Contacts of the strand formed by residues 146 - 153 (chain E) in PDB entry 4GUN
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 ALA 146 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E GLN* 4.2 3.8 - - - +
111E GLN* 3.5 19.1 - - - +
138E VAL 3.8 0.5 - - - +
139E LYS* 3.7 0.4 - - - -
140E ASN* 2.9 28.4 + - - +
143E ASN* 3.4 36.2 + - - +
144E GLY 3.3 1.6 - - - -
145E GLY* 1.3 76.7 - - - +
147E LEU* 1.3 62.5 + - - +
148E ASP* 5.2 1.2 - - - +
111G GLN* 4.2 7.4 - - - +
143G ASN* 5.2 0.4 - - - +
146G ALA* 4.5 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E LEU* 4.0 10.1 - - + -
107E GLN* 3.9 26.2 - - + -
108E ILE* 3.7 33.0 - - + +
111E GLN* 2.8 13.8 + - - +
112E TYR* 3.4 22.0 + - + +
118E LEU* 4.9 3.6 - - + -
137E ILE* 4.4 9.0 - - + -
138E VAL 3.2 22.4 - - - +
139E LYS* 4.2 1.1 - - - -
146E ALA* 1.3 74.3 - - - +
148E ASP* 1.3 56.2 + - - +
166E ILE* 4.3 5.8 - - + -
204E TYR* 3.6 29.2 - - + -
143G ASN* 2.8 30.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 148 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E TYR* 3.6 6.8 + - - -
137E ILE* 3.5 5.1 - - - +
138E VAL* 2.9 44.4 + - + +
140E ASN* 6.5 1.3 - - + -
146E ALA 5.2 0.9 - - - +
147E LEU* 1.3 76.8 - - - +
149E VAL* 1.3 83.6 + - - +
150E VAL* 5.4 3.3 - - - +
140G ASN* 2.9 30.6 + - - -
142G GLN* 4.9 5.0 + - - +
143G ASN* 4.1 3.8 + - - +
148G ASP* 4.8 10.8 - - - +
162G HIS* 5.4 0.7 - - - -
163G LEU* 6.0 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 149 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E TYR* 4.2 4.2 + - - +
118E LEU* 3.7 17.7 - - + -
121E ILE* 3.7 24.9 - - + -
122E THR* 3.7 39.0 - - + +
125E LYS* 3.3 39.3 + - + -
135E ALA* 5.0 1.3 - - + -
136E PHE 3.3 12.8 - - - +
137E ILE* 4.5 2.9 - - + -
148E ASP* 1.3 91.5 + - - +
150E VAL* 1.3 65.3 + - - +
142G GLN* 5.4 3.4 + - - +
162G HIS* 5.8 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 150 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E LYS* 4.2 4.3 - - - +
135E ALA* 3.3 4.2 - - - +
136E PHE* 2.8 36.4 + - + +
138E VAL* 3.8 23.6 - - + -
148E ASP* 5.4 3.6 - - - +
149E VAL* 1.3 73.8 - - - +
151E THR* 1.3 84.0 + - - +
152E THR* 5.2 1.3 - - + -
158E ILE* 3.6 30.5 - - + -
163E LEU* 6.3 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 151 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E LYS* 3.7 48.5 + - + +
129E ILE* 3.7 22.6 - - + +
134E TRP 3.1 10.3 - - - +
135E ALA* 4.3 3.4 - - + -
136E PHE 4.9 0.2 - - - +
150E VAL* 1.3 89.5 - - - +
152E THR* 1.3 69.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 152 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E ILE* 4.8 3.3 - - - +
133E GLY* 3.2 3.6 - - - -
134E TRP* 2.9 35.7 + - - +
136E PHE* 3.4 29.9 - - + -
150E VAL* 5.2 1.6 - - + -
151E THR* 1.3 82.6 - - - +
153E ALA* 1.3 59.8 + - - +
156E ASP* 2.7 40.3 + - + +
157E THR 4.3 5.4 - - - +
158E ILE* 4.2 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E ILE* 5.9 0.7 - - - -
130E GLN 5.9 1.6 - - - +
132E SER 3.5 8.3 - - - +
152E THR* 1.3 74.7 - - - +
154E ASN* 1.4 77.8 - - - +
155E GLN 3.2 0.2 + - - -
156E ASP* 3.0 34.9 + - - +
154H ASN* 5.8 5.8 - - - +
----------------------------------------------------------
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