Contacts of the helix formed by residues 141 - 150 (chain B) in PDB entry 2AY5
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
----------------------------------------------------------
15B ASP* 5.4 4.7 - - - +
17B ILE* 4.3 24.2 - - + -
139B THR* 3.1 11.1 - - + +
140B TRP* 1.3 90.8 - - + +
142B ASN* 1.3 66.2 + - - +
143B HIS 3.0 1.2 + - - -
144B VAL* 3.2 9.1 + - + +
145B SER* 3.2 19.5 + - - -
194B ASN* 5.5 2.0 - - - +
195B PRO* 5.6 4.0 - - + -
386B ARG* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ARG* 3.9 27.6 + - - +
293A GLN* 5.2 0.2 - - - +
15B ASP* 3.0 27.9 + - - -
109B THR* 4.3 1.4 - - - +
140B TRP* 3.1 31.7 + - + +
141B PRO* 1.3 80.3 - - - +
143B HIS* 1.3 62.0 + - - +
145B SER* 3.9 8.0 - - - -
146B ILE* 3.1 38.5 + - + +
414B IOP 3.4 32.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LEU* 3.6 26.0 - - + +
116B LEU* 5.3 0.2 - - - +
135B VAL* 4.9 0.2 - - + -
139B THR* 2.9 31.6 + - + -
140B TRP* 2.8 33.6 + + + +
142B ASN* 1.3 81.3 - - - +
144B VAL* 1.3 62.6 + - + +
146B ILE* 3.5 5.3 + - + +
147B MET* 3.2 40.2 + - + +
187B LEU* 3.4 26.8 - - + +
189B HIS* 3.9 11.4 - + - -
222B ASP* 2.8 31.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B VAL* 4.2 17.0 - - + -
139B THR* 4.6 9.2 - - + -
140B TRP 5.4 0.2 - - - +
141B PRO* 3.2 8.4 + - + +
143B HIS* 1.3 72.6 - - - +
145B SER* 1.3 55.8 + - - +
147B MET* 3.2 6.8 + - - -
148B ASN* 2.7 63.6 + - - +
155B VAL* 4.1 25.6 - - + -
157B THR* 6.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A PHE* 5.3 0.2 - - - -
292A ARG* 2.7 32.1 + - - -
293A GLN* 2.8 24.0 + - - +
141B PRO 3.2 12.9 + - - -
142B ASN* 3.3 17.3 - - - -
144B VAL* 1.3 77.4 - - - +
146B ILE* 1.3 62.8 + - - +
148B ASN* 3.1 9.1 + - - +
149B PHE* 3.0 22.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
292A ARG 4.6 0.2 - - - +
293A GLN* 3.4 40.2 - - + +
109B THR* 3.8 35.2 - - + +
112B LEU* 5.2 6.3 - - + -
113B ARG* 3.9 24.0 - - + +
116B LEU* 4.0 17.3 - - + -
140B TRP* 5.5 2.2 - - + -
142B ASN* 3.1 25.7 + - + +
143B HIS* 3.9 5.2 - - + +
145B SER* 1.3 79.3 - - - +
147B MET* 1.3 58.2 + - - +
149B PHE* 3.3 5.7 + - - +
150B MET* 2.9 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 3.9 28.7 - - + -
133B VAL* 3.6 33.9 - - + -
135B VAL* 3.8 14.4 - - + -
143B HIS* 3.2 31.9 + - + +
144B VAL 3.2 2.0 + - - +
146B ILE* 1.3 73.8 - - - +
148B ASN* 1.3 64.8 + - - +
150B MET* 3.7 5.1 - - - -
151B GLY 3.0 3.1 + - - -
152B LEU* 2.9 36.9 + - + +
155B VAL* 3.6 22.0 - - + -
187B LEU* 3.6 31.2 - - + -
220B LEU* 5.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B VAL* 2.7 50.4 + - - +
145B SER* 3.1 8.0 + - - +
147B MET* 1.3 70.7 - - - +
149B PHE* 1.3 62.7 + - - +
151B GLY* 2.8 21.5 + - - -
152B LEU 4.9 1.8 + - - -
155B VAL* 4.1 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLU* 4.9 13.9 - - - -
121A MET* 4.6 11.7 - - + -
289A PHE* 3.6 33.9 - + + -
290A LEU* 4.3 19.7 - - + -
293A GLN* 4.1 17.5 - - + -
294A THR* 5.6 0.9 - - - -
113B ARG* 3.8 37.0 - - - -
145B SER 3.0 12.2 + - - +
146B ILE* 3.4 12.6 - - - +
148B ASN* 1.3 76.9 - - - +
150B MET* 1.3 67.4 - - + +
151B GLY* 3.2 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ARG* 4.0 26.5 - - - +
116B LEU* 3.6 48.2 - - + +
117B GLU* 3.6 21.8 - - - +
120B ARG* 3.1 49.8 + - - +
146B ILE* 2.9 18.9 + - + +
147B MET* 3.9 4.9 - - - +
149B PHE* 1.3 83.7 - - + +
151B GLY* 1.3 60.3 + - - +
152B LEU* 3.4 15.9 + - + +
----------------------------------------------------------
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