Contacts of the helix formed by residues 92 - 97 (chain C) in PDB entry 4SBV
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 MET 92 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C LEU* 2.7 18.6 + - + +
91C VAL* 1.3 73.4 - - - +
93C PRO* 1.3 70.9 - - + +
94C PHE* 3.2 14.8 + - + +
95C THR* 3.2 22.1 + - - +
96C VAL* 2.9 27.8 + - - +
110C TYR* 4.3 6.5 - - - +
112C TRP* 4.0 0.2 - - - -
200C LYS* 3.7 28.5 - - - +
201C THR 4.2 4.0 - - - +
202C ALA* 4.3 7.4 - - - -
205C TYR* 4.2 25.6 - - + -
219C LEU 4.5 4.0 - - - +
220C VAL* 3.1 35.9 - - + -
221C PRO* 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C MET* 1.3 87.2 - - + +
94C PHE* 1.3 62.6 + - + +
96C VAL* 3.6 8.7 + - + -
97C GLY 3.9 0.3 + - - -
100C LEU* 3.6 42.5 - - + +
101C ARG* 3.6 8.2 + - - -
104C ALA* 4.3 1.3 - - + -
110C TYR* 3.4 49.1 - - + +
112C TRP* 3.8 5.6 - - + -
199C PHE* 3.9 23.6 - - + -
200C LYS 5.5 1.1 - - - +
248C ILE* 4.2 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C MET* 3.2 8.7 + - + +
93C PRO* 1.3 82.3 - - - +
95C THR* 1.3 68.3 - - - +
97C GLY 3.8 1.3 - - - +
101C ARG* 2.8 81.6 + - + +
105C GLN* 5.7 5.8 - - - -
199C PHE* 4.3 15.9 - + + -
200C LYS 3.5 17.7 - - - +
201C THR* 3.8 20.9 - - + -
202C ALA* 3.9 33.9 - - + -
203C THR* 5.8 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C SER* 5.3 1.7 + - - -
89C GLU* 4.1 21.9 - - + +
90C LEU* 2.6 54.4 - - + +
92C MET* 3.4 17.4 - - - +
94C PHE* 1.3 89.1 - - - +
96C VAL* 1.3 62.2 - - - +
101C ARG* 4.9 3.1 + - - +
202C ALA* 5.5 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C GLU* 4.6 2.8 - - + +
74C LEU 5.0 0.2 - - - +
75C SER* 4.1 19.0 + - - -
89C GLU* 6.2 0.7 - - - -
90C LEU 4.6 0.4 - - - +
91C VAL* 4.2 0.9 - - - -
92C MET 2.9 33.5 + - - +
93C PRO 3.6 3.9 + - - +
94C PHE 3.4 0.6 - - - -
95C THR* 1.3 80.2 - - - +
97C GLY* 1.3 61.2 - - - +
100C LEU* 4.5 2.7 - - + -
112C TRP* 3.8 21.8 - - + -
115C ILE* 4.0 12.6 - - + -
117C TYR* 3.8 20.2 - - + +
244C ALA* 3.6 29.7 - - + +
246C TYR* 4.6 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C GLU* 3.2 23.3 - - - -
74C LEU 5.6 1.1 - - - -
93C PRO 3.9 4.0 + - - -
94C PHE 3.8 0.2 - - - +
95C THR 3.5 0.6 - - - -
96C VAL* 1.3 83.6 - - - +
98C THR* 1.3 61.6 + - - -
99C TRP 3.1 2.7 - - - -
100C LEU* 3.8 5.2 - - - +
101C ARG* 3.1 38.2 + - - +
----------------------------------------------------------
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