Contacts of the strand formed by residues 108 - 113 (chain B) in PDB entry 1G83
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 LYS 108 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 5.2 6.7 - - + -
87B PHE 3.3 9.2 - - - +
88B VAL* 4.6 8.5 - - + +
106B GLY 4.0 12.2 + - - +
107B GLU* 1.3 82.7 - - - +
109B PHE* 1.3 74.2 + - - +
125B LEU* 3.0 44.4 + - + +
126B THR* 4.6 3.8 + - - -
141B VAL* 4.8 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 3.7 11.6 - - - +
87B PHE* 3.0 40.4 + - + +
89B ALA* 4.2 13.5 - - + -
101B LEU* 3.7 26.2 - - + -
103B PHE* 3.7 31.0 - + + -
107B GLU* 3.7 37.0 - - + -
108B LYS* 1.3 77.5 - - - +
110B GLN* 1.3 67.8 + - - +
111B ILE* 4.9 5.8 - - + -
122B ALA* 4.2 12.8 - - + -
123B ARG 3.1 10.8 - - - +
124B SER* 3.6 16.2 - - - -
125B LEU* 4.1 7.3 - - - +
133B ILE* 5.0 6.3 - - + -
138B VAL* 4.5 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B THR 5.2 1.3 - - - -
86B LEU* 4.4 15.9 - - + +
109B PHE* 1.3 75.6 - - - +
111B ILE* 1.3 61.1 + - - +
112B LEU* 3.8 15.1 - - + +
122B ALA* 3.3 2.9 - - - +
123B ARG* 2.6 79.4 + - + +
125B LEU* 4.1 16.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B THR 5.1 4.8 + - - +
87B PHE* 3.7 43.5 - - + -
109B PHE* 4.9 2.7 - - + -
110B GLN* 1.3 76.0 - - - +
112B LEU* 1.3 66.7 + - - +
113B ASN 3.8 9.4 - - - +
114B SER* 3.8 26.9 - - - +
120B TRP* 4.0 19.7 - - + -
121B GLU 3.5 10.1 - - - +
122B ALA* 4.0 14.6 - - + -
133B ILE* 4.6 6.7 - - + -
138B VAL* 5.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B GLN* 3.8 26.5 - - + +
111B ILE* 1.3 78.7 - - - +
113B ASN* 1.3 60.3 + - - +
121B GLU* 2.7 26.1 + - + +
122B ALA* 4.3 8.1 - - - -
123B ARG* 4.3 15.5 - - + +
130B THR* 3.6 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ILE* 3.5 3.6 - - - -
112B LEU* 1.3 80.3 - - - +
114B SER* 1.3 61.8 + - - +
115B SER* 2.8 27.3 + - - -
116B GLU* 2.5 33.0 + - - +
119B TRP 4.5 0.9 - - - +
120B TRP* 3.2 5.5 - - - +
121B GLU* 2.6 52.3 + - + +
132B TYR* 4.7 1.4 + - - -
----------------------------------------------------------
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