Contacts of the strand formed by residues 185 - 190 (chain C) in PDB entry 5DM6
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 ARG 185 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ARG* 5.4 0.4 - - - -
115C GLY 3.6 14.6 + - - -
116C LYS* 3.3 44.5 - - - +
118C VAL* 4.6 19.7 - - + +
141C GLY 4.6 10.1 + - - -
142C LEU* 4.2 21.1 - - + +
146C GLU* 3.3 32.7 + - + -
147C LYS 2.9 7.3 + - - +
148C VAL* 3.5 25.7 - - + -
149C LEU* 3.0 24.8 + - - +
180C ILE 5.5 0.3 - - - +
183C HIS* 4.0 5.0 - - - +
184C ASP* 1.3 77.4 - - + +
186C LEU* 1.3 63.7 + - - +
187C VAL* 5.5 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 186 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C ILE* 4.8 9.2 - - + -
111C ARG* 5.0 9.0 - - + +
116C LYS 3.3 7.1 + - - +
117C LEU* 3.8 26.0 - - + -
118C VAL* 3.2 29.3 + - - +
149C LEU* 3.5 22.9 - - + +
151C VAL* 4.0 17.3 - - + -
175C VAL* 5.7 1.1 - - + -
180C ILE* 4.2 32.1 - - + -
185C ARG* 1.3 76.4 - - - +
187C VAL* 1.3 79.8 + - - +
188C ILE* 3.3 22.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 187 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C VAL* 3.9 16.8 - - + +
120C VAL* 4.8 5.8 - - + -
123C PHE* 3.8 32.3 - - + -
133C PHE* 6.6 0.2 - - + -
136C TRP* 5.0 7.0 - - + -
142C LEU* 4.8 13.2 - - + -
148C VAL* 3.8 21.3 - - + -
149C LEU 2.7 14.5 + - - +
150C LEU* 3.9 18.2 - - + -
151C VAL* 2.8 31.9 + - - +
185C ARG* 5.5 2.2 - - + -
186C LEU* 1.3 74.4 - - - +
188C ILE* 1.3 62.2 + - - +
189C ASP* 3.4 5.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 188 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C ILE* 4.8 5.4 - - + -
117C LEU* 3.4 32.3 - - + -
118C VAL 3.1 34.5 + - - +
119C ALA* 3.5 5.8 - - + +
151C VAL* 3.6 18.2 - - - +
175C VAL* 5.8 1.2 - - - +
186C LEU* 3.3 39.7 - - + +
187C VAL* 1.3 71.6 - - - +
189C ASP* 1.3 64.0 + - - +
190C ALA 3.9 0.7 - - - -
192C ALA* 5.0 7.9 - - - +
193C LEU* 3.7 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 189 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C ALA* 2.9 12.8 - - - -
120C VAL* 2.6 36.7 + - + +
123C PHE* 4.3 12.1 - - + -
151C VAL 3.0 16.1 + - - +
152C THR* 3.0 34.3 - - + +
153C ASP* 4.4 1.9 + - - +
187C VAL 3.8 2.0 - - - -
188C ILE* 1.3 77.3 + - - +
190C ALA* 1.3 75.8 + - - +
191C ALA* 2.8 23.5 + - - +
192C ALA* 3.2 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 190 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ASN* 3.8 17.9 - - - +
119C ALA* 3.6 13.5 - - + -
120C VAL 3.1 26.5 - - - +
121C ASP* 5.0 1.8 - - - +
188C ILE 3.9 0.2 - - - -
189C ASP* 1.3 91.5 + - - +
191C ALA* 1.3 56.4 + - - +
192C ALA 3.1 1.3 - - - -
193C LEU* 2.8 37.9 + - + +
194C GLU* 3.5 13.5 + - + +
----------------------------------------------------------
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