Contacts of the helix formed by residues 100 - 106 (chain A) in PDB entry 1Z9X
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 GLU 100 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLY 4.9 0.5 - - - +
99A GLY* 1.3 74.2 - - - -
101A LEU* 1.3 65.5 + - - +
102A PHE* 4.3 2.4 - - + +
103A ASP* 3.2 27.5 + - + +
104A PHE* 3.3 11.8 + - - +
142A PRO* 4.0 17.6 - - - +
143A GLU* 4.0 33.0 + - - +
145A ILE 3.7 5.4 - - - -
146A MET* 3.7 18.4 - - + -
147A LEU* 4.2 0.6 - - - +
300A TYR* 4.0 20.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLY 3.8 1.2 + - - -
100A GLU* 1.3 70.7 - - - +
102A PHE* 1.3 68.4 + - + +
104A PHE* 3.1 7.0 + - + +
105A LEU* 2.9 49.7 + - + +
119A PHE* 3.9 38.8 - - + -
123A ILE* 4.5 6.3 - - + -
145A ILE* 3.0 41.1 + - + +
147A LEU* 4.0 28.0 - - + +
157A ILE* 3.8 12.1 - - + -
210A LEU* 4.5 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLU* 3.3 4.2 - - + +
101A LEU* 1.3 87.3 - - + +
103A ASP* 1.3 63.7 + - - +
105A LEU* 4.3 5.2 - - + -
106A ALA* 3.2 20.6 + - - +
142A PRO* 3.6 42.1 + - + -
145A ILE* 6.0 0.9 - - + -
206A ILE* 3.9 34.8 - - + -
209A ILE* 3.6 25.4 - - + -
210A LEU* 4.1 25.8 - - + -
296A PHE* 3.3 31.8 - + + -
300A TYR* 3.7 26.2 - + + -
303A ARG* 5.1 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLY* 5.3 2.2 - - - -
100A GLU* 3.2 21.0 + - + +
102A PHE* 1.3 78.0 - - - +
104A PHE* 1.3 60.8 + - - +
106A ALA* 3.4 8.7 + - - +
107A GLN* 2.7 47.3 + - - +
150A LYS* 4.5 11.3 + - - -
300A TYR* 3.1 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLY 5.7 0.2 - - - +
100A GLU 3.3 2.4 + - - +
101A LEU* 3.1 10.6 + - + +
103A ASP* 1.3 79.8 - - - +
105A LEU* 1.3 71.9 + - + +
107A GLN* 3.0 31.8 + - + +
108A LYS* 3.7 34.0 - - + +
119A PHE* 4.0 11.7 - + - -
147A LEU* 3.5 23.6 - - + -
150A LYS* 3.5 38.1 - - + -
152A ILE 4.8 2.0 - - - -
153A PRO 4.3 8.3 - - - -
155A PRO* 3.6 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 2.9 37.4 + - + +
102A PHE* 4.3 3.1 - - + -
104A PHE* 1.3 72.9 - - + +
106A ALA* 1.3 58.7 + - - +
107A GLN 2.9 10.4 + - - -
108A LYS* 3.0 23.9 + - + +
111A LEU* 3.8 34.2 - - + +
119A PHE* 3.9 24.0 - - + -
210A LEU* 3.9 32.8 - - + +
293A LEU* 3.2 17.8 - - + +
296A PHE* 3.9 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PHE 3.2 18.1 + - - +
103A ASP 3.5 7.6 - - - +
105A LEU* 1.3 75.4 - - - +
107A GLN* 1.3 61.3 + - - +
108A LYS 3.4 0.2 - - - -
293A LEU* 4.0 10.5 - - - -
296A PHE* 3.7 9.3 - - + -
297A ARG* 2.9 47.2 + - + +
300A TYR* 4.2 17.5 - - + -
301A VAL* 6.4 0.2 - - + -
----------------------------------------------------------
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