Contacts of the strand formed by residues 145 - 151 (chain B) in PDB entry 3TDD
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 145 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B TYR* 1.3 77.8 - - - +
141B TYR* 3.2 25.0 - - - -
142B ASP 2.8 28.4 + - - -
143B ASP 4.7 0.6 - - - -
144B ARG 3.7 1.0 - - - +
146B TYR* 1.3 57.8 + - - -
147B GLN* 3.1 20.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B TYR 3.3 1.0 + - - +
21B VAL* 3.0 43.4 + - + +
41B MET* 3.3 17.5 - - + +
42B ALA 4.5 2.7 - - - +
43B SER 3.9 16.2 - - - -
44B ASP* 3.5 9.3 + - - -
45B GLY* 3.6 20.2 - - - -
46B ILE* 3.7 28.7 - - + -
140B GLY 3.5 1.8 - - - -
141B TYR* 3.8 28.9 - + + -
145B GLY* 1.3 71.6 - - - -
147B GLN* 1.3 59.0 + - - +
215B ILE* 3.3 28.5 - - + -
216B ARG 3.5 0.7 - - - -
62C ARG* 2.9 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B TYR* 3.4 21.0 - - + +
41B MET* 4.2 2.5 - - - -
46B ILE* 3.2 8.7 - - - +
109B VAL* 3.4 15.2 - - + +
110B GLU* 4.0 3.3 + - - +
138B TYR 3.5 2.2 - - - +
140B GLY 2.8 33.5 + - - +
142B ASP* 2.6 34.4 + - - +
145B GLY 3.1 18.1 + - - +
146B TYR* 1.3 80.5 - - - +
148B LEU* 1.3 62.0 + - - +
149B TYR* 2.7 41.6 + - + -
62C ILE* 3.6 23.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLY* 3.1 36.3 - - - +
40B ILE 3.7 2.5 - - - +
41B MET* 3.8 11.4 - - + +
46B ILE* 3.7 25.4 - - + -
137B ILE* 4.0 20.0 - - + -
138B TYR 3.1 15.5 - - - +
139B ALA* 4.0 5.4 - - + -
147B GLN* 1.3 74.8 - - - +
149B TYR* 1.3 62.0 + - - +
159B GLY* 3.3 5.7 - - - -
160B TRP* 2.8 43.8 + - - +
161B LYS 3.8 18.6 - - - +
162B ALA* 4.1 2.2 - - - +
163B ILE* 4.4 7.9 - - + +
62C ILE* 3.5 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B TYR* 5.1 0.7 - - - -
109B VAL* 3.6 22.2 - - + -
110B GLU* 3.5 21.8 - - + +
113B VAL* 3.9 13.9 - - + -
137B ILE* 3.2 9.7 - - - +
138B TYR* 2.6 50.9 + - + -
147B GLN* 2.7 42.4 + - + -
148B LEU* 1.3 75.9 - - - +
150B THR* 1.3 63.0 + - - +
157B TYR* 4.1 21.8 - + - -
158B THR 3.2 21.3 - - - -
159B GLY* 3.9 2.5 - - - -
160B TRP* 4.6 2.2 - - - -
163B ILE* 5.0 0.8 - - - +
62C ILE* 3.0 43.3 + - + +
63C THR* 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PHE 3.2 14.6 + - - -
137B ILE* 4.3 1.9 - - - +
138B TYR* 4.3 1.8 - - - -
149B TYR* 1.3 76.7 - - - +
151B SER* 1.3 61.8 + - - +
152B ASN* 5.9 4.0 - - - +
156B ASN 5.5 0.4 - - - +
157B TYR* 2.9 25.1 - - - +
158B THR* 3.0 16.9 + - - +
160B TRP* 3.3 31.4 - - + +
163B ILE* 4.6 9.7 - - + +
165B VAL* 3.5 22.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B SER* 3.6 25.4 - - - -
120B LYS* 2.9 17.8 + - - -
135B SER* 3.2 5.1 - - - -
136B PHE* 2.8 31.4 + - - +
138B TYR* 2.7 31.2 + - - -
150B THR* 1.3 78.2 + - - +
152B ASN* 1.3 62.5 + - - +
155B GLY 5.4 0.2 - - - -
156B ASN 3.2 9.9 - - - -
157B TYR* 3.9 0.9 - - - -
----------------------------------------------------------
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