Contacts of the strand formed by residues 89 - 92 (chain C) in PDB entry 3GUT
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 GLU 89 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LYS* 4.8 11.2 + - - -
76C LEU* 3.9 3.1 - - - -
87C PRO 4.2 2.0 - - - +
88C HIS* 1.3 72.2 - - - +
90C LEU* 1.3 61.8 + - - +
91C VAL* 3.7 15.1 - - + +
97C ASP* 5.0 0.9 + - - -
98C GLY* 3.8 18.7 + - - -
118C ILE* 3.6 0.9 - - - -
119C GLN* 2.7 62.4 + - + +
121C VAL* 5.1 7.4 - - + +
132C GLN* 3.5 19.3 + - - +
133C ARG* 3.3 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ILE* 3.4 45.8 - - + +
76C LEU* 3.1 36.4 - - + +
89C GLU* 1.3 71.1 - - - +
91C VAL* 1.3 61.6 + - - +
95C CYS* 3.6 16.7 - - - +
96C ARG 4.9 0.2 + - - -
98C GLY* 3.4 28.7 + - - +
99C TYR* 4.3 2.5 - - - -
100C TYR* 4.4 7.9 - - + +
116C LEU* 4.7 15.5 - - + -
117C GLY 3.2 5.6 - - - +
118C ILE* 3.7 26.2 - - + -
159C LEU* 4.2 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ARG 5.6 4.5 - - - +
42C SER* 6.3 0.2 - - - -
43C ALA* 5.2 10.8 - - + +
89C GLU* 4.0 20.9 - - - +
90C LEU 1.3 75.2 - - - +
92C GLY* 1.3 58.1 + - - +
95C CYS* 4.3 6.7 - - - -
115C ASN 4.1 0.2 - - - +
117C GLY* 2.4 58.9 + - - +
118C ILE 4.7 1.1 - - - +
119C GLN* 4.0 38.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C VAL* 1.3 79.0 - - - +
93C LYS* 1.3 65.4 + - - -
94C ASP 3.4 0.5 + - - -
95C CYS* 3.4 17.6 + - - +
115C ASN* 3.9 7.0 - - - -
----------------------------------------------------------
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