Contacts of the helix formed by residues 157 - 169 (chain A) in PDB entry 1RYF
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 157 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ARG* 3.7 8.1 - - - +
155A PRO 4.2 7.0 - - - +
156A ILE* 1.3 79.6 - - - +
158A TYR* 1.3 65.4 + - - +
159A PRO* 3.4 12.2 - - - +
160A GLN* 3.1 39.5 + - - +
161A GLY* 3.0 19.2 + - - -
175A GLU* 4.2 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ARG* 3.5 12.5 - - - +
157A THR* 1.3 72.9 - - - +
159A PRO* 1.3 69.7 - - + +
161A GLY 3.2 2.1 + - - -
162A LEU* 2.9 54.1 + - + +
173A TYR* 3.6 35.3 + + - -
174A LEU* 5.9 0.2 - - - -
175A GLU* 3.5 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A THR* 3.4 14.8 - - - +
158A TYR* 1.3 103.2 - - + +
160A GLN* 1.3 55.4 + - + +
162A LEU* 3.7 7.8 - - + +
163A ALA* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PHE* 3.4 17.1 - - + -
154A THR* 5.4 3.3 + - - -
155A PRO 4.0 3.2 + - - +
156A ILE* 3.5 22.3 - - + +
157A THR* 3.1 41.6 + - - +
159A PRO* 1.3 79.1 - - + +
161A GLY* 1.3 56.5 + - - +
163A ALA* 3.4 7.2 + - - +
164A MET 3.0 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PHE* 4.0 14.8 - - - -
131A LEU* 3.6 6.8 - - - +
156A ILE* 4.0 1.9 - - - +
157A THR 3.0 10.7 + - - -
158A TYR 3.2 0.4 + - - -
160A GLN* 1.3 75.3 - - - +
162A LEU* 1.3 56.6 + - - +
164A MET* 3.1 3.8 + - - +
165A ALA* 2.9 25.6 + - - +
173A TYR* 3.4 32.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A TYR* 2.9 44.4 + - + +
159A PRO* 3.7 8.7 - - + +
161A GLY* 1.3 75.5 - - - +
163A ALA* 1.3 58.3 + - - +
165A ALA* 3.3 5.9 + - + +
166A LYS* 3.1 26.3 + - - +
173A TYR* 3.6 27.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A PRO 2.9 17.3 + - - +
160A GLN* 3.7 7.4 - - - +
162A LEU* 1.3 74.6 - - - +
164A MET* 1.3 59.0 + - - +
166A LYS* 3.3 9.3 + - - +
167A GLU* 2.9 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PHE* 3.5 66.4 - - + +
110A GLU* 4.6 2.7 - - - +
112A VAL* 3.9 14.8 - - + -
113A ARG* 3.9 45.3 - - + +
131A LEU* 3.8 13.7 - - + -
160A GLN 3.0 6.5 + - - -
161A GLY 3.1 4.7 + - - +
163A ALA* 1.3 71.7 - - - +
165A ALA* 1.3 66.3 + - - +
167A GLU* 3.1 10.0 + - - +
168A ILE* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU* 3.6 11.1 - - + +
161A GLY 2.9 13.2 + - - +
162A LEU* 3.3 11.6 + - + +
164A MET* 1.3 75.8 - - - +
166A LYS* 1.3 56.8 + - - +
168A ILE* 3.4 1.4 + - - +
169A GLY 3.0 9.0 + - - -
170A ALA* 2.9 49.4 + - + +
172A LYS 4.5 1.8 - - - +
173A TYR* 3.8 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A LEU 3.1 10.1 + - - +
163A ALA* 3.7 10.5 - - - +
164A MET 3.3 0.4 - - - -
165A ALA* 1.3 79.4 - - - +
167A GLU* 1.3 62.3 + - - +
169A GLY* 3.2 13.1 + - - -
170A ALA 5.4 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ARG* 4.6 24.2 + - + +
117A TYR* 4.5 10.0 + - - -
163A ALA 2.9 16.7 + - - +
164A MET* 3.1 21.1 + - - +
166A LYS* 1.3 78.4 - - - +
168A ILE* 1.3 59.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ILE* 4.4 8.7 - - + -
112A VAL* 3.6 30.5 - - + -
113A ARG* 4.2 13.7 - - + -
117A TYR* 3.2 57.8 - - + -
121A ARG* 5.0 2.1 + - - -
129A ILE* 4.2 27.9 - - + +
131A LEU* 4.2 14.4 - - + -
164A MET* 3.1 19.6 + - - +
165A ALA 3.6 7.0 - - - +
167A GLU* 1.3 78.2 - - - +
169A GLY* 1.3 59.2 + - - +
170A ALA* 3.4 9.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 4.6 11.6 + - - -
129A ILE* 5.2 1.4 + - - +
165A ALA 3.0 5.0 + - - -
166A LYS* 3.2 12.5 + - - -
167A GLU 3.4 0.6 - - - -
168A ILE* 1.3 79.5 - - - +
170A ALA* 1.3 64.3 + - - +
171A VAL* 3.7 7.4 + - - +
----------------------------------------------------------
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