Contacts of the helix formed by residues 143 - 151 (chain D) in PDB entry 3P3W
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 143 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B TYR* 5.7 2.7 - - - +
139B THR* 6.1 2.5 - - + -
146B LEU* 6.0 3.8 - - + -
104D ASP* 3.9 5.8 + - - +
142D GLY* 1.3 70.8 - - - -
144D SER* 1.3 67.6 + - - +
145D VAL 3.1 2.5 - - - -
146D LEU* 2.6 33.3 + - + -
147D GLN* 2.7 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D PRO* 5.1 14.5 + - - +
103D THR 5.6 1.3 - - - -
104D ASP* 3.1 27.4 + - - -
118D LYS* 3.9 20.2 - - - +
141D ARG 5.3 4.2 + - - -
142D GLY 3.6 2.3 + - - -
143D PHE* 1.3 76.0 - - - +
145D VAL* 1.3 64.3 + - - +
147D GLN* 3.7 10.2 + - - +
148D ALA* 3.3 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D LEU* 5.1 2.7 - - + +
118D LYS* 4.9 15.5 - - - +
121D ILE* 4.1 29.4 - - + -
122D LEU* 5.8 1.3 - - + -
135D TYR* 3.4 19.3 - - + +
137D TYR* 6.2 0.2 - - + -
142D GLY 4.7 10.1 + - - +
143D PHE 2.7 3.6 + - - +
144D SER* 1.3 79.8 + - - +
146D LEU* 1.3 61.5 + - + +
148D ALA* 3.6 5.5 + - + +
149D ILE* 3.1 40.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B TYR* 5.5 4.7 - - - +
146B LEU* 4.9 16.8 - - + -
150B MET* 5.5 2.5 - - + -
135D TYR* 3.5 35.0 - - + +
137D TYR* 3.8 36.6 - - + -
142D GLY 5.4 1.1 - - - +
143D PHE* 2.6 25.7 + - + +
145D VAL* 1.3 75.3 - - + +
147D GLN* 1.3 58.9 - - - +
149D ILE* 3.2 4.9 + - + +
150D MET* 3.0 61.3 + - + +
162D ALA* 4.3 3.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
137B TYR* 4.5 8.7 - - - +
139B THR* 5.0 8.7 - - - +
164B SER* 4.2 21.5 + - - -
167B ASN* 3.2 30.3 + - - +
104D ASP* 3.5 16.0 + - - +
143D PHE* 2.7 43.9 + - + +
144D SER* 3.9 8.2 - - - +
146D LEU* 1.3 72.5 - - + +
148D ALA* 1.3 59.9 + - - +
150D MET* 4.2 4.9 - - - +
151D GLU* 3.4 38.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
118D LYS* 3.7 27.6 - - + -
122D LEU* 4.2 20.8 - - + +
144D SER 3.3 15.8 + - - +
145D VAL* 3.8 4.9 - - - +
146D LEU 3.2 0.6 - - - -
147D GLN* 1.3 77.4 - - - +
149D ILE* 1.3 60.7 + - - +
151D GLU* 3.9 3.6 - - - +
152D ALA* 3.1 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 149 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D ILE* 4.2 10.3 - - + -
122D LEU* 3.8 23.1 - - + -
125D LEU* 3.8 22.7 - - + -
133D PHE* 5.0 7.6 - - + -
135D TYR* 4.1 27.6 - - + -
145D VAL* 3.1 29.5 + - + +
146D LEU* 3.2 8.0 + - + +
148D ALA* 1.3 74.9 - - - +
150D MET* 1.3 58.6 + - + +
152D ALA* 3.1 4.0 + - + +
153D ALA* 2.7 34.1 + - - +
160D VAL* 4.1 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 150 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B TYR* 5.6 3.6 - - - +
150B MET* 3.6 31.0 - - + -
160B VAL 6.0 0.7 - - - +
161B THR* 5.5 3.7 - - - +
162B ALA* 3.8 38.8 - - + +
163B ARG* 3.9 7.5 + - - -
164B SER 6.3 0.2 - - - +
146D LEU* 3.0 41.3 + - + +
147D GLN* 4.2 5.8 - - - +
149D ILE* 1.3 76.6 - - + +
151D GLU* 1.3 62.3 + - + +
152D ALA 3.4 0.3 + - - -
153D ALA* 3.5 15.6 + - - +
154D VAL* 3.6 12.3 + - - +
160D VAL* 5.1 14.4 - - + +
162D ALA* 3.9 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ALA 5.4 0.2 - - - +
163B ARG* 4.4 21.9 - - - +
164B SER* 4.4 23.5 - - - +
167B ASN* 5.5 2.8 + - - -
168B ILE* 5.0 10.3 - - - +
177B ILE* 5.9 3.3 - - - +
147D GLN* 3.4 26.8 + - - +
148D ALA* 3.9 3.6 - - - +
149D ILE 3.3 0.4 - - - -
150D MET* 1.3 78.6 - - + +
152D ALA* 1.3 57.6 + - - +
154D VAL* 3.4 19.4 - - - +
155D GLN* 4.1 8.8 - - - +
----------------------------------------------------------
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