Contacts of the strand formed by residues 145 - 151 (chain B) in PDB entry 1A4J
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 GLY 145 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LEU* 2.8 42.2 + - - +
144B LEU* 1.3 79.2 - - - +
146B CYS* 1.3 63.6 + - - -
160B TRP* 3.5 13.8 - - - -
186B SER 3.0 13.9 - - - -
187B VAL* 3.9 0.7 - - - -
217B VAL* 3.8 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B VAL* 4.1 10.3 - - + -
128B PHE 3.4 8.5 - - - +
129B PRO* 4.8 1.1 - - - -
130B LEU* 3.8 5.1 - - - +
145B GLY* 1.3 78.6 - - - -
147B LEU* 1.3 60.1 + - - +
148B VAL* 3.9 4.3 + - + +
158B VAL* 5.7 0.4 - - + -
160B TRP* 3.8 3.3 - - + -
185B SER* 3.3 4.2 - - - -
186B SER* 2.8 36.2 + - - +
202B CYS* 2.0 53.4 - - + -
204B VAL* 5.2 2.5 - - + -
215B LYS* 4.2 3.4 - - - -
217B VAL* 3.8 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLN* 4.4 11.0 - - - +
136A SER* 3.5 33.9 - - - +
138A VAL* 4.9 10.5 - - + -
183A THR* 5.3 8.3 - - + +
126B SER 3.1 6.6 - - - +
127B VAL* 3.4 2.3 - - - -
128B PHE* 2.7 45.3 + - + +
130B LEU* 3.6 19.2 - - + +
146B CYS* 1.3 71.6 - - - +
148B VAL* 1.3 59.3 + - - +
149B LYS* 4.2 10.3 - - + -
183B SER* 3.7 19.7 - - - +
184B LEU* 3.5 20.2 - - - +
185B SER* 4.4 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B PRO* 3.7 16.2 - - + -
126B SER 3.5 5.4 - - - -
127B VAL* 4.6 5.2 - - + +
146B CYS* 4.4 8.5 - - + +
147B LEU* 1.3 71.0 - - - +
149B LYS* 1.3 60.2 + - - +
151B TYR* 3.4 27.4 - - + -
156B VAL* 4.1 13.0 - - + -
158B VAL* 4.2 16.2 - - + -
183B SER* 3.4 3.1 - - - -
184B LEU* 2.8 56.4 + - + +
186B SER* 5.2 0.7 - - - +
204B VAL* 4.1 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLN* 3.7 24.0 - - - +
134A THR* 4.3 18.5 - - - +
136A SER* 3.6 16.3 + - - +
185A THR* 3.6 15.2 - - - +
125B PRO* 3.4 1.6 - - - +
126B SER* 2.9 34.7 + - - +
128B PHE* 4.6 12.3 - - + -
147B LEU* 3.6 13.9 + - + -
148B VAL* 1.3 76.0 - - - +
150B ASP* 1.3 94.8 + - - +
151B TYR 3.6 1.8 - - - -
177B GLN* 3.2 21.5 - - - +
183B SER* 3.4 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A THR* 5.6 0.2 + - - -
123B LYS* 2.8 34.2 + - - +
124B GLY 3.4 1.9 - - - +
126B SER* 5.3 2.6 + - - +
149B LYS* 1.3 101.6 - - - +
151B TYR* 1.3 57.9 + - - +
177B GLN* 2.5 31.2 + - - +
179B SER* 4.7 1.9 + - - -
181B LEU* 3.7 28.5 - - + +
182B TYR 2.8 13.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LYS* 3.2 15.5 - - - +
125B PRO* 3.5 22.4 - - + -
148B VAL* 3.4 42.8 - - + -
150B ASP* 1.3 76.7 - - - +
152B PHE* 1.3 67.0 + - - +
153B PRO 3.8 15.9 - - - -
154B GLU* 3.4 16.4 + - - -
156B VAL* 4.0 15.9 - - + +
174B ALA* 3.1 27.9 - - - +
181B LEU* 3.8 2.5 - - - -
182B TYR* 2.8 56.8 + + + +
183B SER* 4.0 2.7 - - - -
184B LEU* 3.3 12.9 - - + +
206B HIS* 4.0 8.3 - + - +
----------------------------------------------------------
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