Contacts of the helix formed by residues 287 - 297 (chain A) in PDB entry 3ZHP
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 287 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ILE 5.6 0.6 + - - -
250A SER* 3.0 45.8 + - - +
285A HIS 3.8 4.9 + - - +
286A LYS* 1.4 73.7 - - - +
288A GLN* 1.3 65.5 + - - +
289A PRO* 3.8 11.2 - - - +
290A ILE* 3.1 18.6 + - - +
291A VAL* 3.0 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A LYS 3.8 2.0 + - - +
287A THR* 1.3 69.9 - - - +
289A PRO* 1.4 69.9 - - + +
291A VAL* 3.1 27.1 + - - +
292A GLU* 2.9 44.1 + - + +
335A THR* 2.7 36.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A SER 4.4 7.9 - - - +
252A PRO* 4.2 24.2 - - + -
287A THR* 3.6 15.7 - - - +
288A GLN* 1.4 89.9 - - + +
290A ILE* 1.4 60.0 + - - +
292A GLU* 3.6 12.4 + - + +
293A ILE* 3.3 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ILE 3.3 24.0 - - - +
250A SER 3.6 5.4 - - - +
251A LYS 3.4 25.8 - - - +
252A PRO* 3.8 8.5 - - + -
255A LEU* 3.8 28.7 - - + +
280A PHE* 4.0 8.3 - - + +
286A LYS* 4.1 20.0 - - + -
287A THR* 3.1 24.1 + - - +
289A PRO* 1.4 72.5 - - - +
291A VAL* 1.4 60.5 + - - +
293A ILE* 3.2 4.4 + - - +
294A LEU* 3.0 47.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A LYS* 3.7 28.7 - - + +
287A THR 3.0 15.1 + - - +
288A GLN* 3.1 30.3 + - - +
290A ILE* 1.4 73.9 - - - +
292A GLU* 1.3 58.4 + - + +
294A LEU* 3.5 7.7 + - - +
295A LEU* 2.9 49.4 + - + +
332A LEU* 3.9 20.2 - - + -
333A LYS 4.3 7.6 - - - +
334A LYS* 5.5 1.3 - - - -
335A THR* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A GLN* 2.9 36.5 + - - +
289A PRO* 3.6 10.8 - - - +
291A VAL* 1.3 72.7 - - + +
293A ILE* 1.4 55.5 + - + +
295A LEU* 3.4 7.3 + - + +
296A LYS* 2.9 36.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
252A PRO* 3.6 41.7 - - + +
255A LEU* 3.8 22.2 - - + -
256A LYS* 5.3 7.0 - - + +
259A MET* 3.8 20.2 - - - -
289A PRO 3.3 17.4 + - - +
290A ILE* 3.2 6.6 + - - +
292A GLU* 1.4 74.8 - - + +
294A LEU* 1.4 61.2 - - - +
296A LYS* 3.3 5.1 + - - -
297A ASN* 3.0 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A LEU* 4.0 16.2 - - + -
259A MET* 5.6 0.7 - - - -
277A PHE* 4.7 4.5 - - + -
280A PHE 4.6 4.9 - - - +
281A VAL* 3.8 28.0 - - + -
286A LYS* 3.7 33.4 - - + -
290A ILE* 3.0 29.3 + - + +
291A VAL* 3.9 3.8 - - - +
293A ILE* 1.4 74.4 - - - +
295A LEU* 1.4 56.8 + - - +
297A ASN 3.5 2.3 - - - -
298A GLN* 3.0 27.4 + - - +
301A LEU* 4.0 25.7 - - + +
329A ILE* 4.5 11.0 - - + +
332A LEU* 3.8 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A VAL* 2.9 39.6 + - + +
292A GLU* 3.9 6.5 - - + +
293A ILE 3.3 0.2 - - - -
294A LEU* 1.4 72.7 - - - +
296A LYS* 1.3 63.1 + - - +
297A ASN 3.2 0.7 - - - -
298A GLN* 3.3 50.9 + - - +
299A PRO* 4.8 1.7 - - - +
332A LEU* 3.8 22.7 - - + +
333A LYS* 4.1 17.3 - - - +
334A LYS* 4.3 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A GLU 2.9 19.2 + - - +
293A ILE* 3.3 8.5 + - - +
295A LEU* 1.3 75.4 - - - +
297A ASN* 1.3 66.6 + - - +
298A GLN 3.6 0.2 - - - -
299A PRO* 5.2 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A MET* 3.8 29.4 - - + +
293A ILE* 3.0 30.1 + - - +
294A LEU 3.5 4.0 - - - -
296A LYS* 1.3 89.5 + - - +
298A GLN* 1.4 54.2 + - - +
299A PRO* 3.6 2.5 - - - -
300A LYS* 3.3 20.9 + - + +
301A LEU* 2.8 39.1 + - + +
----------------------------------------------------------
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