Contacts of the strand formed by residues 154 - 158 (chain C) in PDB entry 3NT7
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 VAL 154 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ARG 3.2 6.3 + - - +
62C VAL* 3.4 7.2 - - + +
63C CYS 3.1 24.9 + - - +
152C VAL* 4.0 5.4 - - - +
153C SER* 1.3 85.3 - - - +
155C LEU* 1.3 69.6 + - - +
156C TYR* 4.6 1.1 - - + +
175C THR* 3.5 13.0 - - + +
177C ILE* 4.8 4.5 - - + -
198C ILE* 4.1 33.9 - - + +
201C LEU* 4.0 35.9 - - + +
202C LEU* 4.1 19.7 - - + +
205C ASP* 6.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C CYS* 3.8 20.2 - - + +
65C CYS* 4.1 15.3 - - + -
145C LEU* 4.3 21.1 - - + -
149C THR* 4.0 23.1 - - + -
152C VAL* 4.9 3.8 - - + +
154C VAL* 1.3 75.5 - - - +
156C TYR* 1.3 63.9 + - - +
157C CYS* 3.8 28.5 - - - -
174C VAL* 4.6 8.2 - - + +
175C THR 2.8 15.4 + - - +
176C THR* 3.2 20.4 - - + +
177C ILE 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C VAL* 5.0 0.7 - - + -
63C CYS 2.8 15.5 + - - +
64C VAL* 3.5 18.9 - - + +
65C CYS 2.7 32.2 + - - +
154C VAL* 4.0 3.1 + - + -
155C LEU* 1.3 73.3 - - - +
157C CYS* 1.3 57.8 + - - +
158C LEU* 3.6 29.6 + - + +
177C ILE* 3.4 38.8 - - + -
179C GLY* 4.0 16.8 - - - -
180C TYR 5.0 1.2 + - - -
191C LYS* 4.4 8.3 + - - +
194C SER* 3.2 32.1 - - - -
195C PHE* 4.1 23.3 + + - -
198C ILE* 3.7 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 157 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C CYS* 3.4 6.1 - - - -
145C LEU* 6.0 2.7 - - - -
155C LEU* 3.8 34.3 - - - -
156C TYR* 1.3 75.0 - - - +
158C LEU* 1.3 58.9 + - - +
163C PHE* 3.7 38.6 - - + -
176C THR* 4.7 7.6 - - - -
177C ILE 2.9 9.5 + - - +
178C VAL* 3.6 14.0 - - + -
179C GLY* 2.8 32.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
64C VAL* 3.6 28.7 - - + -
65C CYS 2.9 15.4 + - - +
66C GLY* 4.6 6.5 - - - -
67C ILE 4.8 0.2 + - - -
79C PHE* 3.6 27.1 - - + -
92C ILE* 4.7 5.2 - - + -
156C TYR* 3.6 32.3 - - + +
157C CYS* 1.3 74.2 - - - +
159C GLY* 1.3 60.1 + - - +
162C ASP* 4.0 9.0 - - - +
163C PHE* 3.5 12.9 - - - -
180C TYR 3.5 19.3 - - - +
181C HIS* 4.1 6.1 - - - -
182C PRO* 3.9 25.4 - - + -
191C LYS* 6.2 1.6 - - + -
195C PHE* 5.1 8.1 - - + -
----------------------------------------------------------
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