Contacts of the strand formed by residues 114 - 119 (chain D) in PDB entry 3CJC
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 ALA 114 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 4.0 22.9 - - + -
68D SER* 4.9 0.2 - - - -
80D TYR* 3.9 24.2 - - + -
82D PHE* 3.9 11.4 - - + -
95D TYR 3.9 2.2 - - - -
96D GLN* 3.6 18.8 - - - +
112D GLU 3.5 1.2 + - - -
113D PRO* 1.3 70.5 - - - +
115D VAL* 1.3 61.9 + - - +
116D VAL* 4.8 1.1 - - + -
130D ILE 3.7 2.9 - - - +
132D ALA* 3.3 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 115 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D THR* 3.4 5.9 - - - +
95D TYR* 3.0 62.4 + - + +
97D TYR* 5.2 2.9 - - + -
113D PRO 4.3 6.7 - - - +
114D ALA* 1.3 75.6 - - - +
116D VAL* 1.3 62.6 + - - +
129D ALA* 4.5 6.1 - - + -
130D ILE 4.0 3.8 - - - +
131D VAL* 3.9 31.2 - - + -
150D VAL* 4.1 15.0 - - + -
154D VAL* 4.2 7.6 - - + -
158D TRP* 3.5 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D VAL* 4.3 4.5 - - + -
82D PHE* 3.5 37.5 - - + -
91D VAL* 3.5 28.3 - - + -
93D ASP 3.6 2.5 - - - -
94D THR* 3.6 17.0 - - + +
114D ALA 4.5 0.7 - - - +
115D VAL* 1.3 82.7 - - - +
117D LYS* 1.3 63.1 + - - +
118D PHE* 3.2 35.6 - - + -
129D ALA* 3.5 2.1 - - - -
130D ILE 3.0 31.6 + - - +
158D TRP* 4.3 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 117 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D VAL* 3.4 7.4 - - - +
92D LEU* 2.7 50.2 + - + +
93D ASP* 2.7 28.8 + - + +
116D VAL* 1.3 71.5 - - - +
118D PHE* 1.3 61.2 + - - +
127D GLU* 3.7 25.3 + - - -
128D PHE 3.8 3.1 - - - +
129D ALA* 4.5 0.4 - - - +
158D TRP* 3.6 55.4 + - + +
160D LEU* 4.5 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 118 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D ILE* 4.2 13.7 - - + -
82D PHE* 4.6 12.8 - + + -
84D PHE* 3.8 30.1 - + + -
89D VAL* 4.0 16.8 - - + -
90D SER 3.4 7.4 - - - -
91D VAL* 3.4 24.5 - - + -
92D LEU* 4.2 4.9 - - - +
116D VAL* 3.2 38.6 - - + -
117D LYS* 1.3 75.1 - - - +
119D SER* 1.3 61.6 + - - +
120D SER 4.1 1.1 - - - -
127D GLU* 3.4 9.4 - - - +
128D PHE* 2.9 50.0 + + + +
130D ILE* 3.5 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 119 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D VAL* 3.5 5.3 - - - -
90D SER* 2.7 39.5 + - - -
92D LEU* 3.6 24.4 - - - +
118D PHE* 1.3 76.4 - - - +
120D SER* 1.3 60.3 + - - +
121D HIS* 3.8 8.0 + - - +
126D LYS* 3.3 9.4 + - - +
127D GLU* 4.6 5.5 - - - +
----------------------------------------------------------
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