Contacts of the strand formed by residues 146 - 149 (chain D) in PDB entry 1CCW
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 LEU 146 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D LYS 4.5 1.8 + - - -
48D PHE* 3.9 3.0 - - - -
79D LEU* 3.9 8.3 - - + -
91D LEU* 3.5 14.4 - - + +
92D PRO 3.6 14.4 - - - +
93D SER* 3.5 24.9 - - - +
138D VAL* 3.8 9.4 - - + +
139D LEU* 3.6 34.8 - - + +
142D VAL* 4.4 11.2 - - + -
144D LEU 3.7 0.2 + - - -
145D PRO* 1.3 76.4 - - - +
147D GLN* 1.3 58.4 + - - +
166D GLY 5.5 0.2 + - - -
167D TRP* 3.4 44.4 - - + +
168D THR* 3.0 28.2 + - - +
169D SER 3.5 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D PHE* 3.5 15.6 - - + -
64D GLN* 2.9 21.7 + - - +
91D LEU 3.1 5.7 + - - -
92D PRO* 3.4 4.0 - - - +
93D SER 2.8 27.4 + - - -
146D LEU* 1.3 73.5 - - - +
148D ALA* 1.3 73.0 + - - +
149D ARG* 2.8 29.1 + - + +
167D TRP* 4.3 4.7 - - - -
169D SER* 2.9 33.4 + - - +
171D GLU* 4.0 7.7 - - - +
212D ASN* 4.4 0.8 - - - +
214D GLU* 2.9 33.3 + - - +
322D LYS* 3.2 9.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D SER 3.6 7.9 - - - +
95D ILE* 4.5 5.8 - - + -
147D GLN* 1.3 72.7 - - - +
149D ARG* 1.3 59.0 + - - +
150D HIS* 3.7 10.9 - - + +
158D LEU* 5.2 1.8 - - + -
162D ILE* 4.0 23.3 - - + -
167D TRP* 4.0 17.0 - - + -
169D SER 3.2 7.1 + - - -
170D ASN* 3.8 16.2 - - - +
171D GLU* 3.1 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 149 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D GLN* 3.4 18.2 + - - +
65D PRO 4.3 4.9 - - - -
66D ARG* 4.8 5.0 - - - +
92D PRO* 3.8 21.8 - - + -
93D SER 3.1 7.6 + - - +
94D THR* 3.2 13.2 - - - +
95D ILE* 3.0 24.4 + - - +
147D GLN* 2.8 43.1 + - + +
148D ALA* 1.3 76.7 - - - +
150D HIS* 1.3 62.5 + - - +
171D GLU* 3.2 17.5 + - - +
214D GLU* 2.9 34.1 + - - -
291D HIS* 3.6 10.1 + - - -
322D LYS* 3.6 1.0 - - - +
324D ILE* 3.6 18.8 - - - +
900D TAR 2.8 44.6 + - - +
----------------------------------------------------------
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