Contacts of the helix formed by residues 129 - 139 (chain A) in PDB entry 2C0O
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 SER 129 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLY 3.8 3.0 + - - -
128A ILE* 1.3 79.9 - - - +
130A ARG* 1.3 64.4 + - - +
131A LYS* 3.4 8.1 + - - +
132A ASP* 3.0 33.3 + - - -
133A ALA* 3.0 20.7 + - - +
150A ARG* 4.6 0.4 - - - -
153A GLU* 3.2 31.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A SER* 1.3 71.5 - - - +
131A LYS* 1.3 66.4 + - - +
133A ALA 3.6 0.3 + - - -
134A GLU* 3.2 30.0 + - - +
150A ARG* 3.7 20.8 - - - +
153A GLU* 3.0 20.2 + - - +
176A HIS* 3.6 35.9 - - + +
491A ASP* 5.9 0.8 - - - +
492A ASP* 2.8 43.6 + - - -
495A THR* 5.2 3.0 + - - +
500A GLN* 3.4 33.4 + - - +
501A PTR 3.8 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A SER* 3.1 7.2 + - - +
130A ARG* 1.3 84.1 - - + +
132A ASP* 1.3 59.6 + - - +
134A GLU* 3.0 42.0 + - - +
135A ARG* 3.0 46.6 + - - +
153A GLU* 4.8 0.2 + - - -
339A ASP* 4.4 15.3 + - - -
490A LEU 5.1 0.6 + - - -
491A ASP* 2.7 56.1 + - + +
492A ASP* 5.3 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLY 4.9 1.4 - - - +
128A ILE* 3.8 23.0 - - + +
129A SER* 3.0 32.3 + - - +
131A LYS* 1.3 72.5 - - - +
133A ALA* 1.3 57.9 + - - +
134A GLU 3.1 1.6 - - - -
135A ARG* 3.6 20.3 + - - +
136A GLN* 2.6 40.0 + - + +
295A LYS* 5.1 7.8 + - - -
346A GLU* 5.0 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ILE* 3.4 8.0 - - + +
129A SER 3.0 11.5 + - - +
130A ARG 3.6 4.7 - - - +
132A ASP* 1.3 77.1 - - - +
134A GLU* 1.3 57.1 + - - +
136A GLN* 4.1 0.4 - - - -
137A LEU* 3.0 37.8 + - - +
148A MET* 3.8 16.3 - - - +
150A ARG* 3.3 36.1 - - - +
162A SER* 4.1 9.4 - - - +
176A HIS* 4.6 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ARG* 3.2 17.9 + - - +
131A LYS* 3.0 46.8 + - - +
132A ASP 3.1 0.2 - - - -
133A ALA* 1.3 77.5 - - - +
135A ARG* 1.3 59.0 + - - +
137A LEU* 3.4 1.7 + - - +
138A LEU* 2.9 54.5 + - + +
174A VAL* 3.9 27.1 - - + +
176A HIS* 4.1 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LYS* 3.0 37.4 + - - +
132A ASP* 3.1 24.2 + - - +
134A GLU* 1.3 75.8 - - + +
136A GLN* 1.3 66.0 + - + +
138A LEU* 3.4 6.6 + - - +
139A ALA* 3.2 19.8 + - - +
295A LYS* 4.9 4.8 - - - +
339A ASP* 2.8 46.4 + - - +
342A ALA* 3.9 3.2 - - - +
343A GLN* 3.4 35.9 - - - +
346A GLU* 4.6 9.1 + - - -
373A VAL* 6.4 0.2 - - - -
491A ASP* 3.8 19.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A PHE* 3.7 27.9 - - - -
128A ILE* 3.7 31.5 - - - +
132A ASP* 2.6 21.6 + - + +
133A ALA 4.2 2.7 - - - +
135A ARG* 1.3 73.4 - - - +
137A LEU* 1.3 62.3 + - - +
139A ALA* 3.1 20.1 + - + +
142A ASN* 3.1 13.7 + - - -
148A MET* 4.2 10.9 - - + +
220A CYS* 4.0 3.4 - - - -
221A MET 3.8 12.8 - - - +
222A SER* 4.1 7.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ALA 3.0 24.2 + - - +
134A GLU 3.8 2.9 - - - +
136A GLN* 1.3 76.4 - - - +
138A LEU* 1.3 59.7 + - - +
142A ASN* 3.1 28.3 + - - +
146A SER* 3.6 39.7 - - - +
147A PHE* 3.7 5.6 - - - +
148A MET* 4.1 8.3 - - + -
162A SER* 3.6 34.5 - - - +
163A VAL 4.7 0.2 - - - +
164A ARG* 3.4 14.4 + - + +
174A VAL* 3.7 22.4 - - + -
220A CYS* 3.8 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLU* 2.9 45.4 + - + +
135A ARG* 3.4 6.5 + - - +
136A GLN 3.3 0.2 - - - -
137A LEU* 1.3 73.4 - - - +
139A ALA* 1.3 63.4 + - - +
140A PRO* 3.8 1.7 - - - +
164A ARG* 4.1 19.6 + - - +
172A ASP* 3.8 41.1 - - + +
173A THR* 4.4 2.9 - - - +
174A VAL* 4.0 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ARG 3.2 10.7 + - - +
136A GLN* 3.1 20.3 + - + +
137A LEU 3.7 0.9 - - - +
138A LEU* 1.3 81.0 - - - +
140A PRO* 1.3 80.5 - - + +
141A GLY 3.3 2.1 + - - -
142A ASN* 3.4 17.0 + - - +
164A ARG* 4.0 2.8 + - - -
----------------------------------------------------------
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