Contacts of the helix formed by residues 135 - 141 (chain C) in PDB entry 1C2O
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 GLY 135 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C TRP* 3.4 26.6 - - - +
133C TYR 3.0 9.2 + - - -
134C ASP* 1.3 69.1 + - - +
136C ARG* 1.3 61.4 + - - +
137C PHE 3.5 0.9 - - - -
138C LEU 4.3 2.5 - - - -
139C ALA* 3.4 21.8 + - - +
146C LEU* 3.4 33.8 - - - +
455C PHE* 4.2 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LEU* 3.4 36.1 - - + +
23C LYS 3.9 24.1 + - - +
24C ALA* 3.8 19.9 - - + +
25C PRO* 5.2 0.6 - - - +
29C VAL* 4.0 14.7 - - + +
102C TRP* 3.3 18.7 - - + -
134C ASP* 3.0 41.5 + - - +
135C GLY* 1.3 73.7 - - - +
137C PHE* 1.3 82.3 + - + +
139C ALA* 3.1 2.4 + - - +
140C GLN* 2.6 38.4 + - - +
460C ASP* 5.8 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ALA* 4.8 1.1 - - + -
25C PRO* 3.6 35.0 - - + -
134C ASP* 3.8 16.2 - - - -
135C GLY 3.5 0.2 - - - -
136C ARG* 1.3 99.9 - - + +
138C LEU* 1.3 58.9 + - - +
139C ALA 3.0 0.3 + - - -
140C GLN* 4.2 5.4 - - - -
141C VAL* 2.7 39.3 + - + +
455C PHE 3.5 21.3 - - - +
456C GLY* 3.7 18.6 - - - +
457C LEU* 3.9 22.9 - - + -
459C LEU* 4.1 11.2 - - + -
460C ASP* 4.0 27.8 - - + -
463C LEU* 5.3 1.3 - - + -
477C MET* 3.8 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C LEU* 4.5 11.9 - - + -
135C GLY* 3.8 1.9 + - - -
136C ARG 3.5 0.4 - - - -
137C PHE* 1.3 74.9 - - - +
139C ALA* 1.3 58.0 + - - +
142C GLU* 3.5 12.8 + - - +
144C ALA* 3.2 26.6 + - + +
146C LEU* 3.9 21.5 - - + -
200C PHE* 5.0 6.3 - - + -
454C ILE* 3.5 11.4 - - + +
455C PHE* 3.5 50.9 - - + +
477C MET* 3.2 40.2 - - + +
480C TRP* 5.2 5.6 - - + -
481C THR* 4.3 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C VAL* 4.0 16.8 - - + -
102C TRP* 4.2 14.4 - - + +
104C PRO* 3.9 12.2 - - - +
135C GLY 3.4 13.4 + - - +
136C ARG 3.1 7.1 + - - +
138C LEU* 1.3 76.8 - - - +
140C GLN* 1.3 69.9 + - - +
143C GLY* 2.8 24.3 + - - -
144C ALA 2.9 25.1 - - - +
146C LEU 5.1 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ALA* 3.3 27.4 - - + +
25C PRO* 5.5 0.3 - - - +
26C GLY* 3.1 42.8 + - - -
27C GLY* 3.8 14.2 - - - +
28C PRO* 4.4 6.9 - - - +
29C VAL* 4.2 8.4 - - + +
104C PRO* 5.0 6.6 - - - +
136C ARG 2.6 21.8 + - - +
137C PHE* 3.7 3.5 - - - +
139C ALA* 1.3 79.1 - - - +
141C VAL* 1.3 82.9 + - - +
143C GLY* 3.8 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C GLY* 5.8 0.2 - - - -
137C PHE* 2.7 24.5 + - + +
140C GLN* 1.3 95.7 - - - +
142C GLU* 1.3 86.0 + - + +
143C GLY 3.2 1.5 + - - -
459C LEU* 3.5 33.0 - - + -
474C GLN* 5.7 7.0 - - + +
477C MET* 4.6 6.5 - - + -
----------------------------------------------------------
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