Contacts of the strand formed by residues 146 - 153 (chain D) in PDB entry 4GUN
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 146 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLN* 4.3 6.3 - - - +
143A ASN* 5.4 0.2 - - - +
146A ALA* 4.5 7.9 - - + -
107D GLN* 4.1 4.0 - - - +
111D GLN* 3.5 18.2 - - - +
138D VAL* 3.8 0.7 - - - +
139D LYS* 3.6 1.1 - - - -
140D ASN* 2.8 31.9 + - - +
143D ASN* 3.3 36.9 + - - +
144D GLY 3.3 1.6 - - - -
145D GLY* 1.3 76.8 - - - +
147D LEU* 1.3 63.1 + - - +
148D ASP* 4.1 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ASN* 3.0 22.9 + - - -
104D LEU* 3.9 13.9 - - + -
107D GLN* 3.9 25.1 - - + -
108D ILE* 3.8 35.2 - - + +
111D GLN* 2.7 18.7 + - - +
112D TYR* 3.4 20.7 + - + +
118D LEU* 5.1 3.1 - - + -
137D ILE* 4.3 14.4 - - + -
138D VAL 3.2 22.7 - - - +
139D LYS* 4.3 0.9 - - - -
146D ALA* 1.3 74.3 - - - +
148D ASP* 1.3 59.7 + - - +
166D ILE* 4.4 1.8 - - + -
204D TYR* 3.7 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 148 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ASN* 2.9 30.5 + - - -
143A ASN* 4.0 4.6 + - - +
148A ASP* 4.7 11.2 - - - +
162A HIS* 5.3 1.6 - - - -
163A LEU* 5.9 0.3 - - - +
112D TYR* 3.6 7.0 + - - -
125D LYS* 5.4 1.2 + - - -
137D ILE* 3.6 3.0 - - - +
138D VAL* 2.8 46.3 + - + +
146D ALA 5.3 0.7 - - - +
147D LEU* 1.3 77.2 - - - +
149D VAL* 1.3 81.6 + - - +
150D VAL* 5.5 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 149 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D TYR* 4.3 3.6 + - - +
118D LEU* 3.8 21.3 - - + -
121D ILE* 3.9 18.4 - - + -
122D THR* 3.6 39.7 - - + +
125D LYS* 3.1 48.8 - - + +
135D ALA* 4.8 1.1 - - + -
136D PHE 3.3 11.2 - - - +
137D ILE* 4.4 4.3 - - + -
148D ASP* 1.3 92.4 + - - +
150D VAL* 1.4 64.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 150 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D LYS* 4.8 3.1 - - - +
135D ALA* 3.3 4.5 - - - +
136D PHE* 2.8 35.8 + - + +
138D VAL* 3.7 22.7 - - + -
148D ASP* 5.5 2.9 - - - +
149D VAL* 1.4 75.0 - - - +
151D THR* 1.3 76.3 + - - +
152D THR* 5.3 1.6 - - + -
158D ILE* 3.5 31.9 - - + -
163D LEU* 6.2 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D LYS* 3.7 43.8 - - + +
129D ILE* 3.7 22.9 - - + +
134D TRP 3.1 9.4 - - - +
135D ALA* 4.3 3.1 - - + -
150D VAL* 1.3 88.1 - - - +
152D THR* 1.3 71.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 152 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D ILE* 5.0 3.1 - - - +
133D GLY* 3.2 3.5 - - - -
134D TRP* 2.9 36.1 + - - +
136D PHE* 3.6 29.5 - - + -
150D VAL* 5.2 1.8 - - + -
151D THR* 1.3 81.8 - - - +
153D ALA* 1.4 59.4 + - - +
156D ASP* 2.6 40.3 + - + +
157D THR 4.2 5.6 - - - +
158D ILE* 4.2 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C ASN* 6.0 3.6 - - - +
129D ILE* 6.1 0.4 - - - -
130D GLN 6.0 1.3 - - - +
132D SER 3.5 8.5 - - - +
152D THR* 1.4 74.1 - - - +
154D ASN* 1.4 77.3 + - - +
156D ASP* 3.1 34.7 + - - +
----------------------------------------------------------
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