Contacts of the helix formed by residues 89 - 99 (chain B) in PDB entry 2CUY
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 SER 89 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLY* 5.3 1.8 - - - -
9B GLN* 5.1 9.9 + - - -
87B GLY 3.3 0.6 + - - -
88B HIS* 1.3 79.3 + - - +
90B LEU* 1.3 71.4 + - - +
92B GLU* 3.1 9.9 + - - +
93B TRP* 3.8 3.6 - - - -
114B ARG* 2.9 18.7 + - - -
118B MET* 5.2 0.5 - - - +
194B HIS* 2.7 32.7 + - - -
224B ASN* 2.8 20.5 + - - -
243B GLN* 3.1 26.0 + - - +
248B VAL* 4.4 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PRO 3.8 12.1 - - - +
8B GLY* 4.2 9.0 - - - -
9B GLN* 4.7 5.2 - - + +
60B GLN* 3.7 42.2 - - + +
63B LEU* 3.8 21.1 - - + -
64B LEU* 4.1 2.9 - - + +
88B HIS 2.8 1.2 + - - -
89B SER* 1.3 82.5 + - - +
91B GLY* 1.3 65.9 + - - +
93B TRP* 3.0 21.1 + - + +
94B THR* 3.5 16.3 + - - +
111B VAL* 3.6 37.9 - - + -
114B ARG* 4.1 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PHE* 3.4 24.6 - - - +
7B PRO 3.5 10.0 + - - -
87B GLY* 3.1 13.8 - - - -
88B HIS 2.9 8.8 + - - -
90B LEU* 1.3 83.2 - - - +
92B GLU* 1.3 62.4 + - - +
94B THR* 3.0 9.0 + - - -
95B ALA 2.9 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLY* 3.3 19.6 - - - +
89B SER 3.1 14.3 + - - +
90B LEU 3.1 0.2 + - - -
91B GLY* 1.3 76.4 - - - +
93B TRP* 1.3 61.9 + - - +
95B ALA* 3.3 3.8 + - - +
96B HIS* 3.1 42.6 + - + -
221B VAL* 4.6 1.1 - - + -
222B TYR 3.4 19.8 - - - +
223B SER* 3.5 16.8 + - - -
224B ASN* 2.8 29.5 + - - -
236B ILE* 6.0 0.2 - - - +
239B LEU* 4.9 3.5 - - - +
240B LEU* 3.6 21.6 + - + +
243B GLN* 3.0 20.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 3.9 15.7 - - + -
89B SER 3.8 11.7 - - - -
90B LEU* 3.0 16.3 + - - +
92B GLU* 1.3 80.3 - - - +
94B THR* 1.3 61.4 + - - +
96B HIS* 3.1 10.1 + - - +
97B VAL* 3.1 25.5 + - - +
102B LEU* 4.2 20.1 - - + +
107B ALA* 4.9 2.7 - - + -
110B LEU* 3.7 33.4 - - + -
111B VAL* 3.8 17.3 - - + -
114B ARG* 3.3 28.0 - - - +
205B LEU* 3.7 32.3 - - + -
209B LEU* 4.0 21.5 - - + -
240B LEU* 3.9 42.3 + - + +
243B GLN* 4.4 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PHE* 3.2 34.0 - - + +
7B PRO 4.8 0.7 + - - -
63B LEU 4.3 1.1 + - - +
64B LEU* 3.4 36.4 - - + +
67B GLY* 4.0 4.3 - - - -
68B TYR* 3.8 23.6 - - + +
90B LEU* 3.6 15.4 - - - +
91B GLY* 3.0 10.0 + - - -
93B TRP* 1.3 77.5 - - - +
95B ALA* 1.3 63.2 + - - +
97B VAL* 3.2 5.9 + - - +
98B ALA* 3.0 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PHE* 3.6 28.9 - - + -
85B ALA* 4.3 7.4 - - + -
86B ALA 4.1 13.7 - - - -
91B GLY 2.9 10.5 + - - +
92B GLU 3.5 9.4 - - - +
94B THR* 1.3 77.6 - - - +
96B HIS* 1.3 57.4 + - - +
98B ALA* 3.3 2.4 + - - +
99B ALA* 2.9 29.9 + - - +
219B PHE* 4.1 2.1 - - - -
221B VAL* 3.9 18.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B GLU* 3.1 40.8 + - + +
93B TRP* 3.1 9.8 + - + +
95B ALA* 1.3 76.9 - - - +
97B VAL* 1.3 57.7 + - - +
99B ALA* 3.4 2.0 + - - -
100B GLY 3.0 6.6 + - - -
101B THR* 2.8 59.6 + - + +
102B LEU* 3.8 11.7 - - + -
217B PRO* 5.0 0.9 - - + -
221B VAL* 3.3 37.0 + - + +
222B TYR 4.8 0.2 + - - -
230B GLU* 4.9 1.9 - - - +
236B ILE* 3.6 43.0 - - + +
240B LEU* 4.4 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 4.5 8.1 - - + -
68B TYR* 3.8 37.1 + - + -
93B TRP 3.1 12.7 + - - +
94B THR* 3.2 8.7 + - - +
96B HIS* 1.3 73.6 - - - +
98B ALA* 1.3 67.9 + - - +
100B GLY* 3.0 13.2 + - - -
102B LEU* 3.6 20.5 - - + +
103B GLU 4.4 0.4 - - - +
104B LEU* 4.0 23.6 - - + +
107B ALA* 3.3 34.5 - - + -
218B ARG* 5.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PHE* 3.8 18.8 - - + -
68B TYR* 3.8 17.0 - - + -
71B TYR* 3.6 33.5 - - + -
94B THR 3.0 12.8 + - - +
95B ALA 3.6 7.2 - - - +
97B VAL* 1.3 77.1 - - - +
99B ALA* 1.3 60.5 + - - +
100B GLY 3.5 0.5 + - - -
218B ARG* 5.0 5.7 + - - -
219B PHE* 3.5 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ALA 2.9 18.9 + - - +
96B HIS 3.7 4.7 - - - +
97B VAL 3.1 0.4 - - - -
98B ALA* 1.3 78.3 - - - +
100B GLY* 1.3 58.8 + - - +
101B THR* 4.1 0.2 - - - +
217B PRO* 3.6 15.4 - - + +
218B ARG* 2.9 37.0 + - - +
219B PHE* 3.3 28.9 - - + +
221B VAL* 3.6 16.2 - - + -
----------------------------------------------------------
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