Contacts of the strand formed by residues 138 - 142 (chain C) in PDB entry 4IXU
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 138 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C ASP 3.7 0.2 + - - -
137C LEU* 1.3 75.1 - - - +
139C VAL* 1.3 59.8 + - - +
140C VAL 4.3 0.2 - - - -
192C SER 3.4 12.8 - - - +
238C LEU* 3.8 34.3 - - + -
239C ILE* 4.3 11.2 - - - -
244C ARG* 4.0 20.2 - - - +
245C PRO 2.9 10.0 + - - -
246C ILE* 3.6 28.0 - - - -
247C HIS* 2.8 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C ILE* 4.2 18.8 - - + -
137C LEU* 3.6 20.0 - - + -
138C CYS* 1.3 78.4 - - - +
140C VAL* 1.3 71.9 + - - +
141C TRP* 4.0 27.4 - - + -
188C ILE* 4.1 17.7 - - + -
192C SER 2.8 12.9 + - - +
193C ILE* 3.2 16.8 - - + -
194C VAL 2.9 25.8 + - - +
238C LEU* 3.8 4.3 - - - +
247C HIS* 3.3 15.3 - - + +
249C SER* 4.7 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C CYS 4.3 0.4 - - - -
139C VAL* 1.3 75.0 - - - +
141C TRP* 1.3 61.6 + - - +
142C VAL* 3.9 5.8 - - + -
194C VAL 3.5 5.2 - - - +
196C ILE* 3.8 28.9 - - + -
231C MET* 5.2 1.8 - - + -
234C THR* 4.1 12.3 - - + -
235C PHE* 4.8 4.0 - - + -
238C LEU* 3.7 20.9 - - + -
246C ILE* 4.2 10.1 - - + -
247C HIS 2.9 7.8 + - - +
248C LEU* 3.5 24.8 - - + +
249C SER 2.9 26.3 + - - -
279C ILE* 5.3 0.4 - - + -
283C ILE* 4.2 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C HIS* 3.2 29.6 - + - -
123C ALA* 3.6 13.9 - - + -
127C ILE* 3.8 24.5 - - + -
139C VAL* 3.9 12.7 - - + -
140C VAL* 1.3 71.4 - - - +
142C VAL* 1.3 61.1 + - - +
143C ASP* 3.1 35.5 + - + +
145C HIS 4.1 0.4 + - - -
147C ASP* 3.4 26.1 + - + +
163C PRO* 3.7 10.1 - - + -
164C VAL* 3.6 28.5 - - + -
167C LEU* 4.9 1.8 - - + -
193C ILE* 4.0 10.8 - - + -
194C VAL 2.9 11.7 + - - +
195C TYR* 3.2 32.4 - + + +
196C ILE 2.9 24.3 + - - +
249C SER* 3.5 19.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C VAL* 3.9 11.4 - - + -
141C TRP* 1.3 73.2 - - - +
143C ASP* 1.3 62.3 + - - +
196C ILE* 3.3 17.0 - - + +
248C LEU* 3.7 26.9 - - + -
249C SER 2.9 9.5 + - - +
250C PHE* 3.6 33.7 - - + -
251C ASP* 2.8 30.5 + - - +
254C ALA* 3.6 15.3 - - + -
271C LEU* 3.9 9.9 - - + -
279C ILE* 4.2 16.6 - - + -
----------------------------------------------------------
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