Contacts of the helix formed by residues 121 - 131 (chain A) in PDB entry 2DOU
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 TYR 121 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLN* 3.1 18.1 + - - -
120A ALA* 1.3 73.5 - - - +
122A PRO* 1.3 86.5 - - + +
123A SER* 2.8 33.0 - - - -
124A TYR* 2.9 47.4 + + + +
125A PHE* 4.1 2.3 - - - -
165A ASN* 5.5 0.4 - - - +
169A ASN* 3.5 30.2 + - + +
345A PHE* 4.5 2.7 - + - -
501A EPE 3.1 76.9 + - - +
261B PHE* 3.6 12.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A VAL* 5.6 0.7 - - - +
5A PRO* 4.7 8.9 - - + +
10A PHE* 4.5 16.6 - - + -
120A ALA 3.2 7.8 - - - +
121A TYR* 1.3 98.8 - - + +
123A SER* 1.3 62.1 + - - +
124A TYR 3.0 1.9 + - - -
125A PHE* 3.1 27.2 + - + +
126A GLY 3.4 5.9 + - - -
344A GLY 4.0 16.8 - - - +
345A PHE* 3.5 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLN* 2.8 36.1 + - - -
100A LEU* 5.7 0.6 - - - +
121A TYR* 2.8 21.8 + - - -
122A PRO* 1.3 79.7 - - - +
124A TYR* 1.3 59.0 + - - +
126A GLY 3.6 2.5 - - - +
127A ALA* 2.7 32.1 + - - +
257B GLY 5.0 0.9 - - - -
258B VAL* 3.7 30.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLN* 4.9 2.0 - - - -
100A LEU* 3.3 27.8 - - + -
104A LEU* 4.8 2.8 - - - +
114A LEU* 5.1 1.0 - - - +
116A LEU* 3.9 19.3 - - + +
117A PRO* 5.7 2.2 - - + -
120A ALA* 3.8 22.9 - - + -
121A TYR* 2.9 35.4 + + + +
123A SER* 1.3 81.9 - - - +
125A PHE* 1.3 62.9 + - - +
127A ALA* 3.2 6.9 + - - +
128A ALA* 2.9 23.6 + - - +
163A LEU* 3.6 28.2 - - + +
164A LEU 5.3 0.9 - - - -
165A ASN* 3.4 24.2 - - + +
197A ASP* 2.5 35.8 + - + +
501A EPE 3.0 11.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A VAL* 3.9 31.1 - - + +
5A PRO* 3.8 18.2 - - + -
116A LEU* 3.8 15.9 - - + -
117A PRO 3.8 14.1 - - - -
118A GLU 4.6 1.6 - - - -
120A ALA* 3.9 19.7 - - + -
121A TYR 4.1 4.0 - - - -
122A PRO* 3.1 14.9 + - + +
124A TYR* 1.3 76.4 - - - +
126A GLY* 1.3 62.9 + - - +
128A ALA* 3.1 10.3 + - - +
129A ARG* 3.0 20.8 + - - +
135A THR* 5.7 3.4 - - + -
137A LEU* 3.7 35.0 - - + -
345A PHE 3.5 30.1 - - - -
346A GLY* 4.4 7.9 - - - -
347A PRO* 5.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A VAL* 4.4 6.5 - - - +
122A PRO 3.4 6.0 + - - -
123A SER 3.3 5.3 + - - -
124A TYR 3.2 0.6 - - - -
125A PHE* 1.3 79.3 - - - +
127A ALA* 1.3 55.5 + - - +
129A ARG* 3.0 6.6 + - - +
130A VAL* 2.9 31.4 + - - +
254B ARG* 3.9 13.2 + - - -
258B VAL* 3.8 23.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 5.0 5.2 - - + -
101A ALA* 4.1 25.7 - - + +
104A LEU* 3.8 19.4 - - + +
123A SER 2.7 21.3 + - - +
124A TYR* 3.5 7.2 - - - +
126A GLY* 1.3 68.4 - - - +
128A ALA* 1.3 68.1 + - - +
130A VAL* 3.1 15.6 + - - +
131A ALA* 3.1 13.9 + - - +
258B VAL* 3.8 13.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 4.0 9.1 - - - +
114A LEU* 3.8 23.3 - - + -
116A LEU* 5.7 0.4 - - + -
124A TYR 2.9 13.4 + - - +
125A PHE* 3.1 12.5 + - - +
127A ALA* 1.3 76.3 - - - +
129A ARG* 1.3 61.2 + - - +
131A ALA 3.2 2.8 + - - -
132A SER 3.1 3.3 + - - -
133A LEU* 3.0 37.9 + - + +
135A THR* 4.0 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A VAL* 3.3 45.7 - - + +
125A PHE 3.0 12.2 + - - +
126A GLY* 3.0 12.1 + - - +
128A ALA* 1.3 74.7 - - - +
130A VAL* 1.3 62.3 + - + +
132A SER* 2.8 23.1 + - - +
133A LEU 4.8 3.8 - - - +
254B ARG* 4.0 20.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ALA* 6.0 1.3 - - + -
105A LEU* 4.1 10.0 - - + +
126A GLY 2.9 16.9 + - - +
127A ALA* 3.4 7.9 - - - +
129A ARG* 1.3 77.9 - - + +
131A ALA* 1.3 59.2 + - - +
132A SER* 3.5 4.7 + - - -
105B LEU* 3.8 42.2 - - + +
254B ARG* 4.8 9.2 - - - +
255B VAL* 4.5 18.6 - - + -
258B VAL* 3.6 22.7 - - + -
259B ILE* 4.4 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 4.4 11.0 - - + -
105A LEU* 3.7 22.7 - - + +
108A THR* 4.3 7.9 + - - +
109A GLU 4.6 0.3 - - - -
110A PRO* 3.9 10.9 - - - +
127A ALA 3.1 10.5 + - - +
128A ALA 3.6 3.6 - - - +
129A ARG 3.0 0.8 - - - -
130A VAL* 1.3 75.9 - - - +
132A SER* 1.3 71.2 + - - +
133A LEU* 3.3 35.3 + - + +
----------------------------------------------------------
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