Contacts of the strand formed by residues 159 - 164 (chain C) in PDB entry 3VD1
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 159 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C TRP* 4.3 10.8 - - - -
151C LEU* 3.2 42.2 - - - -
153C CYS* 3.4 28.7 - - - -
157C LYS 2.9 1.4 + - - -
158C THR* 1.3 69.3 - - - +
160C PRO* 1.3 61.6 - - - +
161C ILE* 3.9 8.9 + - - +
253C LEU* 4.2 2.2 - - - -
254C TYR* 2.5 51.4 + - + +
256C PHE* 3.8 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 160 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C PHE* 4.6 1.6 - - - +
133C GLN* 5.9 0.9 - - + -
142C TRP* 3.6 46.7 - - + +
158C THR* 3.5 13.7 - - - +
159C CYS* 1.3 84.1 - - - +
161C ILE* 1.3 64.1 + - - +
162C GLN* 3.9 13.3 + - - +
251C THR* 4.2 13.7 - - + -
252C ILE 3.9 4.9 - - - +
253C LEU* 3.9 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 161 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C VAL* 4.1 20.6 - - + -
130C THR 4.1 3.8 - - - +
131C PHE* 3.5 31.9 - - + -
151C LEU* 5.0 2.9 - - + -
159C CYS* 3.9 11.4 + - - +
160C PRO* 1.3 77.8 - - + +
162C GLN* 1.3 62.4 + - - +
163C ILE* 4.1 4.4 + - + -
250C THR 3.8 0.2 - - - +
251C THR* 3.5 4.2 - - - +
252C ILE* 3.0 40.8 + - + +
254C TYR* 3.3 34.8 - - + -
256C PHE* 6.5 0.4 - - + -
275C ILE* 3.7 22.4 - - + -
290C PHE* 5.1 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 162 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C GLU 3.5 2.4 - - - +
129C VAL* 3.7 1.1 - - - -
130C THR* 2.9 49.0 + - - +
131C PHE 4.1 0.5 - - - -
132C GLN* 3.3 43.3 + - - +
133C GLN 5.0 0.8 - - - +
142C TRP* 5.5 0.2 - - - -
160C PRO* 3.9 22.8 + - - +
161C ILE* 1.3 75.5 - - - +
163C ILE* 1.3 64.7 + - - +
249C PHE* 3.6 34.8 - - + -
250C THR 3.3 2.5 - - - +
251C THR* 3.5 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 163 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C PHE* 3.4 47.8 - - + -
128C GLU 3.3 7.0 - - - +
129C VAL* 4.4 13.0 - - + -
161C ILE* 5.0 5.8 - - + -
162C GLN* 1.3 73.6 - - - +
164C LYS* 1.3 72.5 + - - +
165C VAL* 4.5 6.3 - - + -
175C ILE* 4.7 11.4 - - + -
240C TYR* 5.2 4.9 - - + -
249C PHE* 2.7 12.1 - - - +
250C THR* 2.6 54.3 + - + +
252C ILE* 4.1 21.5 - - + -
275C ILE* 3.9 15.7 - - + -
277C LEU* 5.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 164 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C HIS 3.3 1.8 - - - +
127C PHE* 3.6 0.3 - - - -
128C GLU* 2.9 62.9 + - + +
130C THR* 5.8 0.7 - - - +
163C ILE* 1.3 80.3 - - - +
165C VAL* 1.3 83.4 + - - +
243C PRO* 6.1 2.0 - - - -
248C GLU* 3.3 51.1 + - - +
249C PHE* 3.9 19.2 - - + +
250C THR* 5.8 0.4 - - - -
----------------------------------------------------------
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