Contacts of the helix formed by residues 141 - 147 (chain A) in PDB entry 5NJ8
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 141 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 3.3 42.6 + - + +
120A GLN* 4.6 9.6 - - + +
124A GLY 3.5 13.8 + - - -
125A PHE* 3.4 8.9 - - - +
139A SER* 3.0 19.9 + - - -
140A SER* 1.3 74.9 - - - +
142A ILE* 1.3 64.1 + - - +
143A GLN 3.1 0.9 - - - -
144A ASP* 2.9 38.4 + - - +
145A TYR* 3.5 15.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A PHE* 3.6 33.6 - - + +
127A LEU* 5.3 2.0 - - + -
138A ALA* 4.1 11.0 - - + -
139A SER 3.0 20.5 + - - +
140A SER 4.0 1.3 - - - +
141A THR* 1.3 76.6 - - - +
143A GLN* 1.3 60.9 + - - +
145A TYR 3.4 0.2 + - - -
146A LEU* 2.9 51.9 + - + +
147A GLY 3.6 0.3 + - - -
148A PHE* 3.4 19.2 - - + +
150A GLN* 3.8 20.6 - - + +
153A VAL* 3.9 31.2 - - + -
161A LEU* 4.9 7.2 - - + -
224A LEU* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A SER* 3.3 11.0 + - - +
141A THR 3.1 0.4 - - - -
142A ILE* 1.3 80.8 - - - +
144A ASP* 1.3 66.1 + - - +
147A GLY* 2.9 22.9 + - - -
148A PHE 2.9 29.2 + - - +
149A GLN* 3.0 28.3 + - - +
150A GLN 5.3 0.2 - - - +
228A LEU* 4.6 2.6 - - - +
58C GLN* 3.2 53.3 + - - +
59C ASP* 3.2 11.3 + - - +
62C ASN* 4.5 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLN* 5.5 0.9 + - - +
140A SER 4.5 1.0 - - - +
141A THR* 2.9 32.5 + - - +
143A GLN* 1.3 98.4 + - - +
145A TYR* 1.3 74.4 + - + +
228A LEU* 4.1 11.8 - - - +
58C GLN* 3.6 16.1 - - - +
151D ASP* 3.9 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLN 4.9 1.0 + - - -
122A LEU 3.5 6.4 + - - -
123A ASN* 2.9 33.3 + - - -
124A GLY* 3.3 33.7 - - - -
125A PHE* 4.4 14.8 - + + -
141A THR* 3.6 19.5 - - + +
142A ILE 3.4 1.6 + - - -
143A GLN 3.2 0.4 - - - -
144A ASP* 1.3 93.1 - - + +
146A LEU* 1.3 67.2 + - + +
147A GLY 3.8 0.7 - - - -
226A CYS* 3.9 11.3 - - - -
228A LEU* 4.1 8.9 - - - +
235A LEU* 4.8 7.2 - - + +
237A MET* 5.7 2.5 - - - -
271A PRO* 4.4 17.0 - - + -
260B ARG* 4.1 11.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A PHE* 3.7 22.9 - - + -
142A ILE* 2.9 23.5 + - + +
145A TYR* 1.3 85.5 - - + +
147A GLY* 1.3 63.9 + - - +
148A PHE* 3.2 13.2 + - + +
161A LEU* 5.7 3.4 - - + -
224A LEU* 4.2 17.0 - - + +
225A ARG 3.4 24.0 - - - +
226A CYS* 3.8 12.8 - - + -
227A LEU* 3.2 25.0 + - - +
228A LEU* 3.6 6.3 - - - -
235A LEU* 4.3 7.9 - - + -
237A MET* 3.7 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ILE 3.6 0.2 + - - -
143A GLN* 2.9 20.2 + - - -
146A LEU* 1.3 77.9 - - - +
148A PHE* 1.3 58.7 + - - +
149A GLN 4.2 0.7 + - - -
227A LEU* 3.6 18.0 - - - +
228A LEU* 3.3 17.1 - - - +
62C ASN* 2.6 31.1 - - - +
----------------------------------------------------------
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