Contacts of the helix formed by residues 163 - 168 (chain D) in PDB entry 3DLX
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 THR 163 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160D GLY* 2.8 22.5 + - - +
161D TYR 3.5 11.7 - - - +
162D GLY* 1.3 83.9 - - - +
164D LEU* 1.3 60.1 + - - +
165D VAL* 3.1 8.2 + - - +
166D GLN* 3.2 2.4 + - - -
167D GLU* 3.0 33.9 + - - +
427D MET* 3.5 13.5 - - + +
460D LEU* 3.4 24.9 - - + +
461D THR 3.6 27.4 - - - +
462D GLY* 4.1 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 164 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D THR* 1.3 71.7 - - - +
165D VAL* 1.3 61.9 + - - +
167D GLU* 4.4 12.1 - - + +
168D GLY* 3.0 42.8 + - - +
169D GLY 4.2 9.0 - - - +
170D SER* 4.0 26.7 - - - +
171D PRO* 4.7 0.4 - - + -
184D SER* 3.5 7.6 + - - -
413D TRP* 4.1 11.0 - - + -
414D MET* 3.8 28.5 - - + -
459D PRO* 4.1 19.7 - - + -
460D LEU 4.8 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 165 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D LEU 4.6 5.4 - - - +
137D PRO* 3.8 27.6 - - + -
159D THR 5.0 0.2 - - - +
160D GLY* 4.1 4.9 - - - -
163D THR* 3.1 12.7 - - - +
164D LEU* 1.3 80.4 - - + +
166D GLN* 1.3 60.1 + - - +
168D GLY 4.0 2.4 + - - -
170D SER* 5.6 3.6 - - - +
184D SER* 5.0 2.3 + - - -
185D LYS 4.2 5.9 - - - +
187D ARG* 3.4 23.6 + - + +
198D ILE* 4.0 10.3 - - + -
200D GLU* 3.9 22.2 - - - +
413D TRP* 5.7 1.3 - - + -
423D MET* 3.8 28.9 - - + -
427D MET* 4.0 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 166 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160D GLY 3.2 19.5 + - - +
161D TYR* 3.6 10.6 - - + -
162D GLY* 2.8 30.3 + - - -
163D THR 3.2 2.9 + - - +
165D VAL* 1.3 77.2 - - - +
167D GLU* 1.3 80.9 + - - +
186D PRO* 3.4 3.5 - - - +
187D ARG* 2.9 35.3 + - - +
189D VAL* 3.5 22.6 - - + +
198D ILE* 3.5 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 167 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D GLY* 3.2 28.7 - - - +
163D THR* 3.0 21.5 + - - +
164D LEU* 4.4 10.1 + - + +
166D GLN* 1.3 94.8 - - - +
168D GLY* 1.3 66.8 + - - +
186D PRO* 3.5 19.0 - - - +
463D LYS* 4.7 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 168 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D LEU* 3.0 24.5 + - - +
165D VAL 4.0 0.4 + - - -
166D GLN 3.4 3.0 + - - -
167D GLU* 1.3 85.3 - - - +
169D GLY* 1.3 60.8 + - - -
170D SER 3.4 1.3 - - - -
184D SER* 3.1 22.7 - - - -
185D LYS 3.7 13.0 - - - -
186D PRO* 3.9 2.1 - - - +
----------------------------------------------------------
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