Contacts of the helix formed by residues 142 - 150 (chain A) in PDB entry 3N7T
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 HIS 142 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLY* 4.1 0.8 - - - -
110A GLY 3.5 27.3 + - - +
111A HIS* 3.1 35.1 + + - -
113A ALA* 3.6 13.0 - - + +
114A LEU* 3.7 30.7 - - + -
141A CYS* 1.3 90.5 - - - +
143A GLY* 1.3 65.4 + - - +
144A PRO 3.2 3.4 - - - -
145A ALA* 3.0 23.3 + - - +
167A PHE* 3.6 22.5 - + + +
172A GLU* 2.7 25.8 + - - -
189A ILE* 3.8 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A VAL* 3.5 26.4 - - - +
108A CYS 3.5 17.7 - - - -
109A GLY* 3.8 4.0 - - - -
117A PHE* 3.8 4.8 - - - -
139A ALA* 4.0 4.4 - - - +
140A VAL 2.9 15.3 + - - -
142A HIS* 1.3 76.6 - - - +
144A PRO* 1.4 59.4 - - - +
145A ALA 2.9 5.9 + - - -
146A MET* 3.0 14.0 + - - +
147A LEU* 5.0 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ALA* 3.9 20.4 - - + +
140A VAL 3.7 9.0 - - - +
141A CYS 3.5 15.3 - - - +
142A HIS 3.2 4.9 - - - -
143A GLY* 1.4 87.2 - - - +
145A ALA* 1.3 56.7 + - - +
146A MET 3.0 0.4 - - - -
147A LEU* 2.9 41.1 + - + +
148A PRO* 3.4 9.4 - - - +
159A ILE* 5.4 1.3 - - + +
164A VAL* 5.9 3.1 - - + -
165A THR 3.7 20.0 - - - +
166A GLY* 4.5 2.5 - - - -
189A ILE* 4.1 17.5 - - + -
192A MET* 5.6 1.1 - - - +
219A THR* 4.1 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ALA 4.1 17.7 - - - +
114A LEU* 4.4 4.7 - - + -
117A PHE* 4.1 3.4 - - + -
118A PRO* 3.6 21.1 - - + +
142A HIS 3.0 15.4 + - - +
143A GLY 2.9 1.2 + - - -
144A PRO* 1.3 77.6 - - - +
146A MET* 1.3 60.0 + - - +
147A LEU 3.4 0.2 - - - -
148A PRO* 3.6 10.5 - - - +
149A GLY 5.3 0.3 + - - -
189A ILE* 3.8 9.3 - - + +
192A MET* 3.5 34.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ALA* 4.0 8.3 - - + -
105A MET* 4.1 13.0 - - - +
107A VAL* 3.8 20.0 - - + -
117A PHE* 3.8 47.8 - - + +
120A ALA* 5.0 1.1 - - + -
123A LEU* 3.7 35.0 - - + -
124A GLN* 3.4 25.4 + - + -
143A GLY 3.0 12.5 + - - +
144A PRO 3.0 1.0 - - - -
145A ALA* 1.3 79.6 - - - +
147A LEU* 1.3 63.8 + - + +
148A PRO 3.4 0.4 - - - -
149A GLY 3.2 12.0 + - - -
150A ILE* 3.7 24.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A VAL* 5.9 1.1 - - + -
137A ILE* 4.0 21.3 - - + -
139A ALA* 4.3 7.0 - - + -
143A GLY 5.0 0.9 - - - +
144A PRO* 2.9 34.6 + - + +
146A MET* 1.3 74.6 - - + +
148A PRO* 1.3 66.9 - - + +
150A ILE* 3.0 35.7 + - + +
157A SER* 2.9 13.8 + - - -
158A VAL* 4.2 10.0 - - + +
159A ILE* 4.0 35.2 - - + -
164A VAL* 5.1 1.6 - - + -
217A ILE* 4.3 8.1 - - + -
219A THR* 3.8 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PRO* 6.5 0.4 - - + -
144A PRO 3.4 13.0 - - - +
145A ALA* 3.6 8.7 - - - +
146A MET 3.5 4.0 - - - -
147A LEU* 1.3 90.6 - - + +
149A GLY* 1.3 55.5 + - - +
150A ILE 3.3 0.2 - - - -
151A HIS* 3.3 21.1 + - - -
157A SER* 3.5 17.9 - - - +
159A ILE* 4.5 4.3 - - + -
192A MET* 3.7 36.1 - - + +
193A ALA* 5.3 0.2 - - - -
196A ALA* 4.0 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PRO 4.8 3.9 + - - -
124A GLN* 3.5 34.1 - - - +
128A GLN* 3.2 13.3 - - - +
145A ALA 5.3 0.4 + - - -
146A MET 3.2 4.4 + - - -
147A LEU 3.1 1.2 - - - -
148A PRO* 1.3 77.7 - - - +
150A ILE* 1.3 61.5 + - - +
151A HIS* 3.8 14.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A VAL* 5.6 0.4 - - + -
124A GLN* 3.9 13.9 - - + -
127A ALA* 3.5 25.6 - - + +
128A GLN* 3.6 33.0 - - + +
137A ILE* 4.1 10.1 - - + -
146A MET* 3.7 33.9 - - + +
147A LEU* 3.0 29.6 + - + +
149A GLY* 1.3 78.5 - - - +
151A HIS* 1.3 58.7 + - - +
157A SER* 3.3 5.2 - - - -
158A VAL* 2.8 44.0 + - + +
----------------------------------------------------------
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