Contacts of the helix formed by residues 151 - 161 (chain A) in PDB entry 2ORY
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 151 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TRP* 4.1 0.4 - - - -
137A GLN 3.6 23.3 - - - +
138A LYS* 4.3 5.4 - - - +
139A LEU 3.4 10.3 - - - +
140A LYS* 3.5 27.8 - - + -
150A LYS* 1.3 76.8 - - - +
152A ILE* 1.3 64.9 + - - +
153A LEU* 3.6 6.9 + - - +
154A GLN* 3.0 40.6 + - - +
155A PHE* 2.9 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TRP* 3.8 24.5 - - + +
73A MET* 3.9 21.3 - - + -
75A VAL* 3.4 32.5 - - + -
87A ILE* 4.3 17.3 - - + -
136A LEU 4.2 15.8 + - - +
137A GLN* 4.7 5.1 + - - +
139A LEU 4.3 1.2 + - - -
151A THR* 1.3 73.8 - - - +
153A LEU* 1.3 66.1 + - - +
155A PHE* 3.3 4.0 + - + +
156A LEU* 3.0 46.3 + - + +
183A LEU* 5.0 4.9 - - + -
186A TRP* 4.1 27.4 - - + -
187A LEU* 5.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A GLN 6.0 0.7 - - - +
151A THR* 3.2 7.2 + - - +
152A ILE* 1.3 84.2 - - - +
154A GLN* 1.3 63.0 + - + +
156A LEU* 3.4 4.3 + - + +
157A ASN* 3.0 52.9 + - - +
186A TRP* 4.0 31.4 - - + -
187A LEU* 4.9 3.1 - - + -
190A ILE* 3.9 21.8 - - + -
194A LYS* 3.6 26.2 - - + +
195A LEU* 4.1 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LYS* 4.2 11.6 + - - +
149A ASN 4.3 2.3 - - - +
150A LYS* 3.6 16.6 - - + +
151A THR* 3.0 47.3 + - - +
153A LEU* 1.3 77.8 - - + +
155A PHE* 1.3 62.7 + - - +
157A ASN* 3.4 6.0 + - - +
158A GLU* 3.0 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A VAL* 3.3 46.4 - - + -
56A TRP* 3.4 37.7 - + + +
75A VAL* 4.6 8.5 - - + -
85A TYR* 5.0 2.7 - + - -
147A GLY* 4.4 8.1 - - - -
150A LYS* 4.3 10.0 - - + +
151A THR 2.9 17.8 + - - +
152A ILE* 3.6 8.3 - - + +
154A GLN* 1.3 76.9 - - - +
156A LEU* 1.3 71.1 + - + +
158A GLU* 3.3 17.8 + - - +
159A LYS* 2.8 63.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A VAL* 5.2 4.9 - - + -
85A TYR* 5.6 4.5 - - + -
87A ILE* 4.5 6.5 - - + -
152A ILE* 3.0 40.1 + - + +
153A LEU* 3.9 5.2 - - - +
155A PHE* 1.3 90.6 - - + +
157A ASN* 1.3 55.7 + - - +
159A LYS* 4.4 2.9 - - + -
160A ILE* 2.6 47.5 + - + +
168A ILE* 3.7 28.3 - - + -
187A LEU* 4.1 33.7 - - + -
195A LEU* 4.4 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LEU* 3.0 38.7 + - - +
154A GLN* 3.9 5.1 - - - +
156A LEU* 1.3 75.3 - - - +
158A GLU* 1.3 58.7 + - - +
160A ILE* 5.3 0.2 - - - -
161A GLY* 2.8 36.6 + - - +
162A PRO* 4.1 9.5 - - + +
194A LYS* 2.7 29.3 + - - +
195A LEU* 3.8 16.0 - - - +
196A SER 4.3 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A LYS* 3.4 42.1 + - - +
154A GLN 3.0 17.6 + - - +
155A PHE* 3.7 13.3 - - - +
157A ASN* 1.3 79.3 - - - +
159A LYS* 1.3 63.6 + - + +
161A GLY* 4.2 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A VAL* 4.7 4.5 - - - -
77A GLN* 2.6 38.6 + - - +
85A TYR* 3.0 30.2 + - + +
155A PHE* 2.8 51.6 + - + +
156A LEU* 3.8 4.0 - - + +
158A GLU* 1.3 82.3 - - + +
160A ILE* 1.3 60.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR* 4.3 16.2 - - + +
156A LEU* 2.6 30.5 + - + +
157A ASN* 5.3 0.2 - - - -
159A LYS* 1.3 78.0 - - + +
161A GLY* 1.3 61.3 + - - +
164A GLY* 3.0 44.3 - - - +
165A LYS 4.2 2.2 - - - +
166A ALA* 3.4 30.3 - - + -
168A ILE* 4.1 22.9 - - + -
195A LEU* 5.5 4.7 - - + -
196A SER* 4.4 7.0 - - - -
199A ILE* 4.1 9.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
157A ASN* 2.8 23.8 + - - +
158A GLU 4.2 2.6 + - - -
159A LYS 3.5 2.0 - - - -
160A ILE* 1.3 88.9 - - - +
162A PRO* 1.3 75.5 - - - +
163A GLU 3.1 4.6 + - - -
164A GLY 3.3 3.8 + - - -
195A LEU* 6.1 0.2 - - - +
196A SER* 3.8 4.9 + - - -
----------------------------------------------------------
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