Contacts of the helix formed by residues 138 - 149 (chain L) in PDB entry 5U0A
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 ASN 138 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136L ARG 3.7 2.3 + - - +
137L PRO* 1.3 74.2 - - - +
139L LEU* 1.3 56.1 + - - +
140L GLY* 2.9 13.5 + - - +
141L VAL* 3.2 22.6 + - - +
142L SER* 2.7 27.0 + - - -
190L ILE* 6.4 0.4 - - - -
191L ASP 5.5 0.2 + - - -
194L ILE* 3.2 22.0 - - + -
197L ARG* 6.1 1.8 - - - +
198L ASP* 4.1 11.0 - - - +
212L GLU* 4.3 10.5 + - - +
213L TRP* 3.7 19.5 - - - +
216L ASP* 4.1 18.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 139 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138L ASN* 1.3 78.6 - - - +
140L GLY* 1.3 65.4 + - - +
141L VAL 3.3 0.4 - - - -
142L SER* 3.9 6.1 - - - -
143L LEU* 2.9 60.3 + - + +
161L LEU* 5.9 4.3 - - + -
164L ILE* 5.7 3.4 - - + -
176L LEU* 4.5 5.2 - - + -
179L LEU* 4.5 8.7 - - + -
180L VAL* 4.2 18.4 - - + -
183L LEU* 5.0 2.9 - - + -
190L ILE* 4.8 10.5 - - + -
194L ILE* 4.1 3.8 - - + +
195L LEU* 3.7 36.3 - - + -
198L ASP* 5.8 0.4 - - - +
213L TRP* 4.1 35.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 140 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138L ASN* 2.9 8.6 + - - +
139L LEU* 1.3 78.6 - - - +
141L VAL* 1.3 56.5 + - - +
143L LEU 3.3 1.2 + - - -
144L ALA 3.0 20.8 + - - -
161L LEU* 4.9 3.8 - - - -
213L TRP* 3.4 32.8 - - - +
217L TYR* 3.0 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 141 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137L PRO* 3.3 19.7 - - + -
138L ASN* 3.2 36.4 + - - +
140L GLY* 1.3 73.5 - - - +
142L SER* 1.3 62.6 + - - +
145L GLN* 2.9 50.9 + - + +
216L ASP* 4.6 3.3 - - + +
217L TYR* 4.4 1.6 - - - +
220L THR* 3.8 38.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 142 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137L PRO* 5.1 4.0 + - - +
138L ASN 2.7 22.5 + - - -
139L LEU* 3.7 9.6 - - - -
140L GLY 3.2 0.6 - - - -
141L VAL* 1.3 81.3 - - - +
143L LEU* 1.3 58.6 + - - +
145L GLN* 3.9 3.8 - - - -
146L ALA* 2.9 27.9 + - - +
183L LEU* 4.6 7.2 - - - -
188L VAL* 3.4 10.4 - - - +
189L HIS 3.0 26.3 + - - -
190L ILE* 4.1 17.9 - - - +
191L ASP 4.7 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139L LEU* 2.9 49.4 + - + +
142L SER* 1.3 75.5 - - - +
144L ALA* 1.3 59.8 + - - +
146L ALA* 3.3 6.4 + - - +
147L VAL* 2.9 31.7 + - - +
157L THR* 3.6 27.1 - - - +
161L LEU* 3.8 25.1 - - + -
179L LEU* 3.8 23.6 - - + -
183L LEU* 3.6 28.0 - - + -
217L TYR* 3.5 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 144 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140L GLY 3.0 14.8 + - - +
141L VAL* 3.2 3.3 + - + +
143L LEU* 1.3 76.6 - - - +
145L GLN* 1.3 58.5 + - + +
147L VAL* 3.1 7.2 + - - +
148L PHE* 2.9 28.0 + - - +
217L TYR* 3.4 22.2 - - + +
220L THR* 3.3 27.8 - - - +
221L LEU* 3.8 18.2 - - + +
224L LEU* 4.8 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 145 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137L PRO* 6.0 2.8 - - - +
141L VAL* 2.9 38.0 + - + +
142L SER* 4.2 5.2 - - - +
144L ALA* 1.3 72.8 - - - +
146L ALA* 1.3 60.6 + - - +
148L PHE* 4.3 5.4 - - - +
149L ASP* 2.8 48.8 + - - +
188L VAL* 4.7 8.6 - - + +
189L HIS* 5.5 7.1 - - - +
224L LEU* 4.1 19.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142L SER 2.9 20.2 + - - +
143L LEU* 3.5 6.3 - - - +
144L ALA 3.2 0.2 - - - -
145L GLN* 1.3 76.4 - - - +
147L VAL* 1.3 63.6 + - - +
150L LYS* 3.5 16.1 + - - +
152L LEU* 3.4 27.4 - - + +
183L LEU* 3.6 26.2 - - + -
188L VAL* 3.7 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 147 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143L LEU 2.9 18.5 + - - +
144L ALA* 3.1 8.9 + - - +
146L ALA* 1.3 76.9 - - - +
148L PHE* 1.3 67.3 + - - +
151L GLY* 3.3 21.7 + - - -
152L LEU* 3.5 18.6 + - + +
154L ALA* 3.6 23.8 - - + +
157L THR* 3.5 18.2 - - + -
217L TYR* 3.5 21.8 - - + +
221L LEU* 4.2 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 148 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E LYS* 5.8 0.7 + - - -
144L ALA 2.9 15.0 + - - +
145L GLN 4.0 1.6 - - - +
147L VAL* 1.3 81.9 - - - +
149L ASP* 1.3 85.0 + - - +
151L GLY* 4.0 2.1 + - - -
221L LEU* 4.9 9.6 - - + -
224L LEU* 3.6 61.0 - - + -
225L THR* 4.7 4.9 - - - -
227L GLN* 5.9 1.1 - - + -
228L ALA* 4.3 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 149 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E LYS* 5.3 1.9 + - - -
145L GLN* 2.8 37.2 + - - +
148L PHE* 1.3 95.2 - - - +
150L LYS* 1.3 77.4 + - - +
151L GLY* 2.9 10.2 + - - -
224L LEU* 5.5 0.6 - - - +
----------------------------------------------------------
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