Contacts of the helix formed by residues 289 - 299 (chain A) in PDB entry 4DTP
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 289 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A TRP* 3.8 1.3 - - - +
287A SER* 3.2 9.8 + - - -
288A TYR* 1.3 81.6 - - - +
290A LEU* 1.3 62.8 + - - +
291A ASP* 3.5 10.6 - - - +
292A TYR* 3.0 24.8 + - - +
293A ILE* 3.1 19.9 + - - +
851A GLY* 4.5 11.9 + - - -
852A THR* 6.3 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ASP* 5.8 1.6 - - - +
216A TRP* 3.5 52.4 - - + +
289A SER* 1.3 72.7 - - - +
291A ASP* 1.3 53.7 + - - +
293A ILE 4.6 0.2 - - - +
294A SER* 2.8 53.3 + - - +
327A ALA* 3.3 44.9 - - + +
330A ARG* 4.4 7.9 - - + -
331A VAL* 4.0 12.8 - - + -
334A ILE* 4.1 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A SER* 3.5 9.8 - - - +
290A LEU* 1.3 77.7 - - - +
292A TYR* 1.3 62.2 + - - +
294A SER* 3.9 1.4 - - - -
295A GLU* 3.1 24.3 + - - +
300A VAL 5.1 0.5 - - - +
302A LYS* 3.3 34.6 - - + +
303A LEU* 3.4 29.7 + - - +
330A ARG* 3.8 14.0 + - - +
851A GLY 6.0 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A GLN* 3.5 22.0 + - - -
286A PRO* 3.0 32.8 - - + +
287A SER* 3.7 33.4 - - - +
289A SER* 3.0 17.9 + - - +
291A ASP* 1.3 77.5 - - - +
293A ILE* 1.3 65.9 + - + +
295A GLU* 3.3 11.9 + - + +
296A PHE* 3.0 33.7 + + + +
739A LYS* 3.3 25.9 - - + +
831A TYR* 4.8 10.8 - - - -
851A GLY* 5.1 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A TRP* 3.7 31.9 - - + -
277A TYR* 3.7 31.2 - - + -
285A GLN* 3.6 31.9 - - + +
287A SER 3.5 22.7 - - - +
288A TYR* 4.0 9.6 - - + -
289A SER 3.1 16.1 + - - +
290A LEU* 4.2 1.6 - - - +
292A TYR* 1.3 77.9 - - + +
294A SER* 1.3 58.0 + - - +
296A PHE* 3.2 2.8 + - - +
297A GLU* 2.8 33.7 + - + +
334A ILE* 4.0 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A LEU* 2.8 35.4 + - - +
291A ASP 3.9 0.2 - - - -
293A ILE* 1.3 76.9 - - - +
295A GLU* 1.3 56.4 + - - +
298A LEU* 2.8 39.0 + - - +
299A ASN 3.6 0.5 + - - -
300A VAL* 3.6 7.5 - - - +
330A ARG* 3.5 44.6 - - - +
334A ILE* 3.9 10.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ASP 3.1 17.9 + - - +
292A TYR* 3.6 11.7 - - + +
294A SER* 1.3 76.0 - - - +
296A PHE* 1.3 60.4 + - + +
299A ASN* 3.0 37.4 + - - +
300A VAL 3.0 33.3 + - - +
301A GLY* 4.4 4.2 + - - -
302A LYS 5.6 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A TYR* 3.7 1.3 - - - -
283A THR* 4.3 13.9 - - + -
285A GLN* 3.3 36.3 - - - +
292A TYR* 3.0 23.7 + + + +
293A ILE* 3.5 8.7 - - - +
295A GLU* 1.3 81.6 - - + +
297A GLU* 1.3 84.6 + - - +
299A ASN* 4.2 7.1 + - - +
337A LYS* 4.8 3.0 + - - -
338A ARG* 4.4 3.6 - - - -
739A LYS* 6.5 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A TYR* 2.6 39.3 + - + +
293A ILE* 2.8 25.8 + - + +
296A PHE* 1.3 84.8 - - - +
298A LEU* 1.3 71.9 + - + +
299A ASN* 3.7 3.7 + - - -
334A ILE* 4.2 14.1 - - + -
337A LYS* 2.9 49.3 + - + +
338A ARG* 2.8 40.5 + - - +
547A ARG* 5.3 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A SER* 2.8 20.3 + - - +
297A GLU* 1.3 88.8 - - + +
299A ASN* 1.3 75.4 + - - +
300A VAL* 3.3 23.7 + - + +
330A ARG* 4.1 4.9 - - + +
333A GLN* 3.7 56.8 - - + +
334A ILE* 3.9 19.1 - - + +
337A LYS* 4.7 3.4 - - + -
547A ARG* 4.3 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A GLU* 3.0 29.7 + - - +
296A PHE* 4.2 7.1 - - - +
297A GLU 5.1 2.2 + - - -
298A LEU* 1.3 81.9 + - - +
300A VAL* 1.3 60.4 + - - +
301A GLY 4.3 0.3 + - - -
----------------------------------------------------------
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