Contacts of the helix formed by residues 133 - 144 (chain A) in PDB entry 1Q0R
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 ASP 133 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ASP 3.6 5.2 + - - +
132A ILE* 1.3 69.1 - - - +
134A PHE* 1.3 59.0 + - - +
135A ASP* 3.4 2.6 - - - +
136A ALA* 3.2 25.0 + - + +
137A ASN* 2.9 36.9 + - - +
148A LEU* 6.2 1.9 - - + +
149A ASP* 4.3 2.7 + - - +
224A LEU* 4.8 9.2 - - - +
227A PRO* 5.6 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE* 2.9 11.2 + - + -
133A ASP* 1.3 71.8 - - - +
135A ASP* 1.3 75.0 + - - +
137A ASN* 3.1 10.1 + - + +
138A ILE* 3.1 43.3 + - + +
154A PRO* 3.8 20.9 - - + -
158A PHE* 4.4 1.1 - + - -
224A LEU* 3.7 5.9 - - + +
250A ILE* 3.6 21.3 - - + -
600A AKT 3.3 108.6 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ASP* 3.4 0.6 - - - +
134A PHE* 1.3 79.4 - - - +
136A ALA* 1.3 62.9 + - - +
138A ILE* 3.3 18.0 + - - +
139A GLU* 3.4 11.3 + - - +
222A LEU 4.1 6.4 - - - +
223A THR* 5.3 0.5 - - - -
224A LEU* 4.0 14.0 + - + +
600A AKT 2.9 61.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ASP* 3.2 34.9 + - + +
135A ASP* 1.3 79.3 - - - +
137A ASN* 1.3 61.2 + - - +
139A GLU* 3.3 16.0 + - - +
140A ARG* 2.9 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE* 3.7 17.2 - - - +
133A ASP* 2.9 22.8 + - - +
134A PHE* 3.1 10.5 + - + +
136A ALA* 1.3 75.5 - - - +
138A ILE* 1.3 60.0 + - - +
140A ARG* 3.7 11.1 - - - +
141A VAL* 2.9 34.0 + - - +
147A THR* 3.5 35.4 - - + +
148A LEU* 4.3 2.4 + - - +
149A ASP* 3.0 25.4 + - - +
152A PRO 5.9 0.2 + - - -
153A GLY* 5.4 1.4 - - - -
154A PRO* 4.5 11.4 - - + -
255A HIS* 5.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A PHE* 3.1 39.8 + - + +
135A ASP* 3.3 12.3 + - - +
137A ASN* 1.3 75.0 - - - +
139A GLU* 1.3 62.8 + - - +
141A VAL* 3.1 24.4 - - + +
142A MET* 3.2 31.7 + - + +
154A PRO* 4.1 10.8 - - + -
158A PHE* 3.9 31.0 - - + -
159A LEU* 5.1 1.6 - - + -
162A LEU* 4.9 7.6 - - + -
600A AKT 3.9 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ASP 3.4 7.2 + - - +
136A ALA* 3.3 16.7 + - - +
137A ASN 3.3 0.2 - - - -
138A ILE* 1.3 81.4 - - - +
140A ARG* 1.3 62.8 + - + +
142A MET* 3.4 16.0 + - + +
143A ARG* 3.3 57.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ALA* 2.9 27.2 + - - +
137A ASN* 3.7 20.6 - - - +
138A ILE 3.3 0.2 - - - -
139A GLU* 1.3 78.4 - - + +
141A VAL* 1.3 57.2 + - + +
143A ARG* 3.1 5.3 + - - +
144A GLY 2.9 9.0 + - - -
145A GLU* 2.8 59.0 + - + +
146A PRO* 3.2 27.6 + - - +
147A THR* 4.4 2.9 - - - +
148A LEU* 3.7 37.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ASN 2.9 19.8 + - - +
138A ILE* 3.1 22.2 - - - +
140A ARG* 1.3 75.2 - - - +
142A MET* 1.3 65.5 + - + +
144A GLY* 3.3 11.9 + - - +
145A GLU 4.4 6.5 - - - +
147A THR* 4.9 7.0 - - + -
153A GLY* 3.8 28.9 - - - +
154A PRO* 3.9 21.8 - - + +
159A LEU* 4.7 16.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ILE* 3.2 36.1 + - + +
139A GLU* 3.7 16.2 - - + +
140A ARG 3.2 0.2 - - - -
141A VAL* 1.3 76.2 - - - +
143A ARG* 1.3 62.4 + - + +
144A GLY 3.7 0.3 + - - -
159A LEU* 4.1 30.1 - - + -
162A LEU* 5.9 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLU* 3.3 43.0 + - - +
140A ARG* 3.1 6.7 + - - +
142A MET* 1.3 78.8 - - + +
144A GLY* 1.3 60.4 + - - +
145A GLU* 3.4 20.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG 2.9 3.9 + - - -
141A VAL* 3.3 12.6 + - - -
142A MET 3.4 0.6 - - - -
143A ARG* 1.3 78.7 - - - +
145A GLU* 1.3 66.6 + - - +
146A PRO* 4.2 2.1 - - - +
----------------------------------------------------------
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