
276E ARG* 3.0 35.4 + - - +
277E SER 3.2 14.7 + - - +
278E GLU* 3.2 32.3 + - - +
280E SER* 1.4 73.7 + - - +
282E GLN* 1.4 59.0 + - - +
284E LEU* 3.2 12.1 + - + +
285E ASN* 3.0 36.7 + - - +
298E GLN* 3.5 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 282 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278E GLU* 3.2 33.3 + - - +
279E LYS* 3.4 12.9 - - - +
280E SER 3.2 0.4 - - - -
281E ARG* 1.4 73.1 - - - +
283E GLU* 1.4 55.1 + - - +
285E ASN* 3.3 15.4 + - - +
286E THR* 2.7 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 283 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211E THR* 4.7 0.3 + - - -
243E GLY 4.9 0.3 - - - +
244E GLU* 3.3 29.4 - - + +
245E LYS* 2.8 27.9 + - - +
252E TYR* 2.6 40.8 + - + +
275E PHE* 5.2 4.5 - - + -
279E LYS 3.6 5.1 + - - +
280E SER* 3.1 18.3 + - - +
282E GLN* 1.4 78.5 - - - +
284E LEU* 1.4 55.0 + - - +
286E THR* 3.2 9.0 + - - -
287E ILE* 3.0 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 284 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241E THR* 4.8 2.5 - - + -
268E VAL* 3.2 38.8 - - + +
270E GLY* 3.8 18.4 - - - +
275E PHE* 3.7 41.5 - - + -
280E SER 3.9 0.9 - - - +
281E ARG* 3.2 17.2 + - + +
283E GLU* 1.4 75.4 - - - +
285E ASN* 1.3 58.3 + - - +
287E ILE* 3.4 5.9 + - + -
288E ALA* 3.0 26.7 + - - +
296E VAL* 3.8 13.2 - - + -
298E GLN* 3.9 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 285 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278E GLU* 5.8 2.0 + - - -
281E ARG* 3.0 23.9 + - - +
282E GLN* 3.3 17.3 + - - +
284E LEU* 1.3 75.5 - - - +
286E THR* 1.4 56.9 + - - +
288E ALA 2.9 21.7 - - - +
290E LYS* 4.3 20.3 - - - +
292E PRO* 3.4 35.8 - - + +
296E VAL* 3.6 16.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 286 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252E TYR* 3.6 37.2 - - + -
256E ILE* 3.4 28.2 - - + +
266E ARG* 4.3 0.7 + - - -
282E GLN* 2.7 21.4 + - - +
283E GLU* 3.2 11.9 + - - -
285E ASN* 1.4 74.8 - - - +
287E ILE* 1.4 64.4 + - - +
288E ALA 4.0 2.4 - - - +
290E LYS* 6.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 287 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211E THR* 4.3 9.0 - - + -
215E ILE* 3.9 16.6 - - + -
239E VAL* 4.2 18.4 - - + -
241E THR* 5.0 6.5 - - + -
252E TYR* 3.4 37.9 - - + +
256E ILE* 3.8 7.1 - - - +
266E ARG* 2.6 40.1 + - + +
267E TYR 5.3 0.7 - - - +
268E VAL* 3.8 31.2 - - + -
275E PHE* 6.1 0.7 - - + -
283E GLU* 3.0 27.6 + - + +
284E LEU* 3.4 9.2 + - + +
286E THR* 1.4 75.8 - - - +
288E ALA* 1.4 54.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 288 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266E ARG* 3.4 22.0 + - - +
268E VAL* 3.7 11.7 - - + -
284E LEU 3.0 17.7 + - - +
285E ASN 2.9 18.2 - - - +
286E THR 4.0 0.9 - - - +
287E ILE* 1.4 79.0 - - - +
289E SER* 1.4 65.8 + - - +
290E LYS* 3.8 2.3 + - - +
292E PRO* 5.7 0.2 - - + -
295E HIS* 3.8 11.7 - - + +
296E VAL* 3.6 22.0 - - + -
----------------------------------------------------------
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