Contacts of the strand formed by residues 157 - 162 (chain C) in PDB entry 2HU4
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 THR 157 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LYS* 3.9 18.8 + - + +
104A ASN* 4.0 6.6 + - - +
133C PHE 3.5 0.2 - - - +
134C LEU* 3.6 1.5 - - - -
135C THR* 2.7 50.8 + - - +
137C GLY* 5.5 0.2 - - - -
155C HIS 3.4 12.3 + - - +
156C ARG* 1.3 79.6 - - - +
158C LEU* 1.3 61.9 + - - +
159C MET* 3.5 16.7 + - - +
173C PHE* 3.7 24.2 - - + -
175C SER 3.5 8.3 - - - -
176C VAL* 4.2 8.3 - - + -
177C ALA 3.4 4.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 158 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C PHE* 4.4 5.8 - - + -
132C PHE* 4.1 15.5 - - + -
133C PHE 3.5 27.1 - - - +
134C LEU* 3.8 13.4 - - + +
157C THR* 1.3 69.6 - - - +
159C MET* 1.3 62.4 + - - +
173C PHE* 4.7 0.5 - - - -
174C GLU* 2.9 43.3 + - + +
175C SER* 2.6 25.7 + - - +
177C ALA* 4.0 6.9 - - + +
180C ALA* 3.6 31.0 - - + -
181C SER 4.3 11.7 - - - +
191C THR* 4.4 14.1 - - + -
192C ILE 4.4 4.7 - - - +
193C GLY* 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 159 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A GLY 4.4 8.1 - - - +
165A GLU* 4.6 6.3 - - + -
115C PHE* 3.7 33.7 - - + -
132C PHE* 3.4 5.0 - - - +
133C PHE* 3.1 46.0 + - + -
135C THR* 4.0 11.4 - - + -
157C THR* 3.7 18.4 - - - +
158C LEU* 1.3 80.4 - - - +
160C SER* 1.3 63.9 + - - +
169C PRO* 5.8 1.6 - - + -
171C SER* 3.8 16.6 - - - +
172C ARG 3.2 14.6 - - - +
173C PHE* 3.6 39.0 - - + +
174C GLU* 3.8 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 160 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ARG* 2.8 29.4 + - - -
131C THR 3.1 14.6 - - - -
132C PHE* 3.6 17.5 - - - -
133C PHE* 3.8 4.7 - - - -
159C MET* 1.3 77.7 - - - +
161C CYS* 1.3 60.3 + - - +
171C SER* 3.2 4.0 - - - -
172C ARG* 2.7 39.4 + - - +
174C GLU* 2.6 27.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 161 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ARG* 3.4 12.1 - - - +
131C THR* 2.9 36.1 + - - +
133C PHE* 3.9 18.4 - - - -
160C SER* 1.3 77.3 - - - +
162C PRO* 1.3 79.7 - - + +
165C GLU 3.6 23.8 - - - -
167C PRO* 4.0 12.8 - - - -
170C ASN* 3.4 24.2 - - - +
171C SER* 3.9 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 162 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ARG* 6.5 0.4 - - + -
128C GLU* 5.0 6.5 - - - +
129C CYS 4.2 9.2 - - - +
130C ARG* 4.2 15.3 - - + +
131C THR* 4.5 0.6 + - - -
161C CYS* 1.3 95.1 - - + +
163C VAL* 1.3 69.0 + - + +
165C GLU* 2.8 58.3 + - - +
170C ASN* 4.2 6.7 - - + +
----------------------------------------------------------
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