Contacts of the strand formed by residues 162 - 165 (chain P) 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 ALA 162 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39P GLY 3.1 11.7 - - - +
40P ILE* 4.1 15.5 - - + -
148P LEU* 4.1 0.2 - - - -
160P TRP* 3.4 10.6 - - - +
161P LYS* 1.3 82.4 - - - +
163P ILE* 1.3 65.4 + - - +
173P GLN* 3.3 14.2 + - - -
176P LEU* 4.5 13.5 - - + -
180P TYR* 4.1 16.8 - - + -
58Q LEU* 4.0 19.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 163 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38P ILE* 3.4 4.0 - - - +
39P GLY 2.8 37.5 + - - +
137P ILE* 4.0 27.8 - - + +
148P LEU* 4.4 4.9 - - + -
149P TYR 4.9 0.4 - - - +
150P THR* 4.5 12.3 - - + +
160P TRP* 3.3 66.0 - - + +
162P ALA* 1.3 75.1 - - - +
164P SER* 1.3 75.8 + - - +
165P VAL* 5.2 0.2 - - + -
173P GLN* 3.6 24.2 - - + +
176P LEU* 4.3 4.3 - - - +
56Q LEU* 5.9 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 164 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36P THR* 4.5 2.7 - - - -
37P ALA 3.1 13.0 - - - -
38P ILE* 3.8 14.8 - - - -
137P ILE* 4.2 0.7 - - - -
163P ILE* 1.3 85.3 - - - +
165P VAL* 1.3 71.0 + - - +
169P THR* 3.5 19.8 + - - +
172P ALA* 3.4 24.9 - - - +
173P GLN* 3.1 17.3 + - - +
176P LEU* 4.5 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 165 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35P GLY 4.2 0.3 - - - +
36P THR* 3.5 4.5 - - - +
37P ALA* 2.9 39.8 + - + -
77P ALA 5.0 1.1 - - - +
79P ALA* 3.4 23.6 - - + +
135P SER* 4.4 22.7 - - - +
136P PHE 4.6 0.7 - - - +
137P ILE* 3.7 27.8 - - + -
150P THR* 3.5 24.9 - - - +
163P ILE* 5.2 0.7 - - + -
164P SER* 1.3 80.6 - - - +
166P GLY* 1.3 62.5 + - - +
169P THR* 3.5 7.9 - - - -
----------------------------------------------------------
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