Contacts of the helix formed by residues 141 - 150 (chain B) in PDB entry 5AM8
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 PRO 141 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B SER* 3.7 4.3 - - - +
139B LEU 3.8 0.9 - - - -
140B ASP* 1.3 89.4 - - - +
142B ASP* 1.3 76.8 + - - +
143B LEU 3.5 1.3 - - - -
144B THR* 3.5 2.7 + - - -
145B ASN* 2.9 38.3 + - - +
321B LYS* 3.7 20.4 - - + +
350B ARG* 3.7 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B CYS 4.2 3.6 - - - +
137B TRP* 3.6 29.8 - - + -
138B SER* 3.0 38.0 + - - +
141B PRO* 1.3 90.4 - - - +
143B LEU* 1.3 64.7 + - - +
145B ASN* 3.7 5.5 - - - +
146B ILE* 3.1 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B VAL* 3.6 28.5 - - + -
137B TRP* 3.9 32.8 - - + +
138B SER 2.9 26.6 + - - +
139B LEU* 3.7 7.9 - - + +
142B ASP* 1.3 70.8 - - - +
144B THR* 1.3 60.0 + - - +
146B ILE* 3.3 4.1 + - + +
147B LEU* 2.9 35.9 + - - +
159B ALA* 3.7 29.4 - - + -
163B TRP* 3.8 28.7 - - + -
256B MET* 4.0 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 2.8 33.9 + - - +
140B ASP* 4.0 8.3 - - - +
141B PRO* 3.6 10.8 - - - -
142B ASP 3.4 0.2 - - - -
143B LEU* 1.3 76.8 - - - +
145B ASN* 1.3 56.3 + - - +
147B LEU* 3.4 6.1 + - - +
148B ALA* 2.9 30.1 + - + +
254B GLY 4.8 0.7 - - - +
256B MET* 6.2 2.7 - - - +
257B TRP* 5.8 2.6 - - - -
263B ASN* 6.1 1.6 - - - +
350B ARG* 3.6 34.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B PRO* 2.9 36.7 + - - +
142B ASP* 3.7 5.3 - - - +
144B THR* 1.3 73.6 - - - +
146B ILE* 1.3 61.1 + - + +
148B ALA* 4.2 5.7 - - - +
149B SER* 2.8 39.5 + - - +
350B ARG* 3.5 25.9 + - - +
352B THR* 5.8 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B TRP* 3.6 48.7 - - + -
142B ASP* 3.1 15.6 + - + +
143B LEU* 3.3 14.8 + - + +
145B ASN* 1.3 73.9 - - + +
147B LEU* 1.3 61.2 + - - +
149B SER* 5.2 0.4 - - - -
150B SER* 2.9 38.3 + - - +
155B MET* 3.8 29.4 - - + +
156B LEU* 3.5 7.2 - - + +
159B ALA* 4.0 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU 2.9 22.2 + - - +
144B THR* 3.8 6.1 - - - +
146B ILE* 1.3 78.1 - - + +
148B ALA* 1.3 60.2 + - - +
150B SER 4.8 0.2 - - - +
151B ARG* 4.5 3.5 + - - -
156B LEU* 4.0 16.9 - - + +
159B ALA* 3.7 27.8 - - + -
160B TRP* 4.5 3.6 - - + +
251B HIS* 3.5 34.9 - - + +
254B GLY* 3.2 22.0 + - - +
255B ASP* 3.9 25.1 - - - +
256B MET* 3.7 37.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B THR* 2.9 21.7 + - + +
145B ASN* 3.7 9.6 - - - +
147B LEU* 1.3 78.1 - - - +
149B SER* 1.3 63.2 + - - +
151B ARG* 3.0 17.3 + - - -
254B GLY 3.4 8.9 + - - -
263B ASN* 3.5 40.3 - - - +
350B ARG* 6.1 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ASN* 2.8 23.6 + - - +
146B ILE* 5.2 0.4 - - - -
148B ALA* 1.3 80.2 + - - +
150B SER* 1.3 65.6 + - - +
151B ARG* 3.5 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ILE* 2.9 35.5 + - - +
147B LEU 4.8 0.2 - - - +
149B SER* 1.3 74.2 - - - +
151B ARG* 1.3 70.5 + - - +
152B SER* 3.1 24.4 + - - -
155B MET* 3.7 12.7 - - - +
156B LEU* 3.4 25.5 - - - +
----------------------------------------------------------
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