Contacts of the strand formed by residues 130 - 140 (chain E) in PDB entry 2QC8
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 TRP 130 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128E HIS* 3.4 10.3 - - - +
129E PRO* 1.3 79.1 - - - +
131E PHE* 1.3 62.3 + - - +
208E PRO* 4.1 26.0 - - + -
209E CYS 3.5 2.5 - - - +
210E GLU* 3.0 35.1 + - + +
256E PHE* 3.4 6.8 - - - -
257E SER 2.8 30.0 + - - +
262E ARG* 3.3 52.0 - - - +
501E ADP 3.4 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 131 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E MET* 3.6 28.7 - - + -
129E PRO* 4.3 9.4 - - + -
130E TRP* 1.3 74.2 - - - +
132E GLY* 1.3 58.9 + - - +
207E GLY* 3.7 0.3 - - - -
208E PRO* 3.1 2.9 - - - +
209E CYS 2.7 39.7 + - - -
211E GLY 4.0 7.0 - - - -
214E MET* 3.3 40.3 - - + +
254E THR* 4.0 15.9 - - + -
255E ASN 3.2 10.8 - - - +
256E PHE* 3.2 36.8 - + - -
352E THR* 3.7 30.7 - - + -
355E LEU* 3.9 16.4 - - + -
356E ILE* 4.0 6.5 - - + -
501E ADP 3.9 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 132 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131E PHE* 1.3 74.4 - - - +
133E MET* 1.3 60.4 + - - -
206E ILE 3.3 8.7 - - - -
207E GLY* 4.2 1.1 - - - -
255E ASN* 2.7 46.8 + - - -
501E ADP 3.5 30.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 133 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E GLY* 1.3 77.5 - - - -
134E GLU* 1.3 62.0 + - - +
135E GLN* 3.7 3.3 + - - +
204E PHE 3.8 0.3 - - - +
205E GLN* 3.4 2.0 - - - -
206E ILE* 2.8 33.7 + - - +
214E MET* 3.6 40.4 - - + -
218E LEU* 3.7 15.1 - - + +
252E CYS* 3.7 25.6 - - - -
253E HIS 3.3 3.6 - - - +
254E THR* 3.5 35.2 - - + +
346E CYS* 4.1 9.6 - - - -
348E PRO* 3.8 26.5 - - + -
351E VAL* 4.4 5.8 - - + -
352E THR* 4.3 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 134 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E MET* 1.3 73.7 - - - +
135E GLN* 1.3 60.7 + - - +
136E GLU* 3.2 8.2 + - + +
203E GLU* 2.9 12.4 - - - +
204E PHE 3.6 5.8 - - - -
205E GLN* 4.0 3.8 - - + +
251E GLY 3.2 2.3 - - - +
252E CYS* 3.1 23.6 - - - -
253E HIS* 3.0 21.2 + - + +
255E ASN* 3.1 20.2 + - - +
338E GLU* 3.2 3.5 - - - +
402E MN 2.4 30.5 + - - -
403E MN 2.2 29.1 + - - -
501E ADP 2.6 33.2 + - - +
601E P3S 3.0 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 135 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E MET 3.7 2.2 + - - -
134E GLU* 1.3 69.9 - - - +
136E GLU* 1.3 86.6 + - - +
137E TYR* 3.5 4.3 - - + -
203E GLU* 3.3 3.6 - - - -
204E PHE* 2.8 68.2 + - + -
218E LEU* 4.1 10.5 - - + +
222E ARG* 2.8 37.3 + - - +
238E PHE* 3.8 19.8 - - + -
251E GLY 4.3 0.2 + - - -
252E CYS* 4.0 8.6 - - - +
344E ALA* 3.0 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 136 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134E GLU* 3.2 7.9 + - + +
135E GLN* 1.3 94.1 + - - +
137E TYR* 1.3 62.2 + - - +
196E GLU* 3.1 17.4 - - + -
201E GLN* 5.0 4.5 - - - +
202E TRP 3.3 7.9 - - - +
203E GLU* 3.9 9.6 - - + +
238E PHE* 4.1 0.3 - - - -
249E GLY 4.9 0.2 - - - -
250E ALA* 3.8 6.4 - - + -
251E GLY* 3.0 36.8 + - - +
253E HIS* 4.9 4.0 - - + -
344E ALA* 3.5 9.8 - - - +
401E MN 2.1 39.5 + - - +
601E P3S 2.6 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 137 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135E GLN* 3.5 13.7 - - + -
136E GLU* 1.3 76.5 - - - +
138E THR* 1.3 73.0 + - - +
139E LEU* 3.9 22.4 - - + +
175E ILE* 4.5 1.4 - - - +
176E VAL* 3.6 20.8 - - - +
179E HIS* 5.6 0.9 + - - -
201E GLN* 3.2 6.4 - - - +
202E TRP* 2.9 63.7 + - + +
203E GLU* 3.8 4.7 - - - -
204E PHE* 3.7 24.7 - + - -
225E LEU* 3.7 34.2 - - + +
236E ALA* 4.4 6.3 - - + -
237E THR 3.4 15.7 - - - +
238E PHE* 3.6 15.5 - - + +
250E ALA* 4.6 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 138 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137E TYR* 1.3 80.6 + - - +
139E LEU* 1.3 75.6 + - - +
140E MET* 4.7 4.3 - - - -
146E PRO* 4.6 4.9 - - + -
198E MET* 3.0 36.9 - - + +
200E ALA* 3.6 14.4 - - + +
201E GLN* 3.6 12.1 + - - +
235E ILE 3.6 1.0 - - - +
236E ALA* 3.7 1.0 - - - -
237E THR* 3.1 47.2 + - + +
239E ASP 5.5 0.2 + - - -
242E PRO* 3.7 13.0 - - + +
250E ALA* 4.9 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 139 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137E TYR* 3.9 23.5 + - + -
138E THR* 1.3 79.3 - - - +
140E MET* 1.3 59.3 + - - +
146E PRO* 3.5 6.2 - - - +
147E PHE* 2.9 32.3 + - + +
171E TYR 3.9 6.5 - - - +
172E GLY* 3.7 37.2 - - - +
175E ILE* 4.1 19.1 - - + -
176E VAL* 5.4 0.2 - - + -
200E ALA* 2.9 18.6 + - + +
202E TRP* 4.0 10.3 - - + -
229E CYS* 3.7 30.1 - - - -
234E VAL* 4.3 6.7 - - + -
235E ILE 3.4 6.1 - - - +
236E ALA* 4.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 140 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138E THR* 3.9 5.2 - - - +
139E LEU* 1.3 76.4 - - - +
141E GLY* 1.3 70.3 + - - +
144E GLY* 3.2 28.5 - - - +
145E HIS 3.7 2.9 - - - +
146E PRO* 3.9 24.7 - - + -
147E PHE* 3.8 4.5 - - - +
234E VAL* 3.5 6.3 - - - +
235E ILE* 2.8 48.7 + - + +
237E THR* 3.8 35.2 - - + +
242E PRO* 4.7 15.7 - - + +
243E ILE* 5.4 2.7 - - + -
----------------------------------------------------------
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