Contacts of the strand formed by residues 104 - 109 (chain C) in PDB entry 1G82
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 LEU 104 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C SER* 4.0 1.7 + - - -
100C ILE* 3.2 29.1 + - + -
101C ALA* 2.9 29.9 + - + +
102C VAL 3.8 9.6 - - - +
103C GLY* 1.3 86.7 - - - +
105C VAL* 1.3 69.2 + - - +
135C VAL* 4.1 16.8 - - + -
136C PHE 3.2 10.1 - - - +
137C ARG* 4.1 9.2 - - + -
151C ASN* 4.0 31.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 105 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C PHE* 4.5 10.5 - - + -
98C ILE 3.3 13.9 - - - +
99C SER* 4.9 2.9 - - - -
100C ILE* 3.8 4.9 - - - -
104C LEU* 1.3 81.7 - - - +
106C SER* 1.4 67.9 + - - +
107C ILE* 4.2 13.7 - - + -
134C CYS 3.5 0.2 - - - +
135C VAL* 3.3 5.4 - - - -
136C PHE* 2.7 51.4 + - + +
138C GLU* 3.6 30.1 - - + +
148C TYR* 4.0 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 106 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C PHE* 3.6 1.6 - - - -
98C ILE* 2.7 44.3 + - - -
100C ILE* 3.5 21.3 - - - +
105C VAL* 1.4 75.5 + - - +
107C ILE* 1.4 65.6 + - - +
115C TYR* 4.8 2.0 - - - -
130C LEU* 3.4 26.4 - - - +
134C CYS 2.6 24.7 + - - -
135C VAL* 3.8 2.1 - - - +
136C PHE* 5.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU* 4.0 21.8 - - + -
74C LEU* 5.3 0.4 - - + -
76C ILE* 4.1 5.7 - - + +
95C LEU* 3.8 36.3 - - + -
96C GLU 3.5 2.7 - - - +
97C PHE* 4.1 19.7 - - + -
105C VAL* 4.2 17.0 - - + -
106C SER* 1.4 78.5 - - - +
108C ARG* 1.3 63.0 + - - +
109C GLY 3.9 0.3 + - - -
114C LEU 3.9 0.5 - - - +
115C TYR* 3.4 4.9 - - - +
116C LEU* 2.9 58.6 + - + +
134C CYS 4.5 2.0 + - - -
136C PHE* 4.9 5.8 - - + -
148C TYR* 4.5 11.9 - - + -
164C VAL* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C LEU* 3.3 3.5 - - - -
96C GLU* 2.7 62.4 + - + +
98C ILE* 4.5 5.8 - - + -
107C ILE* 1.3 74.8 - - - +
109C GLY* 1.3 70.7 + - - +
110C VAL* 3.2 2.3 + - - +
113C GLY* 3.0 31.9 + - - +
114C LEU 3.6 9.0 - - - +
115C TYR* 3.1 48.1 + - + -
128C GLU 5.2 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C ILE* 3.7 14.5 - - - +
92C PHE* 5.4 1.8 - - - -
94C ILE 3.7 7.4 - - - -
95C LEU* 3.9 11.7 - - - -
108C ARG* 1.3 70.2 - - - +
110C VAL* 1.3 60.5 + - - -
111C ASP 3.4 2.7 - - - -
112C SER* 4.1 9.0 - - - -
113C GLY* 2.7 31.5 + - - -
114C LEU 2.9 17.1 + - - -
----------------------------------------------------------
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