Contacts of the helix formed by residues 155 - 167 (chain B) in PDB entry 5H1Y
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 MET 155 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B SER* 1.3 80.2 + - - +
156B SER* 1.3 60.6 + - - +
157B GLU 3.6 0.2 - - - -
158B GLU* 3.7 12.2 - - - +
159B ARG* 3.0 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B SER* 3.7 7.3 + - - -
155B MET* 1.3 77.5 - - - +
157B GLU* 1.3 64.3 + - - +
159B ARG* 3.4 6.4 + - - +
160B HIS* 3.2 42.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B SER* 3.3 32.5 + - - +
156B SER* 1.3 79.1 + - - +
158B GLU* 1.3 57.8 + - - +
160B HIS* 3.0 33.1 + - + +
161B GLU* 3.0 16.6 + - - +
164B ARG* 5.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B SER 3.0 32.5 + - - +
155B MET* 3.6 14.8 + - - +
156B SER 3.2 0.6 - - - -
157B GLU* 1.3 80.3 - - - +
159B ARG* 1.3 74.4 + - - +
161B GLU* 3.5 8.7 + - + +
162B ARG* 2.9 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B MET* 3.0 33.3 + - + +
156B SER* 3.4 7.2 + - - +
157B GLU 3.2 0.4 - - - -
158B GLU* 1.3 89.0 + - - +
160B HIS* 1.3 62.4 + - + +
162B ARG* 3.2 64.9 - - - +
163B VAL* 2.9 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B SER* 3.2 32.7 + - - -
157B GLU* 3.0 21.0 + - + +
159B ARG* 1.3 80.5 - - + +
161B GLU* 1.3 55.8 + - - +
162B ARG 3.1 0.4 - - - -
163B VAL* 3.3 5.2 + - + +
164B ARG* 2.9 47.1 + - - +
176B ILE 6.0 0.2 + - - -
178B PRO* 3.4 34.5 - - + +
179B PRO* 3.8 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B GLU 3.0 13.1 + - - +
158B GLU* 4.0 10.5 - - + +
160B HIS* 1.3 75.4 - - - +
162B ARG* 1.3 57.0 + - - +
164B ARG* 3.0 40.6 + - - +
165B LYS* 3.0 29.1 + - - +
169B ILE 5.2 1.6 - - - +
171B VAL* 3.9 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B GLU 2.9 8.3 + - - +
159B ARG* 3.2 81.4 - - - +
160B HIS 3.1 0.2 - - - -
161B GLU* 1.3 76.0 - - - +
163B VAL* 1.3 67.5 + - - +
165B LYS* 3.5 5.2 + - - +
166B LYS* 2.8 34.6 + - + +
181B LYS* 4.9 14.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ARG* 2.9 26.3 + - + +
160B HIS* 3.3 6.3 + - + +
162B ARG* 1.3 81.9 - - - +
164B ARG* 1.3 63.5 + - - +
166B LYS* 3.4 5.9 + - - -
167B TYR* 3.0 50.0 + - + +
169B ILE* 5.3 0.2 - - - -
179B PRO* 3.9 26.2 - - + +
181B LYS* 3.8 36.6 - - + +
209B ILE* 4.3 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B HIS* 2.9 32.5 + - - +
161B GLU* 3.0 46.2 + - - +
163B VAL* 1.3 75.2 - - - +
165B LYS* 1.3 64.6 + - - +
167B TYR* 3.1 3.8 + - - -
168B HIS 3.0 4.0 + - - -
169B ILE* 2.9 60.7 + - + +
171B VAL* 3.9 21.4 - - - +
176B ILE* 3.6 25.6 + - - +
177B PRO 3.6 9.5 + - - -
178B PRO* 4.6 0.6 - - - +
179B PRO* 3.7 11.8 - - + +
210B GLN* 3.1 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B GLU* 3.0 22.5 + - - +
162B ARG* 3.9 4.7 - - - +
164B ARG* 1.3 70.8 - - - +
166B LYS* 1.3 64.4 + - - +
168B HIS* 3.1 24.6 + - - +
169B ILE 4.4 1.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ARG* 2.8 22.9 + - + +
163B VAL* 3.4 7.2 - - - +
165B LYS* 1.3 77.4 - - - +
167B TYR* 1.3 96.2 + - + +
168B HIS* 3.9 10.7 + - - -
181B LYS* 4.5 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B VAL* 3.0 36.4 + - + +
164B ARG 3.1 0.2 + - - -
166B LYS* 1.3 109.0 + - + +
168B HIS* 1.3 76.5 + - - +
169B ILE* 3.2 18.1 + - + -
181B LYS* 3.6 35.4 - - + +
204B PRO 5.4 0.9 - - - -
206B PRO* 3.4 32.7 - - + +
209B ILE* 4.1 23.1 - - + -
398B VAL* 5.6 0.2 - - - +
----------------------------------------------------------
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