Contacts of the strand formed by residues 136 - 143 (chain A) in PDB entry 5A19
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 GLY 136 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLN* 1.3 83.0 - - - +
137A LEU* 1.3 64.6 + - - -
138A MET* 3.5 17.1 - - - +
291A ASP* 5.1 3.1 - - - -
319A SER* 3.2 5.3 - - - -
320A TYR* 2.9 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLY* 1.3 78.1 - - - +
138A MET* 1.3 72.3 + - - +
139A PHE* 3.8 9.4 - - + -
277A HIS 4.7 0.9 - - - +
278A GLY* 3.3 50.0 + - - +
280A GLY 5.2 0.9 + - - -
291A ASP* 4.9 2.8 - - - +
317A GLN* 3.5 27.6 - - - +
318A VAL 3.3 11.0 - - - +
319A SER* 4.3 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLN 4.9 0.9 - - - +
136A GLY* 3.5 25.4 - - - +
137A LEU* 1.3 80.0 - - - +
139A PHE* 1.3 66.5 + - - +
278A GLY* 4.7 2.7 - - - +
290A VAL* 3.5 43.7 - - + +
291A ASP* 3.7 31.0 - - - +
295A ALA* 4.0 19.5 - - + +
298A ALA* 5.1 0.4 - - - +
316A VAL 3.8 0.2 - - - +
317A GLN* 3.3 4.9 - - - +
318A VAL* 2.8 46.2 + - + +
320A TYR* 3.7 26.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 3.8 11.4 - - + -
138A MET* 1.3 75.4 - - - +
140A GLY* 1.3 59.5 + - - +
270A THR* 6.1 0.3 - - - +
271A TYR* 4.1 10.9 - - + -
276A ALA* 3.4 39.6 - - + +
277A HIS* 3.4 36.8 - - - +
278A GLY 3.6 3.2 - - - +
295A ALA* 4.3 15.3 - - - +
298A ALA* 4.0 5.2 - - - -
315A LEU* 3.9 22.9 - - + -
316A VAL 3.1 13.7 - - - +
317A GLN* 3.2 44.0 - - + -
333A PHE* 5.2 3.8 - + - -
380A PHE* 5.6 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A PHE* 1.3 74.4 - - - +
141A TYR* 1.3 59.5 - - - -
271A TYR* 3.7 7.4 - - - -
298A ALA* 3.5 29.6 - - - +
299A ARG 3.7 0.4 - - - -
302A ALA* 4.0 6.3 - - - -
314A VAL 3.9 0.2 - - - +
315A LEU* 3.4 8.5 - - - +
316A VAL 2.8 33.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLY* 1.3 74.6 - - - +
142A ALA* 1.3 63.7 + - - +
143A THR* 3.7 27.7 - - + +
145A GLU* 4.9 1.0 + - - -
151A PRO* 4.0 13.7 - - + -
195A VAL* 5.3 0.2 - - - +
271A TYR* 3.2 49.6 + + + -
274A TRP* 3.8 16.0 - + + -
275A GLY* 3.8 21.5 - - - -
299A ARG* 2.8 23.9 + - - +
302A ALA* 3.6 5.5 - - - +
313A ARG* 2.9 35.8 + - + +
314A VAL 3.3 20.6 - - - -
315A LEU* 4.3 7.0 - - + -
335A TYR* 3.8 26.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A TYR* 1.3 82.4 - - - +
143A THR* 1.3 63.1 + - - +
149A CYS* 3.5 13.0 - - + +
299A ARG* 3.6 11.4 - - - +
302A ALA* 3.6 29.1 - - + +
303A LYS* 3.8 5.8 - - - +
306A VAL* 3.8 11.4 - - + +
313A ARG* 3.3 5.4 - - - +
314A VAL* 3.0 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A TYR* 3.7 27.1 - - + -
142A ALA* 1.3 76.3 - - - +
144A ASP* 1.3 62.0 + - - +
145A GLU* 2.6 35.6 + - - +
146A THR 3.9 0.3 - - - +
149A CYS* 3.0 29.4 + - - +
150A MET* 3.4 32.0 + - - +
151A PRO* 3.5 5.4 - - + -
195A VAL* 4.2 6.1 + - - +
306A VAL* 4.7 0.7 - - - -
312A ARG 3.5 6.0 + - - -
313A ARG* 4.2 6.1 - - - +
----------------------------------------------------------
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