Contacts of the helix formed by residues 167 - 174 (chain A) in PDB entry 5DAH
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 HIS 167 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU 3.9 8.1 - - - -
85A CYS* 4.2 2.0 - - + -
86A PRO* 3.5 20.0 - - + +
137A CYS* 3.4 15.2 - - + +
140A CYS* 3.7 0.2 - - - -
148A LYS 3.0 25.4 - - - -
149A ALA 4.0 4.5 + - - -
151A THR 2.6 28.4 + - - -
153A ALA 3.5 21.1 - - - -
154A CYS* 4.2 5.5 - - - -
166A PHE* 1.3 78.4 - - - +
168A VAL* 1.3 64.5 + - - +
169A THR* 4.1 8.5 - - - +
170A CYS* 3.2 19.1 + - - +
171A ALA 3.2 9.9 + - - -
304A ZN 2.2 36.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A CYS* 5.4 0.2 - - - +
104A VAL* 3.3 42.2 - - + +
105A CYS* 3.9 18.6 - - - +
108A TYR* 3.6 18.6 - - + -
109A ILE* 3.8 26.5 - - + -
153A ALA 4.8 2.4 + - - -
155A MET* 3.5 27.6 - - + +
166A PHE 3.5 1.4 + - - -
167A HIS* 1.3 71.0 - - - +
169A THR* 1.3 63.7 + - - +
171A ALA* 3.3 2.4 + - - +
172A GLN* 3.0 20.1 + - - +
177A LEU* 3.6 9.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A CYS* 3.0 40.8 - - - +
86A PRO* 4.8 1.2 - - - +
87A HIS* 4.0 22.4 + - - +
102A HIS* 3.8 18.8 - - + +
104A VAL* 4.1 15.5 - - + -
105A CYS* 4.0 4.4 - - - -
167A HIS* 4.1 2.3 - - - +
168A VAL* 1.3 78.9 - - - +
170A CYS* 1.3 63.6 + - - +
172A GLN* 3.3 16.1 + - - +
173A PHE* 3.1 27.7 - - - -
303A ZN 3.9 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PRO* 5.2 4.3 - - - -
137A CYS* 3.8 2.2 - - - -
139A ILE* 3.9 29.1 - - + +
140A CYS* 3.9 5.8 - - - -
143A GLN* 5.9 1.8 - - - -
167A HIS* 3.2 16.1 + - + +
169A THR* 1.3 79.5 + - - +
171A ALA* 1.3 63.3 + - - +
173A PHE* 3.5 4.9 + - - +
174A ALA* 3.1 22.5 + - - +
304A ZN 2.3 38.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ILE* 4.0 6.5 - - - +
166A PHE* 3.5 33.7 - - + -
167A HIS 3.2 3.2 + - - -
168A VAL 3.3 2.7 + - - +
170A CYS* 1.3 76.9 - - - +
172A GLN* 1.3 59.1 + - - +
174A ALA* 3.3 0.8 + - - -
175A GLY 2.8 8.7 + - - -
176A LEU* 2.5 51.4 + - + -
177A LEU* 3.8 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 3.5 23.5 - - + +
26A CYS 3.0 29.3 + - - +
27A VAL 3.9 13.1 + - - -
28A CYS 5.6 0.2 - - - -
29A SER* 4.4 10.3 + - - +
87A HIS* 5.5 1.2 - - - -
104A VAL* 4.1 19.6 - - - +
168A VAL 3.0 12.9 + - - +
169A THR* 3.4 14.3 - - - +
170A CYS 3.2 0.4 - - - -
171A ALA* 1.3 78.1 - - - +
173A PHE* 1.3 74.3 + - + +
175A GLY* 3.1 16.1 + - - -
177A LEU* 3.7 19.9 - - + +
143B GLN* 5.1 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A MET* 3.7 44.0 - - + -
22A ILE* 3.7 21.1 - - + -
87A HIS* 3.9 36.8 - + - -
169A THR* 3.1 18.7 + - - +
170A CYS* 3.5 4.2 + - - +
171A ALA 3.3 0.2 - - - -
172A GLN* 1.3 94.7 - - + +
174A ALA* 1.3 59.1 + - - +
175A GLY 3.1 5.5 + - - -
139B ILE* 4.1 7.6 - - - +
143B GLN* 2.8 48.4 + - + +
173B PHE* 5.8 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ILE* 4.3 7.9 - - + -
170A CYS 3.1 18.0 + - - +
171A ALA 3.8 0.2 - - - +
172A GLN 3.3 0.2 - - - -
173A PHE* 1.3 76.7 - - - +
175A GLY* 1.3 62.1 + - - +
176A LEU* 3.6 32.0 - - + +
138B TYR* 5.2 3.5 + - - -
139B ILE* 5.5 6.7 - - - +
142B GLU* 5.1 0.3 - - - +
173B PHE 5.6 0.2 - - - +
174B ALA* 4.3 31.8 - - + +
176B LEU* 5.7 1.2 - - - +
195B LYS* 4.4 8.8 - - - +
----------------------------------------------------------
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