Contacts of the helix formed by residues 154 - 165 (chain C) in PDB entry 4CYM
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 154 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C LYS* 5.2 0.2 - - - -
153C GLN* 1.3 74.6 - - - +
155C PRO* 1.3 71.9 - - - +
156C SER* 2.6 29.3 + - - -
157C GLN* 2.9 37.5 + - - +
158C VAL* 3.2 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C LYS* 4.7 8.0 - - - +
153C GLN 4.0 4.9 - - - +
154C SER* 1.3 83.1 - - - +
156C SER* 1.3 57.1 + - - +
158C VAL* 3.2 5.1 + - + +
159C ASP* 2.8 38.2 + - - +
170C TRP* 3.7 29.6 - - + -
172C GLU* 5.4 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLY 5.7 4.9 - - - -
154C SER* 2.6 25.4 + - - -
155C PRO* 1.3 76.1 - - - +
157C GLN* 1.3 58.3 + - - +
159C ASP* 3.4 13.5 + - - +
160C GLN* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 157 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C SER 4.6 4.3 + - - +
153C GLN* 3.9 19.5 - - + +
154C SER* 2.9 41.5 + - - +
156C SER* 1.3 73.1 - - - +
158C VAL* 1.3 61.4 + - - +
160C GLN* 3.1 8.0 + - - +
161C PHE* 2.8 28.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
106C PHE* 5.5 5.4 - - + -
114C PHE* 5.0 6.1 - - + -
140C LEU* 4.5 11.0 - - + -
149C LYS* 5.8 3.1 - - - +
153C GLN* 3.4 30.1 - - + +
154C SER 3.2 13.6 + - - +
155C PRO 3.5 6.7 - - - +
157C GLN* 1.3 73.4 - - - +
159C ASP* 1.3 65.7 + - - +
161C PHE* 3.4 7.9 - - - +
162C CYS* 3.0 27.7 + - - -
170C TRP* 3.2 50.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 159 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C PRO* 2.8 30.3 + - - +
156C SER* 3.4 14.3 - - - +
158C VAL* 1.3 73.4 - - - +
160C GLN* 1.3 63.6 + - - +
162C CYS* 3.5 2.8 + - - +
163C LYS* 3.3 27.8 + - + +
170C TRP* 2.8 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 160 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C SER 3.1 13.7 + - - +
157C GLN* 3.1 11.2 + - - +
159C ASP* 1.3 72.6 - - - +
161C PHE* 1.3 67.7 + - - +
163C LYS* 3.0 30.0 + - - +
164C GLU* 2.9 48.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 161 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C PHE* 3.7 35.9 - + + -
117C VAL* 3.7 32.5 - - + -
118C LEU* 3.9 26.7 - - + -
140C LEU* 4.1 16.8 - - + -
157C GLN 2.8 17.3 + - - +
158C VAL* 3.4 13.0 - - - +
160C GLN* 1.3 72.1 - - - +
162C CYS* 1.3 66.2 + - - +
164C GLU* 3.0 5.4 + - - -
165C HIS* 2.9 52.4 + + - +
167C PHE* 4.0 15.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 162 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C LEU* 4.1 14.6 - - - -
158C VAL 3.0 21.4 + - - +
159C ASP* 3.8 6.3 - - - +
161C PHE* 1.3 76.9 - - - +
163C LYS* 1.3 64.6 + - + +
165C HIS 3.3 0.2 + - - -
166C GLY* 3.1 6.1 + - - -
167C PHE* 2.9 51.7 + - + +
169C GLY* 3.5 24.9 - - - +
170C TRP* 3.7 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 163 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A SER* 5.2 7.9 + - - -
164A GLU 6.2 0.2 - - - +
165A HIS* 5.7 8.5 - - + +
159C ASP* 3.4 14.8 - - + +
160C GLN* 3.0 30.1 + - - +
162C CYS* 1.3 78.8 - - + +
164C GLU* 1.3 62.8 + - - +
165C HIS 3.4 0.5 + - - -
166C GLY* 3.9 5.7 + - - -
167C PHE 5.0 2.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
160C GLN* 2.9 37.2 + - - +
161C PHE* 3.5 10.1 - - - +
163C LYS* 1.3 79.1 - - - +
165C HIS* 1.3 82.4 + - + +
166C GLY 3.7 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C LEU* 3.4 30.3 - - + +
121C LYS* 3.3 22.5 + - + +
161C PHE* 2.9 53.9 + + - +
162C CYS 3.6 0.4 - - - -
164C GLU* 1.3 104.1 + - + +
166C GLY* 1.3 65.4 + - - +
167C PHE* 3.2 18.7 + - + -
----------------------------------------------------------
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