Contacts of the helix formed by residues 288 - 292 (chain I) in PDB entry 4HOK
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 PHE 288 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104I THR* 3.4 15.9 - - + +
107I LEU* 3.8 31.0 - - + -
108I LEU* 4.1 11.2 - - + -
111I GLN* 4.8 4.5 - - - -
136I MET* 3.8 26.7 - - + -
142I GLY 4.6 1.6 - - - -
143I ASN* 4.1 18.8 - - + -
286I TYR* 3.2 37.7 + + + -
287I VAL* 1.3 81.2 - - - +
289I ASP* 1.3 67.1 + - - +
290I TRP* 3.1 47.8 - + + -
291I ASN* 2.9 29.5 + - - +
292I MET* 3.8 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 289 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96I CYS* 3.9 15.7 - - + -
99I LYS 4.0 2.5 - - - +
100I PHE* 3.2 15.4 - - + -
101I SER* 2.4 50.3 + - - -
104I THR* 3.0 14.6 + - - +
287I VAL 5.1 0.7 - - - +
288I PHE* 1.3 73.5 - - - +
290I TRP* 1.3 58.7 + - - +
291I ASN 3.0 4.4 + - - -
292I MET* 3.1 15.1 + - - +
294I LYS* 2.7 27.5 + - - -
13K ARG* 3.1 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 290 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89I LEU* 4.4 3.6 - - + -
92I LEU* 3.6 51.4 - - + +
95I PHE* 3.5 26.6 - - + -
96I CYS* 3.6 10.7 - - - -
100I PHE* 3.7 34.8 - + - -
104I THR* 3.7 13.9 - - + -
108I LEU* 4.1 17.5 - - + -
136I MET* 4.0 13.9 - - + +
288I PHE* 3.1 53.0 - + + +
289I ASP* 1.3 78.8 - - - +
291I ASN* 1.3 74.8 + - - +
292I MET 3.4 0.4 - - - -
294I LYS* 3.9 4.9 - - - +
87K PRO* 3.7 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 291 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286I TYR 3.4 10.6 - - - +
287I VAL* 3.8 11.8 - - + -
288I PHE* 2.9 39.6 + - - +
289I ASP 3.0 1.0 + - - -
290I TRP* 1.3 91.2 + - - +
292I MET* 1.3 60.7 + - - +
85K LEU 3.9 0.2 - - - +
86K GLY* 2.9 24.9 + - - -
87K PRO* 3.4 3.1 - - - +
137K GLY 5.0 0.3 - - - +
138K LEU* 4.1 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 292 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103I LYS* 5.7 0.4 - - + +
287I VAL* 4.0 18.6 - - + +
288I PHE 4.3 3.4 - - - +
289I ASP* 3.1 19.2 + - - +
291I ASN* 1.3 82.4 - - - +
293I LEU* 1.3 66.8 + - + +
294I LYS* 2.4 23.0 + - - +
13K ARG* 4.2 15.5 - - - +
15K ILE* 4.6 10.8 - - + -
25K LEU* 3.6 28.5 - - + -
34K GLU* 3.1 27.4 - - - +
84K LEU* 3.9 28.3 - - + -
85K LEU 3.5 6.3 - - - +
86K GLY* 3.7 1.1 - - - -
87K PRO* 3.2 11.3 - - - +
138K LEU* 5.3 0.7 - - - -
----------------------------------------------------------
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