Contacts of the strand formed by residues 90 - 94 (chain C) in PDB entry 1VCW
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 TYR 90 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ILE* 3.6 2.4 - - - +
85C MET* 2.9 25.6 + - - -
86C ASP* 3.4 18.9 + - - +
88C ARG* 2.9 55.6 - - + -
89C GLY* 1.3 78.0 - - - +
91C ILE* 1.3 63.3 + - - +
119C VAL* 4.6 7.4 - - + -
129C VAL* 4.0 7.0 - - + -
130C LEU 3.6 10.5 - - - +
131C LYS* 3.4 31.8 - - + +
245C MET* 4.5 15.7 - - - -
249C ILE* 3.4 42.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C VAL* 4.8 2.5 - - + -
61C VAL* 5.2 6.3 - - + -
82C GLY* 4.0 8.1 - - - -
83C VAL 3.3 18.4 - - - +
84C ILE* 3.9 18.8 - - + +
85C MET* 4.6 0.2 - - - -
89C GLY 4.1 7.4 - - - +
90C TYR* 1.3 81.4 - - - +
92C ILE* 1.3 76.1 + - - +
93C THR* 5.3 0.2 - - - -
106C VAL* 3.8 34.3 - - + -
129C VAL* 3.4 6.4 - - - +
130C LEU* 2.8 50.1 + - + +
132C ILE* 3.9 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C GLY* 3.2 3.6 - - - -
83C VAL 2.9 32.5 + - - +
85C MET* 3.4 42.6 - - + -
91C ILE* 1.3 74.3 - - - +
93C THR* 1.3 70.4 + - - +
127C LEU* 3.6 28.0 - - + -
128C ALA 3.4 6.5 - - - +
129C VAL* 4.8 2.5 - - + -
202C GLY 4.1 1.3 - - - +
215C ILE* 3.8 20.6 - - + -
241C ALA* 3.8 32.8 - - + +
245C MET* 3.9 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C VAL* 4.3 8.6 - - + +
81C SER 2.9 21.4 + - - -
82C GLY* 4.4 1.8 - - - -
91C ILE* 5.3 0.4 - - - -
92C ILE* 1.3 83.2 - - - +
94C ASN* 1.3 72.0 + - - +
97C VAL* 4.0 8.5 - - - +
98C ILE* 4.5 6.1 - - + -
127C LEU* 3.1 9.7 - - - +
128C ALA* 2.4 60.2 + - + +
130C LEU* 4.2 22.2 - - + -
202C GLY* 4.0 10.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C THR* 1.3 87.4 + - - +
95C LYS* 1.3 66.0 + - - +
96C HIS* 3.4 5.8 - - + -
97C VAL* 2.9 34.7 + - + +
98C ILE* 3.8 2.6 + - - +
126C ASP* 2.7 36.6 + - - +
127C LEU* 4.6 2.8 - - - +
128C ALA* 4.0 1.3 - - - -
201C SER* 2.7 15.9 + - - -
202C GLY* 2.4 27.3 + - - +
215C ILE* 4.6 5.1 - - - +
216C ASN 2.9 12.1 + - - +
217C THR* 3.7 15.7 + - - +
----------------------------------------------------------
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