Contacts of the strand formed by residues 148 - 154 (chain I) in PDB entry 6IY6
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 VAL 148 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139I HIS* 4.3 4.5 - - + +
142I LEU* 4.0 14.1 - - + +
143I CYS* 3.6 38.7 - - - +
146I PHE* 3.5 22.9 + - + +
147I ARG* 1.3 72.6 - - - +
149I LEU* 1.3 57.5 - - - +
150I SER* 3.2 14.7 + - - +
181I TYR* 4.3 7.5 - - - -
183I LEU* 3.3 17.3 - - + +
184I GLY 4.7 0.4 - - - -
185I PHE* 3.6 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 149 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601G PO4 5.8 4.3 - - - +
148I VAL* 1.3 66.4 - - - +
150I SER* 1.3 66.4 + - - +
151I THR* 3.9 16.3 + - + -
180I ASP* 6.0 0.2 - - - +
181I TYR* 3.8 50.3 - - + +
183I LEU 3.0 11.5 + - - +
184I GLY* 3.7 6.1 - - - -
185I PHE 3.2 18.8 + - - +
186I THR* 5.4 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 150 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139I HIS* 3.1 37.6 + - - -
143I CYS* 4.8 2.4 - - - -
148I VAL* 3.2 10.4 + - - -
149I LEU* 1.3 76.3 - - - +
151I THR* 1.3 65.6 + - - +
169I PHE* 4.0 17.3 - - - +
185I PHE* 3.3 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 151 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601G PO4 3.8 24.5 + - - +
149I LEU* 4.3 18.9 + - + +
150I SER* 1.3 78.3 - - - +
152I VAL* 1.3 65.0 + - - +
153I HIS* 3.6 18.5 + - - -
169I PHE* 4.3 1.8 - - - -
185I PHE 3.0 4.9 + - - +
186I THR* 3.5 20.3 + - - -
187I LEU* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 152 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342G PRO* 3.2 17.8 - - - +
151I THR* 1.3 70.0 - - - +
153I HIS* 1.3 68.4 + - - +
165I LEU 3.8 2.7 - - - +
166I LEU* 3.2 30.6 - - + +
167I LYS* 5.2 0.9 - - - -
168I CYS* 4.1 11.2 - - - -
169I PHE* 3.3 39.5 - - + +
187I LEU* 3.3 7.6 - - + +
189I TRP* 3.6 33.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 153 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340G LEU* 3.9 26.2 - - + +
342G PRO* 2.8 43.7 + - + +
344G LEU* 4.6 4.3 - - + -
601G PO4 3.5 41.8 + - - -
151I THR* 3.6 10.5 + - - -
152I VAL* 1.3 86.3 + - - +
154I THR* 1.3 64.0 + - - +
166I LEU* 5.6 0.4 - - - -
186I THR* 3.8 21.1 - - + +
187I LEU 3.0 6.3 + - - +
188I ILE* 3.5 14.9 - - + -
189I TRP* 2.9 30.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 154 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339G PHE* 3.8 0.7 - - - +
340G LEU* 3.3 5.5 - - - -
341G GLU* 2.9 49.4 + - + +
342G PRO* 3.8 5.9 - - - +
153I HIS* 1.3 75.2 + - - +
155I HIS* 1.3 72.1 + - - +
158I VAL* 4.1 8.5 - - + +
159I LYS* 5.7 1.1 - - - -
160I SER 5.7 0.7 - - - +
161I VAL* 3.5 31.6 - - + +
166I LEU* 3.1 29.5 - - + +
189I TRP* 3.6 7.2 - - - +
----------------------------------------------------------
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