Contacts of the strand formed by residues 201 - 210 (chain H) 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 GLN 201 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136H GLU* 4.7 3.2 + - + +
137H TYR 3.3 18.8 - - - +
138H THR* 3.7 14.8 + - - +
195H ALA* 3.9 1.2 - - - +
196H GLU* 2.9 39.9 + - + +
197H VAL 3.9 0.5 + - - -
198H MET* 3.1 50.3 + - + +
199H PRO 3.2 0.2 - - - -
200H ALA* 1.3 76.1 + - - +
202H TRP* 1.3 72.2 + - - +
242H PRO* 5.7 0.8 - - - +
248H ASN* 3.9 12.6 + - - +
249H GLY 3.0 34.1 + - - -
250H ALA* 3.8 11.7 - - - +
601H P3S 4.4 2.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 202 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136H GLU* 3.3 6.6 - - - +
137H TYR* 2.9 53.1 + - + +
139H LEU* 3.9 15.1 - - + +
170H ALA* 4.2 6.5 - - + -
171H TYR 2.9 41.6 + - - +
172H GLY 4.4 0.7 - - - -
173H ARG* 4.0 47.6 - - + -
176H VAL* 3.2 36.1 - - + -
194H ASN* 3.7 8.1 - - - -
195H ALA* 3.5 40.8 - - + -
196H GLU* 4.1 5.3 - - - +
200H ALA* 3.5 16.2 - - - +
201H GLN* 1.3 80.6 + - - +
203H GLU* 1.3 64.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 203 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134H GLU* 3.0 11.9 - - + +
135H GLN 3.5 10.8 - - - +
136H GLU* 4.1 6.1 - - + -
137H TYR* 3.9 4.6 + - - -
176H VAL* 5.3 1.4 - - - +
193H THR* 3.1 9.5 - - - +
194H ASN* 2.9 48.8 + - - +
196H GLU* 2.9 7.6 - - + +
202H TRP* 1.3 82.6 - - - +
204H PHE* 1.3 67.0 + - - +
205H GLN* 2.6 18.8 + - - +
401H MN 2.0 35.5 + - - -
403H MN 2.3 25.2 + - - -
501H ADP 3.0 0.2 + - - -
601H P3S 3.0 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 204 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133H MET 3.8 0.5 - - - +
135H GLN* 2.8 69.7 + - + -
137H TYR* 3.6 24.2 - + - +
179H HIS* 3.7 31.2 - + + +
190H ILE* 4.1 8.3 - - + -
192H GLY 3.5 10.3 - - - +
193H THR* 3.8 11.2 - - + -
203H GLU* 1.3 75.5 - - - +
205H GLN* 1.3 61.4 + - - +
206H ILE* 3.7 33.4 - - + -
218H LEU* 4.2 4.0 - - + -
221H ALA* 3.8 22.4 - - + -
222H ARG* 4.7 4.0 - - - -
225H LEU* 4.1 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 205 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G LYS* 6.1 0.5 - - - +
44G THR 4.5 1.6 - - - +
60G TRP* 5.1 6.1 - - - -
133H MET 3.4 4.3 - - - -
134H GLU* 4.1 6.7 - - + -
190H ILE* 3.5 3.6 - - - +
191H ALA* 2.9 26.4 + - + -
192H GLY* 3.1 37.6 + - - +
193H THR* 3.5 2.3 + - - +
194H ASN* 3.2 15.6 + - - -
203H GLU* 2.6 35.4 + - - +
204H PHE* 1.3 75.0 - - - +
206H ILE* 1.3 69.7 + - - +
501H ADP 3.3 46.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 206 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132H GLY* 3.4 1.7 - - - -
133H MET 2.9 31.1 + - - +
183H CYS* 5.4 0.4 - - - -
188H VAL* 3.8 17.7 - - + -
189H LYS 3.3 5.6 - - - +
190H ILE* 3.7 21.5 - - + -
204H PHE* 3.7 30.7 - - + -
205H GLN* 1.3 83.7 - - - +
207H GLY* 1.3 59.3 + - - +
209H CYS* 4.0 3.8 - - - -
214H MET* 3.3 27.2 - - + +
217H HIS* 4.0 22.2 - - + -
218H LEU* 4.1 11.9 - - + +
221H ALA* 4.1 7.0 - - + -
501H ADP 4.0 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 207 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H PHE 3.8 2.9 - - - -
189H LYS* 2.9 25.5 + - - +
191H ALA* 3.6 16.2 - - - +
205H GLN 4.1 0.8 - - - -
206H ILE* 1.3 74.5 - - - +
208H PRO* 1.3 77.3 - - - +
209H CYS* 3.8 6.5 - - - -
501H ADP 3.6 10.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 208 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H TRP* 4.0 30.2 - - + -
131H PHE 3.2 8.1 - - - +
189H LYS* 3.1 29.5 - - - +
191H ALA* 5.4 0.2 - - + -
207H GLY* 1.3 83.9 - - - +
209H CYS* 1.3 61.2 + - - +
210H GLU 4.2 0.5 + - - -
501H ADP 3.5 45.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 209 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H TRP* 3.5 2.4 - - - -
131H PHE* 2.7 35.9 + - - +
189H LYS* 4.3 11.4 - - - -
206H ILE* 4.0 27.4 - - - -
207H GLY* 4.1 5.6 - - - -
208H PRO* 1.3 78.3 - - - +
210H GLU* 1.3 63.9 + - - +
211H GLY 3.5 1.0 + - - -
213H SER* 3.7 18.2 - - - +
214H MET* 3.5 27.1 - - + +
217H HIS* 4.0 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 210 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H SER* 3.9 6.6 - - - +
128H HIS* 2.7 46.1 + - - +
129H PRO* 3.2 17.1 - - + +
130H TRP* 3.6 21.5 + - + +
208H PRO 4.2 0.8 + - - -
209H CYS* 1.3 70.1 - - - +
211H GLY* 1.3 70.8 + - - +
212H ILE 3.5 0.3 + - - -
213H SER* 2.8 29.2 + - - +
----------------------------------------------------------
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