Contacts of the helix formed by residues 233 - 238 (chain A) in PDB entry 1P7L
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 GLY 233 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A MET 4.4 5.0 - - - +
83A GLY* 5.1 1.6 - - - -
163A ASP* 3.6 8.7 - - - -
188A GLN* 2.9 27.1 + - - +
230A PHE* 3.7 4.9 - - - -
232A ILE* 1.3 75.7 - - - +
234A GLY* 1.3 70.4 + - - +
236A MET* 3.5 10.4 + - - +
237A GLY* 3.3 14.8 + - - -
384A ANP 5.2 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PRO* 3.6 12.9 - - - +
77A TYR* 3.2 23.1 + - - -
163A ASP* 2.8 18.0 + - - -
233A GLY* 1.3 67.5 - - - -
235A PRO* 1.3 74.6 - - - +
236A MET 2.8 8.1 + - - -
237A GLY 2.8 10.0 + - - -
238A ASP* 2.9 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PRO* 3.9 3.6 - - + -
18A ILE* 4.1 21.5 - - + -
45A VAL* 3.6 17.5 - - + +
46A LYS* 3.2 56.8 - - - +
47A THR 3.4 3.4 + - - -
77A TYR* 4.7 1.6 - - + -
83A GLY 6.0 0.2 - - - -
84A PHE* 3.4 38.8 - - + -
234A GLY* 1.3 82.3 - - - +
236A MET* 1.3 60.0 + - - +
238A ASP 3.2 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LYS* 3.6 12.8 + - - -
47A THR* 3.9 22.4 + - + +
80A SER 5.6 0.4 - - - +
83A GLY* 3.6 38.3 + - - +
232A ILE* 4.1 26.0 - - + +
233A GLY 3.5 9.6 + - - +
234A GLY 2.8 5.7 + - - -
235A PRO* 1.3 77.7 - - - +
237A GLY* 1.3 58.8 + - - +
55B GLU* 4.7 0.7 - - - +
97B LYS 5.2 5.0 - - - +
99B SER* 5.4 1.7 + - - -
87D ASN* 3.8 24.7 - - + +
88D SER* 4.0 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ILE* 4.1 18.3 - - - +
233A GLY* 3.3 9.6 + - - -
234A GLY 2.8 5.9 + - - -
236A MET* 1.3 80.2 - - - +
238A ASP* 1.3 65.2 + - - +
384A ANP 5.4 4.0 - - - -
55B GLU* 4.3 12.0 - - - +
99B SER* 4.4 12.7 + - - -
102B ILE* 4.1 17.4 - - - +
385B MET* 4.5 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A HIS* 4.5 1.2 + - - -
15A PRO* 3.0 24.8 - - + +
16A ASP* 5.8 0.3 - - - +
163A ASP* 5.6 0.4 - - - +
234A GLY 2.9 4.6 + - - +
235A PRO* 3.2 13.0 + - - +
236A MET 3.4 2.4 - - - -
237A GLY* 1.3 80.3 - - - +
239A CYS* 1.3 61.1 - - - +
384A ANP 2.9 61.5 + - + +
386A K 3.3 12.3 - - - -
55B GLU* 3.3 4.1 + - - +
385B MET* 2.9 36.8 + - - +
----------------------------------------------------------
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