Contacts of the strand formed by residues 304 - 309 (chain M) in PDB entry 6D6Q
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 304 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114M VAL* 3.3 6.8 - - - +
115M ALA* 2.9 36.2 + - - +
156M SER* 3.6 25.8 - - - -
157M VAL* 4.0 8.1 - - - -
158M LEU* 4.3 3.8 - - - -
281M PHE* 5.2 4.0 - - - -
292M PHE* 6.2 0.2 - - - -
293M ALA* 4.6 20.9 - - + +
296M ILE* 4.5 23.6 - - + -
302M GLN 3.8 2.0 + - - +
303M PRO* 1.3 77.5 - - - +
305M HIS* 1.3 87.0 + - - +
306M VAL* 5.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 305 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112M HIS* 3.1 23.3 + + + +
113M GLU 3.7 2.2 - - - -
114M VAL* 3.0 32.1 - - + +
122M TYR* 4.6 9.0 - + - -
125M LEU* 4.0 17.6 - - + +
150M CYS* 3.1 34.6 - - - -
155M GLN* 2.4 32.8 + - + -
156M SER 3.2 7.5 + - - -
157M VAL* 3.9 9.4 - - + -
158M LEU* 2.9 23.1 + - - +
303M PRO* 5.4 2.6 - - - +
304M CYS* 1.3 84.6 - - - +
306M VAL* 1.3 70.3 + - - +
307M ILE* 5.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 306 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111M THR* 3.6 1.5 - - + +
112M HIS* 3.2 8.3 - - - -
113M GLU* 2.8 52.0 + - + +
114M VAL* 5.5 0.4 - - - -
158M LEU* 3.5 14.4 - - + -
289M ALA* 3.7 31.9 - - + +
290M ARG* 5.4 4.5 - - + +
293M ALA* 3.5 30.1 - - + -
304M CYS 5.2 0.2 - - - +
305M HIS* 1.3 82.5 - - - +
307M ILE* 1.3 70.9 - - - +
308M TYR* 4.9 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 307 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110M CYS* 4.6 8.3 - - + -
111M THR 3.4 3.8 - - - +
112M HIS* 3.2 44.2 - - + +
143M PHE* 3.2 44.4 - - + +
146M GLU* 3.6 19.5 - - + +
147M ALA* 4.9 10.5 - - + +
157M VAL* 4.5 12.3 - - + -
158M LEU 2.9 16.0 + - - +
159M VAL* 3.7 7.6 - - + -
160M SER* 2.9 28.8 + - - +
306M VAL* 1.3 76.6 - - - +
308M TYR* 1.3 63.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 308 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110M CYS* 3.4 1.4 - - - +
111M THR* 2.8 53.3 + - + +
160M SER* 3.3 35.4 - - - -
285M THR* 3.9 31.8 - - + +
286M ILE 4.0 15.1 + - - -
287M PRO* 5.9 2.0 - - + -
289M ALA* 5.9 2.5 - - + -
306M VAL* 5.1 7.2 - - + -
307M ILE* 1.3 75.3 - - - +
309M THR* 1.3 77.2 + - - +
310M ASP* 4.7 9.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 309 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109M GLY 2.6 30.3 + - - +
110M CYS* 3.8 5.2 - - - +
143M PHE* 3.5 22.2 - - + -
160M SER 3.5 2.5 + - - +
161M ALA* 3.5 37.1 - - + -
162M HIS* 4.2 5.2 + - - -
165M ALA* 6.1 1.1 - - + -
285M THR* 4.6 3.6 - - - +
308M TYR* 1.3 88.8 - - - +
310M ASP* 1.3 58.9 + - - +
311M TYR* 3.1 23.9 + - + +
----------------------------------------------------------
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