Contacts of the strand formed by residues 136 - 141 (chain M) in PDB entry 5DST
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 136 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113M LYS 3.4 4.4 + - - +
114M VAL* 3.4 14.7 - - + +
115M VAL* 2.9 23.7 + - - +
134M ALA* 4.1 0.2 - - - +
135M LYS* 1.3 93.9 - - + +
137M VAL* 1.3 68.3 + - - +
138M PHE* 4.1 28.2 - - + -
159M ASP 5.1 0.8 + - - -
160M ASN 3.4 21.1 + - - -
161M ILE* 3.0 32.3 + - - +
163M THR* 3.6 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 137 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115M VAL* 3.3 20.2 - - + +
117M ASP* 4.7 1.8 - - + -
126M SER* 3.7 37.5 - - - +
129M ALA* 4.0 4.3 - - + -
130M ALA* 4.0 17.9 - - - +
134M ALA* 3.8 20.4 - - + -
136M LYS* 1.3 81.6 - - - +
138M PHE* 1.3 70.3 + - - +
161M ILE* 3.0 16.1 + - + +
162M ILE* 3.3 12.1 - - + +
163M THR 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 138 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114M VAL* 4.1 23.3 - - + -
115M VAL 2.8 12.1 + - - +
116M LEU* 3.3 9.4 - - + +
117M ASP* 2.7 32.9 + - - +
136M LYS* 4.1 33.7 - - + -
137M VAL* 1.3 82.6 - - - +
139M GLY* 1.3 54.5 + - - +
163M THR* 3.3 11.7 - - + -
165M PHE* 3.7 25.1 - + + -
174M LEU* 4.1 25.6 - - + -
175M PRO* 3.3 32.8 - - + -
176M VAL* 4.1 17.9 - - + -
179M VAL* 4.8 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 139 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117M ASP* 3.5 10.5 - - - -
120M SER* 3.7 20.4 - - - -
126M SER* 4.3 1.9 + - - -
137M VAL 4.1 0.6 - - - -
138M PHE* 1.3 73.7 - - - +
140M ILE* 1.3 59.3 + - - -
162M ILE* 5.0 0.6 - - - +
163M THR 3.0 9.1 + - - -
164M ILE* 3.4 11.0 - - - +
165M PHE* 2.7 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 140 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116M LEU* 3.8 24.9 - - + -
117M ASP 3.1 7.9 + - - +
118M VAL* 5.9 0.7 - - + -
119M GLY* 2.9 26.9 + - - -
120M SER* 3.0 4.9 + - - -
139M GLY* 1.3 76.4 - - - +
141M GLU* 1.3 64.5 + - - +
165M PHE* 3.5 10.1 - - + +
167M GLY 3.3 17.9 - - - +
169M VAL* 3.5 35.4 - - + -
172M VAL* 3.5 31.0 - - + -
174M LEU* 4.3 8.5 - - + -
207M TRP* 4.0 20.4 - - + -
401M SAH 3.9 1.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 141 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119M GLY 3.6 2.1 - - - -
120M SER* 3.4 15.0 - - - +
121M GLY 2.8 21.5 + - - +
140M ILE* 1.3 78.2 - - - +
142M CYS* 1.3 63.3 + - - +
143M SER* 3.0 27.7 + - - +
145M ILE* 3.6 22.0 - - + -
146M SER* 4.0 13.1 - - - +
164M ILE* 4.9 1.3 - - + -
165M PHE 3.2 4.9 + - - +
166M LYS* 3.6 7.6 - - - +
167M GLY 3.0 19.4 + - - -
401M SAH 2.5 56.5 + - - -
----------------------------------------------------------
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