Contacts of the helix formed by residues 97 - 107 (chain B) in PDB entry 3C0M
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 ASP 97 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B GLY* 1.3 72.7 - - - -
98B GLU* 1.3 68.9 + - - +
99B VAL* 3.3 9.6 - - + -
100B ASP* 2.7 35.2 + - - +
101B VAL* 3.0 9.1 + - - -
233B TYR* 4.0 11.9 - - - +
234B GLY* 3.1 23.0 + - - +
235B LEU 4.2 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B GLY 3.7 2.0 + - - -
97B ASP* 1.3 69.7 - - - +
99B VAL* 1.3 65.4 + - + +
101B VAL* 3.0 5.3 + - - +
102B GLN* 2.9 35.8 + - - +
144B ARG* 5.2 5.1 + - - -
175B PHE* 5.0 0.9 - - - +
177B TYR* 2.7 33.1 + - - +
234B GLY 4.5 2.6 - - - +
235B LEU* 3.9 28.1 - - + +
238B LYS* 3.0 46.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ASP* 4.4 9.6 - - + +
98B GLU* 1.3 77.5 - - + +
100B ASP* 1.3 69.8 + - - +
102B GLN* 3.2 8.8 + - - +
103B TRP* 2.7 37.5 + - - +
144B ARG* 3.5 33.9 - - - +
149B TRP* 4.3 8.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ASP* 2.7 38.0 + - - +
99B VAL* 1.3 80.7 - - - +
101B VAL* 1.3 60.6 + - - +
103B TRP* 3.4 9.9 + - - +
104B ARG* 3.1 52.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 4.1 24.8 - - + +
94B PRO 4.1 17.3 - - - +
95B ASP* 5.0 0.7 - - - -
96B GLY* 3.8 22.2 - - - +
97B ASP 3.0 4.9 + - - +
98B GLU* 3.4 7.2 - - - +
100B ASP* 1.3 74.7 - - - +
102B GLN* 1.3 70.8 + - + +
104B ARG* 3.3 10.6 + - - +
105B LEU* 3.4 12.3 + - - +
177B TYR* 5.2 5.4 - - + -
235B LEU* 3.7 33.7 - - + -
312B VAL* 5.2 7.4 - - + -
398B ALA* 4.3 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLU* 2.9 32.3 + - - +
99B VAL* 3.7 6.0 - - - +
101B VAL* 1.3 80.3 - - + +
103B TRP* 1.3 62.6 + - - +
105B LEU* 3.2 6.1 + - - +
106B VAL* 2.9 28.1 + - - +
144B ARG* 2.8 18.1 + - - +
147B ASP 3.5 7.5 + - - +
149B TRP* 2.8 31.1 + - + +
175B PHE* 3.6 41.1 - - + +
177B TYR* 3.1 24.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL 2.7 21.4 + - - +
100B ASP* 3.7 11.7 - - - +
102B GLN* 1.3 73.1 - - - +
104B ARG* 1.3 66.4 + - + +
106B VAL* 4.8 1.8 - - + -
107B HIS* 2.8 84.4 + + + +
142B VAL* 3.6 37.5 - - + -
149B TRP* 3.7 30.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 4.0 20.0 - - + +
94B PRO* 2.7 49.4 + - - +
95B ASP 3.3 18.2 + - - -
96B GLY* 4.2 5.2 - - - +
100B ASP* 3.1 39.2 + - - +
101B VAL* 3.8 5.8 - - - +
102B GLN 3.3 0.2 - - - -
103B TRP* 1.3 84.1 - - + +
105B LEU* 1.3 61.1 + - - +
107B HIS* 4.7 1.1 - - - -
108B ASP* 3.6 19.1 + - - +
233B TYR* 6.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 4.7 14.1 - - + -
93B ILE* 3.9 15.2 - - + +
101B VAL 3.4 5.6 + - - +
102B GLN* 3.2 8.0 + - - +
103B TRP 3.1 0.8 - - - -
104B ARG* 1.3 78.1 - - - +
106B VAL* 1.3 64.3 + - + +
108B ASP* 3.1 12.7 - - + +
111B ASN 5.4 2.0 - - - +
112B PHE* 3.1 46.5 - - + +
172B VAL* 6.1 0.2 - - + -
175B PHE* 4.3 17.5 - - + -
312B VAL* 4.5 4.0 - - + -
314B TYR* 3.8 30.3 - - + +
396B VAL* 4.1 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B GLN 2.9 18.7 + - - +
103B TRP* 4.2 2.7 - - + +
105B LEU* 1.3 77.5 - - + +
107B HIS* 1.3 57.4 + - - +
108B ASP 3.1 8.6 + - - -
112B PHE* 3.4 18.8 - - + -
113B ILE* 3.3 19.8 - - - +
142B VAL* 3.7 26.9 - - + +
149B TRP* 4.1 26.0 - - + -
151B ILE* 3.9 20.1 - - + +
172B VAL* 4.2 21.5 - - + -
175B PHE* 4.6 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B TRP* 2.8 72.6 + + + +
104B ARG* 4.7 1.6 - - - -
106B VAL* 1.3 73.2 - - - +
108B ASP* 1.3 61.0 + - - +
109B SER* 3.3 4.0 + - - -
113B ILE* 3.8 12.7 - - + +
142B VAL* 3.9 15.0 - - + -
----------------------------------------------------------
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