Contacts of the strand formed by residues 158 - 162 (chain C) in PDB entry 1E50
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 GLN 158 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ASN* 2.9 31.1 + - - +
70C PHE* 3.5 25.9 - - + -
97C VAL* 4.4 6.3 - - - +
150C ILE 3.8 0.3 - - - +
151C THR* 3.4 3.1 - - - +
152C VAL* 2.8 38.6 + - + +
154C THR* 3.0 33.4 + - - +
156C PRO 4.2 2.2 - - - +
157C PRO* 1.3 75.3 - - - +
159C VAL* 1.3 62.4 + - - +
160C ALA 4.3 0.2 + - - -
2D PRO* 3.1 33.8 - - + +
3D ARG* 3.8 6.9 + - - +
102D ILE* 3.4 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 159 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C SER* 4.1 4.7 + - - -
70C PHE* 5.3 1.1 - - - -
149C THR* 3.9 14.6 - - + -
150C ILE 3.3 8.7 - - - +
151C THR* 4.1 17.7 - - + +
157C PRO* 4.9 1.6 - - + -
158C GLN* 1.3 79.2 - - - +
160C ALA* 1.3 66.2 + - - +
161C THR* 4.7 2.0 - - + -
64D LEU* 3.8 16.8 - - + -
65D SER 5.1 4.7 - - - +
101D MET* 3.8 28.0 - - + -
102D ILE 2.7 13.3 + - - +
103D LEU* 3.3 25.4 - - + -
104D ASN* 2.8 29.2 + - - -
105D GLY 4.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 160 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C THR* 3.6 18.6 - - + +
67C SER* 3.5 21.1 - - - -
70C PHE* 4.1 15.5 - - + -
148C LEU 3.8 0.3 - - - +
149C THR* 3.6 0.7 - - - -
150C ILE* 2.6 54.5 + - + +
158C GLN 4.3 0.2 - - - -
159C VAL* 1.3 74.5 - - - +
161C THR* 1.3 61.9 + - - +
104D ASN* 3.4 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 161 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C THR* 3.7 3.0 - - - -
66C ASP* 2.4 53.5 + - - +
147C THR* 4.5 4.3 - - + -
148C LEU 3.2 9.4 - - - +
149C THR* 4.1 14.8 - - - +
150C ILE* 5.8 0.2 - - - -
159C VAL* 4.7 2.9 - - + -
160C ALA* 1.3 77.9 - - - +
162C TYR* 1.3 62.6 + - - +
163C HIS* 3.3 13.3 - - + -
17D PHE* 4.2 14.4 - - + -
62D THR* 5.5 4.9 - - + -
64D LEU* 5.7 1.1 - - + -
103D LEU* 4.6 8.7 - - + -
104D ASN* 2.8 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 162 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C VAL* 3.9 23.1 - - + +
64C ARG 5.0 9.0 - - - -
65C THR* 5.1 4.0 - - - +
66C ASP* 4.1 3.1 - - - +
72C CYS* 3.5 31.0 - - - -
73C SER 4.0 8.7 - - - -
74C VAL* 4.2 4.5 - - - +
75C LEU* 3.8 21.1 + - + -
147C THR* 3.4 2.3 - - - -
148C LEU* 2.7 60.6 + - + +
150C ILE* 5.2 3.1 - - + -
161C THR* 1.3 75.5 - - - +
163C HIS* 1.3 68.7 + - - +
164C ARG 5.1 1.3 - - - -
165C ALA* 3.4 30.1 + - + +
----------------------------------------------------------
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