Contacts of the helix formed by residues 153 - 164 (chain C) in PDB entry 4DOH
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 GLU 153 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C LEU* 1.3 70.8 - - - +
154C PRO* 1.3 76.3 - - + -
155C GLN 3.4 1.3 - - - +
156C ALA* 2.8 26.8 + - + +
157C ALA 2.9 10.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 154 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C PHE* 5.4 0.8 - - + -
152C LEU 3.3 7.5 - - - +
153C GLU* 1.3 83.3 - - + -
155C GLN* 1.3 63.5 + - - +
157C ALA* 3.0 16.9 + - + +
158C VAL* 3.2 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ASN* 3.0 25.9 + - - +
98C TYR* 4.4 1.2 - - - -
99C GLN* 3.4 51.1 + - + +
153C GLU* 3.2 2.6 + - - +
154C PRO* 1.3 79.3 - - + +
156C ALA* 1.3 58.9 + - - +
158C VAL* 3.5 12.6 - - - +
159C VAL* 2.9 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ASP* 4.7 4.0 - - - +
59C ASN* 4.4 16.8 - - - +
152C LEU* 4.7 5.4 - - + +
153C GLU* 2.8 24.1 + - + +
155C GLN* 1.3 76.0 - - - +
157C ALA* 1.3 61.2 + - - +
159C VAL* 3.9 6.5 - - - +
160C LYS* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 157 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ILE* 4.1 0.9 - - - +
149C PHE* 3.3 47.2 - - + +
152C LEU* 3.9 19.7 - - + +
153C GLU 2.9 9.8 + - - +
154C PRO* 3.0 10.3 + - + +
156C ALA* 1.3 76.0 - - - +
158C VAL* 1.3 60.0 + - - +
160C LYS* 3.4 1.6 + - - +
161C ALA* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 158 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ARG 3.3 25.1 - - - +
94C VAL* 3.7 20.1 - - - +
97C ASN* 3.9 20.2 - - + +
98C TYR* 4.0 13.9 - - + -
149C PHE* 4.4 6.3 - - + -
154C PRO 3.2 16.2 + - - +
155C GLN* 3.5 30.5 - - - +
157C ALA* 1.3 74.0 - - - +
159C VAL* 1.3 69.5 + - + +
161C ALA 3.3 0.5 + - - -
162C LEU* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 159 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C VAL* 3.7 18.0 - - - +
56C LYS* 3.6 42.8 - - + +
57C ASP* 4.1 7.1 - - - +
98C TYR* 3.9 22.7 - - + -
155C GLN* 2.9 43.7 + - + +
156C ALA* 3.9 6.5 - - - +
158C VAL* 1.3 78.6 - - - +
160C LYS* 1.3 61.1 + - - +
162C LEU 3.5 0.2 + - - -
163C GLY* 3.3 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 160 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ASP* 2.7 41.3 + - - +
59C ASN* 3.0 28.7 + - - -
62C ILE* 2.8 29.9 + - - +
64C ILE* 3.4 29.4 - - + -
152C LEU* 3.9 13.2 - - + -
156C ALA 3.0 19.1 + - - +
157C ALA* 3.8 4.5 - - - +
158C VAL 3.3 0.2 - - - -
159C VAL* 1.3 74.9 - - - +
161C ALA* 1.3 66.7 + - - +
163C GLY* 3.4 2.6 + - - -
164C GLU* 3.2 32.2 + - - +
76E TYR* 2.8 14.4 + - - +
128E ARG* 5.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ILE* 4.3 10.1 - - + +
90C TYR* 2.5 36.6 + - + +
94C VAL* 3.6 27.4 - - + -
149C PHE* 3.9 12.3 - - + -
157C ALA 2.9 17.4 + - - +
158C VAL 3.8 0.4 - - - +
160C LYS* 1.3 77.6 - - - +
162C LEU* 1.3 62.3 + - - +
164C GLU* 3.2 10.8 + - - -
165C LEU 3.6 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C PHE* 3.1 29.5 - - + -
49C ILE* 4.7 1.3 - - + -
53C VAL* 3.8 17.9 - - + -
90C TYR* 4.3 4.9 - - - -
94C VAL* 4.1 6.7 - - + -
95C PHE* 4.2 24.0 - - + -
98C TYR* 3.4 38.8 - - + -
109C ILE* 3.8 20.6 - - + -
112C LEU* 4.4 8.1 - - + -
158C VAL 3.0 16.2 + - - +
159C VAL 3.9 4.0 - - - +
160C LYS 3.2 0.2 - - - -
161C ALA* 1.3 77.3 - - - +
163C GLY* 1.3 60.4 + - - +
165C LEU* 3.3 24.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 163 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C PHE* 3.8 9.3 - - - -
53C VAL* 3.7 16.1 - - - +
54C GLN* 3.0 28.3 - - - +
57C ASP* 6.5 0.2 - - - -
159C VAL 3.3 9.1 + - - -
160C LYS* 3.4 4.2 + - - -
161C ALA 3.3 0.6 - - - -
162C LEU* 1.3 79.2 - - - +
164C GLU* 1.3 58.4 + - - +
165C LEU 3.2 1.6 - - - -
166C ASP* 3.0 15.4 - - - +
128E ARG* 3.9 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 164 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ARG* 4.3 2.0 - - - -
64C ILE* 3.1 24.3 + - - +
65C LEU* 3.0 44.1 + - + +
90C TYR* 4.2 1.8 - - - +
160C LYS* 3.2 24.6 + - - +
161C ALA* 3.2 10.7 + - - +
162C LEU 3.1 1.2 - - - -
163C GLY* 1.3 78.9 - - - +
165C LEU* 1.3 63.0 + - - +
166C ASP* 3.2 6.3 - - - -
167C ILE* 3.1 25.6 + - + +
168C LEU 3.3 7.6 + - - -
76E TYR* 2.4 35.8 + - - +
128E ARG* 4.0 7.2 - - - +
----------------------------------------------------------
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