Contacts of the strand formed by residues 148 - 153 (chain C) in PDB entry 3DGG
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 ASN 148 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C ASP* 4.1 9.4 + - - +
147C ILE* 1.3 80.6 - - - +
149C VAL* 1.3 66.6 + - - +
150C LYS* 4.3 7.9 - - - -
199C ALA* 3.4 7.6 - - - +
200C THR* 2.9 57.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C CYS* 5.4 1.6 - - - -
139C LEU* 3.3 22.7 - - + -
147C ILE* 4.8 0.9 - - + -
148C ASN* 1.3 78.5 - - - +
150C LYS* 1.3 64.2 - - - +
151C TRP* 4.1 14.4 - - + +
164C ASN* 4.4 5.8 - - - +
178C MET* 3.3 41.1 - - + -
180C SER* 3.2 30.3 - - - +
197C CYS* 5.0 6.3 - - + -
198C GLU 3.5 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C ASN* 4.8 7.6 - - - +
149C VAL* 1.3 77.9 - - - +
151C TRP* 1.3 65.7 + - - +
152C LYS* 5.0 4.9 - - + +
157C GLU* 4.6 21.1 + - + +
196C THR 3.9 0.3 - - - +
197C CYS* 3.4 2.4 - - - +
198C GLU* 2.8 72.1 + - + +
200C THR* 3.4 26.3 + - - +
207C PRO* 5.3 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 151 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C ILE* 4.1 11.0 - - + -
135C VAL* 3.5 47.8 - - + -
136C VAL 4.2 0.4 - - - -
137C CYS* 3.5 32.1 - - + -
149C VAL* 4.1 6.8 - - + +
150C LYS* 1.3 78.1 - - - +
152C LYS* 1.3 69.9 + - - +
157C GLU* 3.4 6.2 - - - +
158C ARG* 3.1 43.6 + - + +
162C VAL* 4.0 24.2 - - + +
180C SER* 3.0 36.5 + - - -
182C LEU* 3.9 26.8 - - + +
195C TYR* 4.9 2.7 - - + -
196C THR 3.3 20.2 - - - -
197C CYS* 4.0 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C LYS* 5.0 5.2 - - + +
151C TRP* 1.3 81.1 - - - +
153C ILE* 1.3 69.4 + - - +
154C ASP 4.2 0.2 - - - -
155C GLY* 3.4 32.4 + - - +
156C SER 3.2 12.6 - - - +
157C GLU* 3.8 23.8 + - + +
194C SER 4.7 0.2 - - - -
195C TYR* 3.6 2.4 - - - +
196C THR* 2.7 49.2 + - + +
198C GLU* 3.4 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C LYS* 1.3 78.8 - - - +
154C ASP* 1.3 71.5 + - - +
156C SER* 2.9 25.4 + - - +
158C ARG* 3.6 48.5 - - + +
182C LEU* 3.9 17.3 - - + -
184C LEU* 4.4 4.7 - - + -
192C HIS* 3.3 45.9 - - + +
194C SER 3.5 8.3 - - - +
195C TYR* 3.9 21.1 - - + -
----------------------------------------------------------
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