Contacts of the helix formed by residues 147 - 159 (chain A) in PDB entry 2HCR
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 ALA 147 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A MET* 4.1 10.9 - - - +
128A ASP* 2.9 22.8 + - - +
146A TYR* 1.3 72.4 - - - +
148A GLU* 1.3 59.0 + - - +
149A PRO* 3.4 1.1 - - - -
150A ALA* 3.1 11.5 + - + +
151A VAL* 2.9 34.8 + - + +
249A THR* 3.8 19.1 - - + -
272A THR* 3.9 18.8 - - + -
292A ILE* 5.1 1.1 - - + -
295A ILE* 5.2 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ASP* 4.6 1.4 + - - +
146A TYR* 4.3 11.5 - - + +
147A ALA* 1.3 76.9 - - - +
149A PRO* 1.4 71.2 - - + +
151A VAL* 3.0 8.1 + - - -
152A LEU* 2.8 36.6 + - + +
180A SER* 3.1 35.5 + - - +
181A ILE* 3.9 24.7 - - + +
184A ARG* 3.9 21.6 + - - +
313A PHE 5.2 3.1 - - - +
102B LYS* 4.8 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A TYR* 3.6 15.0 - - + +
147A ALA 3.6 0.7 - - - -
148A GLU* 1.4 93.3 - - + +
150A ALA* 1.3 56.3 + - - +
152A LEU* 3.4 13.4 - - + +
153A LYS* 3.0 26.5 + - - +
156A ARG* 5.4 0.7 + - - -
312A LEU 4.1 7.2 - - - +
313A PHE 3.3 32.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ALA* 3.1 12.2 + - + +
149A PRO* 1.3 76.5 - - - +
151A VAL* 1.3 61.1 + - - +
153A LYS* 3.6 9.2 - - - +
154A TRP* 3.0 27.0 + - - +
290A ILE* 3.9 30.0 - - + +
292A ILE* 5.2 1.3 - - + -
295A ILE* 4.8 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ALA* 2.9 29.9 + - + +
148A GLU* 3.0 10.1 + - - +
150A ALA* 1.3 75.2 - - - +
152A LEU* 1.3 60.1 + - + +
154A TRP* 3.2 3.8 + - - +
155A ILE* 2.9 46.1 + - + +
181A ILE* 4.6 17.5 - - + -
219A VAL* 5.3 3.6 - - + -
247A ILE* 3.7 34.7 - - + +
249A THR* 5.8 4.3 - - + +
272A THR* 5.5 2.5 - - + -
290A ILE* 4.3 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A GLU* 2.8 31.9 + - + +
149A PRO* 3.4 11.0 - - + +
151A VAL* 1.3 77.0 - - + +
153A LYS* 1.3 62.0 + - - +
155A ILE* 3.3 8.1 + - + +
156A ARG* 3.2 57.0 + - - +
181A ILE* 3.9 36.1 - - + -
184A ARG* 3.9 28.5 - - + -
185A LEU* 4.2 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PRO 3.0 17.4 + - - +
150A ALA* 3.6 10.8 - - - +
151A VAL 3.3 0.2 - - - -
152A LEU* 1.3 76.5 - - - +
154A TRP* 1.3 61.6 + - - +
156A ARG* 3.4 10.8 + - - +
157A GLU* 3.0 59.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ALA 3.0 17.6 + - - +
151A VAL* 3.2 5.6 + - - +
153A LYS* 1.3 76.3 - - - +
155A ILE* 1.3 62.2 + - - +
157A GLU* 4.4 2.5 - - - -
158A ASN* 2.9 69.2 + - + +
159A ILE* 3.7 23.3 - - + -
245A TYR* 4.1 22.2 - + - -
247A ILE* 4.1 15.7 - - + -
268A ALA* 4.5 3.6 - - + -
270A VAL* 3.5 35.9 - - + +
288A GLN* 3.6 32.9 + - - +
289A VAL 6.0 0.9 - - - -
290A ILE* 4.2 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A VAL* 2.9 36.2 + - + +
152A LEU* 3.3 5.8 + - - +
154A TRP* 1.3 80.0 - - - +
156A ARG* 1.3 63.7 + - - +
159A ILE* 3.0 33.7 + - + +
162A TRP* 3.8 21.1 - - + -
167A ILE* 4.4 2.7 - - + -
181A ILE* 4.3 12.6 - - + -
185A LEU* 3.9 30.3 - - + -
217A ILE* 3.8 25.6 - - + -
219A VAL* 5.2 1.6 - - + -
247A ILE* 3.8 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PRO 5.4 0.2 + - - -
152A LEU* 3.2 41.4 + - - +
153A LYS* 3.8 8.4 - - - +
155A ILE* 1.3 78.5 - - - +
157A GLU* 1.3 60.2 + - + +
158A ASN 3.8 0.2 + - - -
159A ILE 4.2 2.1 - - - +
162A TRP* 3.5 56.9 + - + +
184A ARG* 3.9 15.4 + - - +
185A LEU* 3.5 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LYS* 3.0 58.5 + - - +
154A TRP* 4.4 1.4 - - - -
156A ARG* 1.3 80.0 - - + +
158A ASN* 1.3 71.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TRP* 2.9 67.5 + - + +
157A GLU* 1.3 91.5 + - - +
159A ILE* 1.3 64.5 + - - +
160A SER 4.0 2.1 + - - -
245A TYR* 4.5 6.6 + - - -
288A GLN* 4.1 9.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TRP* 3.7 24.0 - - + -
155A ILE* 3.0 20.5 + - + +
156A ARG 4.2 1.9 - - - +
158A ASN* 1.3 81.4 - - - +
160A SER* 1.3 60.0 + - - +
161A GLU* 4.0 13.5 - - - +
162A TRP* 3.0 46.5 - - + +
215A VAL* 4.0 22.2 - - + -
217A ILE* 3.5 31.9 - - + -
245A TYR* 3.8 28.9 - - + +
247A ILE* 5.0 0.7 - - + -
----------------------------------------------------------
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