Contacts of the strand formed by residues 149 - 154 (chain D) in PDB entry 1OJ7
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 149 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D ASP* 3.6 4.5 - - - +
102D LYS* 2.8 26.1 + - - +
144D SER* 3.8 0.7 + - - -
147D ASN* 3.0 13.0 + - - +
148D ALA* 1.3 79.8 - - - +
150D ALA* 1.3 61.2 + - - -
151D VAL* 5.9 0.2 - - - -
163D PHE 3.5 7.6 - - - -
164D HIS* 3.8 15.4 - - - -
168D VAL* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 150 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D ASP* 3.6 32.8 - - + +
102D LYS* 4.0 4.9 - - + -
149D GLY* 1.3 76.9 - - - +
151D VAL* 1.3 64.7 + - - +
152D ILE* 4.2 1.3 - - + -
162D ALA* 3.2 5.2 - - - +
163D PHE* 2.9 62.8 + - + +
164D HIS* 5.4 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D PRO* 3.6 24.1 - - - +
99D ASP* 3.1 16.7 + - - +
150D ALA* 1.3 80.0 - - - +
152D ILE* 1.3 63.0 + - - +
160D LYS* 3.8 41.8 + - + +
161D GLN 3.4 12.8 - - - +
162D ALA* 4.1 7.6 - - + -
271D HIS* 3.9 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 152 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D PRO* 3.7 11.9 - - + +
71D TYR* 4.4 5.2 - - + +
74D LEU* 3.8 21.5 - - + -
99D ASP 3.4 31.0 - - - +
100D GLY* 4.1 1.1 - - - -
103D PHE* 3.7 26.7 - - + -
117D TRP* 3.9 17.8 - - + -
120D LEU* 4.1 17.0 - - + -
150D ALA* 4.4 1.3 - - + -
151D VAL* 1.3 84.9 - - - +
153D SER* 1.3 71.5 + - - +
160D LYS* 3.6 1.1 - - - -
161D GLN 2.9 31.2 + - - +
163D PHE* 4.0 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D ASN* 3.7 26.2 + - - +
69D PRO 2.9 14.0 + - - -
70D ALA* 3.4 1.0 - - - -
71D TYR* 2.6 35.2 + - - +
117D TRP* 4.1 2.7 - - - -
151D VAL 4.4 0.2 + - - -
152D ILE* 1.3 73.6 - - - +
154D ARG* 1.3 55.5 + - - +
155D LYS* 3.9 19.4 + - - -
159D ASP 3.2 9.0 - - - -
160D LYS* 3.6 23.4 + - - +
275D ALA* 6.0 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 154 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D TYR* 4.0 27.8 - - + -
72D GLU* 4.5 0.4 - - - +
115D ASP* 4.8 7.3 + - - -
117D TRP* 3.3 62.7 - - + +
121D GLN* 5.1 3.6 + - - -
153D SER* 1.3 70.6 - - - +
155D LYS* 1.3 65.7 + - - +
156D THR* 3.3 16.4 + - - +
157D THR* 2.8 38.8 + - - +
158D GLY 3.2 17.3 + - - -
159D ASP* 3.0 25.4 + - + -
----------------------------------------------------------
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