Contacts of the helix formed by residues 160 - 164 (chain D) in PDB entry 3AP3
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 PRO 160 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D GLY* 3.3 13.1 - - - -
75D GLY* 2.9 42.8 + - - +
77D PRO* 3.7 31.0 - - + -
81D THR* 4.3 12.1 - - + +
99D GLU* 3.1 31.0 - - - +
158D LYS* 3.9 6.9 - - + -
159D ASP* 1.3 84.6 - - + +
161D PHE* 1.3 62.1 + - + +
162D THR 3.0 4.3 + - - -
163D LEU* 3.5 4.9 + - - +
221D MET* 4.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 161 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D VAL* 5.0 3.1 - - + -
77D PRO* 3.6 28.5 - - + -
104D PRO* 5.3 12.7 - - + +
159D ASP* 2.8 3.6 + - - +
160D PRO* 1.3 79.3 - - + +
162D THR* 1.3 63.6 - - - +
163D LEU 3.1 2.7 - - - -
164D LYS* 2.9 42.0 + - + +
165D SER* 4.6 1.2 + - - -
199D ILE* 3.6 30.7 - - + -
200D ALA* 5.7 4.7 - - + -
202D PHE* 4.8 11.0 - + - -
217D ALA* 4.6 15.3 - - + -
221D MET* 3.5 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 162 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D PHE* 5.0 5.8 - - + +
73D VAL 3.8 5.0 + - - -
103D ILE* 4.5 9.4 - - + -
104D PRO* 4.7 6.8 - - + +
107D LEU* 4.4 22.4 - - + -
157D ASN* 4.2 10.8 + - - +
159D ASP* 2.6 42.2 + - + +
161D PHE* 1.3 71.8 - - - +
163D LEU* 1.3 71.3 + - - +
164D LYS 2.8 4.9 - - - -
165D SER* 2.6 36.1 + - - -
166D SER 3.6 2.6 + - - -
169D LEU* 4.0 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 163 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D PHE* 4.0 16.4 - - + +
73D VAL 3.7 4.3 - - - -
74D GLY* 3.4 32.1 - - - +
75D GLY 4.0 4.5 - - - +
160D PRO 3.5 6.3 + - - +
161D PHE 3.1 0.8 - - - -
162D THR* 1.3 93.2 + - - +
164D LYS* 1.3 56.5 - - - +
165D SER 3.1 1.1 - - - -
166D SER* 3.0 27.7 + - - +
178D PHE* 4.6 17.0 - - + -
179D LEU 3.5 21.3 - - - +
180D LEU* 3.5 32.3 - - + -
221D MET* 4.1 14.1 - - + +
224D GLN* 3.9 8.0 - - - +
225D CYS* 6.0 0.2 - - + -
233D CYS* 5.0 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 164 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D PHE* 2.9 42.0 + - + +
162D THR 2.6 1.8 + - - -
163D LEU* 1.3 78.2 - - - +
165D SER* 1.3 59.8 + - - +
217D ALA* 5.0 12.1 - - - +
220D VAL* 4.1 35.3 - - - +
221D MET* 3.9 22.4 - - + -
224D GLN* 3.0 21.5 + - - +
----------------------------------------------------------
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