Contacts of the helix formed by residues 149 - 157 (chain B) in PDB entry 5I1U
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 CYS 149 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A HIS* 3.7 22.9 - - - -
204A ARG* 5.1 1.1 - - - -
145B TYR* 3.2 32.4 + - - +
146B TYR 3.8 6.3 - - - +
147B PHE 3.2 0.8 + - - -
148B ALA* 1.3 76.4 - - - +
150B HIS* 1.3 64.6 + - - +
151B PRO 3.5 0.4 - - - -
152B ALA* 3.4 6.3 + - - +
153B GLU* 3.2 17.2 + - - +
170B THR 5.2 0.4 - - - -
171B LEU* 3.5 21.1 - - + +
174B GLY* 3.7 22.0 - - - -
175B THR* 4.0 20.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE* 3.8 7.0 - + - -
80B ASP* 2.8 30.3 + - - -
83B PHE* 3.9 20.4 - + + -
94B VAL* 3.7 9.0 - - + +
98B CYS* 3.6 14.1 - - - -
146B TYR* 2.8 60.2 + + - -
147B PHE* 3.1 12.7 + - - +
149B CYS* 1.3 75.7 - - - +
151B PRO* 1.4 72.3 - - + +
153B GLU* 3.1 24.1 + - - +
154B ALA* 2.9 23.0 + - - +
175B THR* 5.1 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A HIS* 3.6 28.9 - - + -
279A MET* 4.1 8.3 - - + -
91B PRO* 3.8 20.0 - - - +
94B VAL* 3.7 10.3 - - + -
95B ALA* 3.4 32.8 - - - +
98B CYS* 4.6 2.9 - - + -
147B PHE 3.8 5.4 - - - +
148B ALA* 3.4 15.0 - - - +
150B HIS* 1.4 91.0 - - + +
152B ALA* 1.3 56.2 + - - +
154B ALA* 3.2 3.4 + - + +
155B ALA* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A HIS 5.4 1.3 + - - +
200A HIS* 3.6 26.4 + - + +
201A PRO* 3.6 32.1 - - + -
279A MET* 4.1 4.8 - - - -
148B ALA 5.0 1.0 + - - +
149B CYS* 3.4 10.8 + - - +
150B HIS 3.3 0.8 - - - -
151B PRO* 1.3 79.5 - - - +
153B GLU* 1.3 62.7 + - - +
155B ALA* 3.3 6.7 + - - +
156B GLY* 3.0 19.8 + - - -
171B LEU* 4.0 8.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASP* 5.1 2.3 - - - +
83B PHE* 5.4 5.9 - - - +
149B CYS 3.2 12.4 + - - +
150B HIS* 3.1 32.0 + - - +
152B ALA* 1.3 75.0 - - - +
154B ALA* 1.3 63.6 + - - +
156B GLY* 3.1 11.7 + - - -
157B ARG* 3.4 10.6 + - - +
171B LEU* 4.0 20.3 - - + +
172B ARG* 5.3 1.6 + - - -
175B THR* 3.9 25.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PHE* 6.1 4.0 - - + -
88B GLY* 5.5 2.1 - - - -
89B ARG* 3.7 26.5 - - + +
91B PRO* 4.1 7.0 - - + +
94B VAL* 4.0 19.3 - - + -
150B HIS 2.9 12.4 + - - +
151B PRO 3.2 7.2 + - - +
153B GLU* 1.3 78.5 - - - +
155B ALA* 1.3 62.5 + - - +
157B ARG* 3.2 21.3 + - - +
158B THR* 4.1 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A HIS* 5.9 1.3 - - - +
278A SER* 3.6 40.7 - - - +
279A MET* 4.5 2.9 - - + -
91B PRO* 3.7 9.5 - - + +
151B PRO 2.9 13.8 + - - +
152B ALA* 3.6 11.2 - - - +
154B ALA* 1.3 76.7 - - - +
156B GLY* 1.3 62.5 + - - +
158B THR* 2.7 30.1 + - - -
159B ILE 4.2 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ALA 3.0 14.0 + - - -
153B GLU* 3.1 6.8 + - - -
155B ALA* 1.3 76.9 - - - +
157B ARG* 1.3 60.2 + - - +
158B THR 3.1 1.4 + - - -
159B ILE* 3.1 18.5 + - - +
171B LEU* 6.2 1.6 - - - -
233B ALA* 6.1 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B SER 5.8 1.9 + - - +
86B PRO 4.9 11.9 + - - -
87B LEU 4.4 18.6 - - - +
88B GLY* 4.5 12.8 - - - +
153B GLU 3.4 8.0 + - - +
154B ALA* 3.2 15.6 + - - +
155B ALA 3.1 0.6 - - - -
156B GLY* 1.3 76.5 + - - +
158B THR* 1.3 59.5 + - + +
159B ILE* 3.2 7.5 + - - +
232B VAL 5.9 4.5 - - - +
----------------------------------------------------------
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