Contacts of the strand formed by residues 142 - 147 (chain B) in PDB entry 3IU3
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 142 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ALA* 1.3 73.7 - - - +
143B VAL* 1.3 65.4 + - - +
144B GLN* 3.9 38.2 + - + +
158B GLU* 5.5 0.2 - - - -
192B GLU* 3.5 3.5 - - - +
193B VAL* 3.5 1.9 - - - +
194B THR* 2.8 64.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B CYS* 4.7 0.7 - - - -
133B LEU* 3.7 35.4 - - + -
141B ALA 4.2 0.6 - - - -
142B LYS* 1.3 82.3 - - - +
144B GLN* 1.3 72.5 + - - +
145B TRP* 4.7 3.4 - - - +
158B GLU* 3.9 22.8 + - - +
172B LEU* 4.0 15.7 - - + -
174B SER* 3.9 22.3 + - - +
191B CYS* 3.6 29.8 - - - -
192B GLU 3.3 3.8 - - - +
193B VAL* 4.6 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LYS* 3.9 34.3 + - + +
143B VAL* 1.3 80.8 - - - +
145B TRP* 1.3 67.8 + - - +
146B LYS* 5.0 3.1 - - - +
151B LEU* 3.4 37.2 - - + +
152B GLN 5.8 0.4 - - - +
190B ALA 3.7 0.5 - - - +
191B CYS* 3.6 4.2 - - - -
192B GLU* 2.8 67.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ILE* 3.8 14.8 - - + -
129B VAL* 3.6 44.2 - - + -
131B CYS* 3.6 25.8 - - + -
143B VAL* 4.7 2.8 - - + +
144B GLN* 1.3 79.0 - - - +
146B LYS* 1.3 67.3 + - - +
147B VAL* 6.1 0.2 - - + -
151B LEU* 3.5 4.8 - - - +
152B GLN* 2.8 47.6 + - + +
156B SER* 3.7 29.4 - - - -
174B SER* 2.8 44.5 + - - -
176B LEU* 3.7 26.7 - - + +
189B TYR* 5.2 2.7 - + + -
190B ALA 3.4 22.9 - - - -
191B CYS* 4.3 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B GLN* 5.0 3.3 - - - +
145B TRP* 1.3 80.3 - - - +
147B VAL* 1.3 64.0 + - - +
148B ASP 4.0 0.9 + - - -
149B ASN* 4.5 17.3 + - + +
150B ALA 3.3 9.0 - - - +
151B LEU* 3.8 34.5 - - + +
188B VAL* 3.7 2.1 - - - +
189B TYR* 3.9 0.2 - - - -
190B ALA* 2.9 49.1 + - + +
192B GLU* 3.0 38.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B TRP* 5.6 0.7 - - + -
146B LYS* 1.3 74.5 - - - +
148B ASP* 1.3 64.9 + - - +
149B ASN 3.1 0.4 - - - -
150B ALA* 2.9 33.3 + - - +
152B GLN* 3.7 26.9 - - + +
176B LEU* 4.2 9.9 - - + -
178B LEU* 5.0 4.0 - - + -
186B HIS* 3.3 46.8 + - + +
188B VAL 3.3 12.6 - - - +
189B TYR* 3.5 31.0 - - + -
----------------------------------------------------------
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