Contacts of the strand formed by residues 141 - 146 (chain B) in PDB entry 4IBU
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 CYS 141 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B CYS* 3.7 6.7 - - - -
133B MET* 3.6 22.7 - - + -
135B CYS* 3.5 39.9 - - - -
139B LYS 3.5 15.0 - - - -
140B THR* 1.3 74.2 - - - +
142B PRO* 1.3 67.0 - - - +
143B VAL* 3.4 4.0 + - - +
232B ILE 3.5 0.2 - - - +
234B TYR* 2.8 45.7 + - + +
236B TYR* 3.9 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLY 4.7 0.9 - - - +
113B PHE* 4.3 11.3 - - - +
114B LEU* 3.7 26.4 + - + -
124B CYS* 4.2 11.7 - - + -
133B MET* 4.2 7.6 - - - +
140B THR* 3.5 15.3 - - + +
141B CYS* 1.3 84.5 - - - +
143B VAL* 1.3 64.4 + - - +
144B GLN* 4.2 2.7 - - + -
231B THR* 4.0 5.2 - - + -
232B ILE 3.5 6.5 - - - +
233B HIS* 4.1 5.4 - - + -
302B EDO 3.3 35.4 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
111B LEU* 3.9 29.8 - - + -
112B GLY 4.0 2.9 - - - +
113B PHE* 4.3 13.9 - - + -
133B MET* 4.0 18.2 - - + -
141B CYS 3.9 3.6 - - - +
142B PRO* 1.3 79.0 - - - +
144B GLN* 1.3 65.5 + - - +
145B LEU* 3.9 4.9 + - + +
230B THR 3.6 0.5 - - - +
231B THR* 3.4 2.2 - - - +
232B ILE* 2.8 34.7 + - - +
234B TYR* 3.6 36.6 - - + -
236B TYR* 6.6 0.2 - - + -
255B ILE* 4.9 2.0 - - + -
270B PHE* 4.1 14.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
111B LEU* 3.3 12.8 - - - +
112B GLY* 2.9 46.5 + - - +
113B PHE* 3.9 7.9 + - - +
114B LEU* 3.5 31.2 - - + +
142B PRO* 5.5 1.8 - - + -
143B VAL* 1.3 72.8 - - - +
145B LEU* 1.3 61.1 + - - +
146B TRP* 2.9 32.2 + - - +
229B CYS* 3.8 18.1 - - - -
230B THR 3.4 4.5 - - - -
231B THR* 3.7 19.5 + - + +
302B EDO 5.2 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B PHE* 3.9 21.8 - - + -
110B ARG 3.9 2.7 - - - -
111B LEU* 3.8 22.9 - - + -
143B VAL* 4.8 6.7 - - + +
144B GLN* 1.3 74.7 - - - +
146B TRP* 1.3 60.7 + - - +
147B VAL* 4.3 2.2 + - + +
157B VAL* 3.6 39.3 - - + -
220B TYR* 4.1 20.3 + - + -
223B PRO* 5.4 0.5 - - - +
229B CYS* 3.3 5.5 - - - +
230B THR* 2.6 51.8 + - + +
232B ILE* 3.8 21.3 - - + -
234B TYR* 5.7 0.4 - - + +
255B ILE* 4.3 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B GLY 3.3 1.4 - - - +
109B PHE* 3.4 0.5 - - - -
110B ARG* 2.9 74.5 + - + +
111B LEU 4.1 2.0 - - - -
112B GLY* 3.7 24.8 - - - -
144B GLN* 2.9 34.3 + - + +
145B LEU* 1.3 77.4 - - - +
147B VAL* 1.3 68.4 + - - +
228B ASP* 3.5 45.5 - - + -
229B CYS* 3.5 16.4 - - + -
----------------------------------------------------------
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