Contacts of the helix formed by residues 95 - 104 (chain B) in PDB entry 2CX9
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 LEU 95 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B SER* 2.9 37.9 + - - +
94B SER* 1.3 78.2 - - - +
96B ALA* 1.3 59.0 + - - +
99B HIS* 2.7 38.6 + - - +
125B TRP* 3.3 49.8 - - + +
160B THR* 5.4 4.9 - - - +
244B VAL* 3.9 20.4 - - + +
245B LEU* 4.7 4.9 - - + -
248B GLY* 4.8 0.7 - - - -
369B GLU* 3.7 33.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B SER 4.0 2.8 + - - -
92B HIS 4.3 2.5 - - - +
95B LEU* 1.3 79.8 - - - +
97B THR* 1.3 63.3 + - - +
100B ILE* 3.2 31.3 + - - +
116B LEU* 4.8 3.1 - - + -
123B GLY* 3.6 39.3 - - - +
124B ALA 3.7 15.3 - - - +
125B TRP* 3.7 10.2 - - - +
167B VAL* 4.9 2.0 - - + +
169B VAL* 3.8 10.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PHE 5.0 4.3 - - - +
57B VAL* 3.5 32.3 - - + -
92B HIS* 2.8 41.0 + - - -
93B ASN* 3.5 12.3 - - - +
96B ALA* 1.3 76.7 - - - +
98B GLY* 1.3 59.3 - - - +
100B ILE* 3.1 4.2 + - - +
101B LEU* 2.8 29.2 + - + +
113B LEU* 4.0 11.1 - - + +
116B LEU* 3.7 24.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 6.6 0.2 - - - -
93B ASN 2.8 21.6 + - - -
94B SER* 3.6 11.9 - - - -
95B LEU 3.5 1.0 + - - -
96B ALA 3.4 0.4 - - - -
97B THR* 1.3 75.3 - - - +
99B HIS* 1.3 57.6 + - - +
101B LEU* 3.4 11.2 + - - +
102B LEU* 2.9 31.2 + - - +
244B VAL* 4.6 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B SER 4.1 1.0 + - - -
95B LEU 2.7 23.6 + - - +
96B ALA 3.8 3.4 - - - +
98B GLY* 1.3 72.3 - - - +
100B ILE* 1.3 58.2 - - - +
102B LEU* 3.3 0.6 + - + +
103B ALA* 3.0 35.1 + - + +
125B TRP* 3.0 24.6 + - + +
169B VAL* 3.6 5.4 - - + +
171B MET* 3.8 11.0 - - - -
189B ALA* 3.6 28.4 - - + +
231B LEU* 3.4 22.6 + - + +
237B GLY* 4.6 1.1 + - - -
240B ASP* 3.8 19.1 + - + +
241B VAL* 4.2 16.2 - - + -
244B VAL* 3.7 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ALA 3.2 14.3 + - - +
97B THR 3.1 7.0 + - - +
99B HIS* 1.3 75.7 - - - +
101B LEU* 1.3 57.0 + - - +
104B GLY* 2.9 26.2 + - - -
108B GLN* 4.4 11.4 - - + +
109B LYS* 4.0 6.7 - - - +
112B PHE* 3.7 30.3 - - + -
113B LEU* 3.9 20.2 - - + -
116B LEU* 3.7 21.3 - - + -
167B VAL* 4.0 8.3 - - + -
169B VAL* 3.9 21.3 - - + -
191B ALA* 4.1 7.9 - - + -
231B LEU* 4.1 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 3.6 34.1 - - + +
57B VAL* 4.3 7.4 - - + +
58B PRO* 3.7 25.6 - - + -
61B TYR* 5.5 1.1 - - + -
97B THR* 2.8 17.9 + - + +
98B GLY* 3.7 9.9 - - - +
100B ILE* 1.3 77.3 - - - +
102B LEU* 1.3 63.6 + - - +
109B LYS* 3.6 25.9 + - + +
113B LEU* 4.1 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLY 2.9 18.0 + - - +
99B HIS 3.7 2.7 - - - +
101B LEU* 1.3 81.3 - - - +
103B ALA* 1.3 61.8 + - + +
104B GLY 3.6 1.3 + - - +
109B LYS* 5.5 0.5 - - - -
240B ASP* 3.9 23.8 - - + +
243B ARG* 3.7 55.5 + - + +
244B VAL* 3.9 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B HIS* 3.0 24.5 + - + +
102B LEU* 1.3 74.1 - - - +
104B GLY* 1.3 64.1 + - - +
105B SER 3.8 0.9 + - - -
108B GLN* 4.2 0.9 - - - +
231B LEU* 3.8 6.3 - - + -
232B GLY* 3.8 25.1 + - - -
240B ASP* 3.5 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ILE 2.9 20.8 + - - -
101B LEU 4.5 0.2 - - - -
102B LEU 3.6 1.9 - - - +
103B ALA* 1.3 79.9 - - - +
105B SER* 1.3 68.3 + - - -
106B GLU* 4.9 0.7 - - - +
108B GLN* 3.3 15.9 - - - -
109B LYS* 3.1 19.6 + - - -
231B LEU* 3.5 7.9 - - - +
----------------------------------------------------------
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