Contacts of the strand formed by residues 185 - 190 (chain A) in PDB entry 1DVM
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 HIS 185 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A SER 2.8 23.1 + - - +
184A THR* 1.3 76.9 - - - +
186A ARG* 1.3 81.9 + - - +
187A ARG* 3.4 29.6 + - - +
200A PRO* 3.5 3.2 - - - +
201A MET* 2.8 39.2 + - + +
203A ALA* 3.9 19.5 - - + -
274A VAL* 4.2 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A HIS* 1.3 87.7 - - - +
187A ARG* 1.3 67.1 + - - +
198A SER* 2.8 45.7 + - - +
199A VAL 3.4 20.2 - - - -
200A PRO* 3.5 24.1 - - - +
207D LYS* 6.0 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A HIS* 3.4 21.8 + - - +
186A ARG* 1.3 77.0 - - - +
188A LEU* 1.3 70.9 + - - +
189A PHE 3.6 0.3 + - - -
198A SER* 4.5 2.9 + - - -
199A VAL* 3.0 32.9 + - - +
201A MET* 3.5 31.2 - - + -
274A VAL* 3.3 40.2 - - - +
351A GLU* 4.3 7.9 + - - -
353A ILE* 3.7 29.4 - - + +
355A ASP* 5.6 0.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ARG* 1.3 80.1 - - - +
189A PHE* 1.3 58.9 + - - +
190A HIS* 4.8 7.6 + - + +
196A THR* 3.9 30.3 - - + +
197A VAL* 3.4 22.7 - - - +
198A SER* 3.9 11.7 - - - +
201A MET* 3.7 2.6 - - - +
355A ASP* 3.4 20.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LEU* 1.3 73.9 - - - +
190A HIS* 1.3 70.8 + - - +
191A LYS* 3.4 5.4 + - + -
196A THR* 3.0 26.0 - - - -
197A VAL* 3.0 19.3 + - + +
199A VAL* 3.8 15.5 - - + -
201A MET* 3.6 12.3 - - + -
276A PRO* 3.6 14.6 - - + -
354A ILE 3.4 16.4 - - - -
355A ASP* 3.5 13.5 - - - -
356A ARG 3.3 32.5 - - - -
357A PRO* 3.8 6.1 - - + -
358A PHE* 4.2 9.2 - + - -
376A VAL 4.2 1.1 - - - -
377A MET 3.2 26.7 - - - -
378A GLU* 4.5 2.0 - - - -
379A PRO* 3.3 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LEU* 4.8 8.2 + - + +
189A PHE* 1.3 75.0 - - - +
191A LYS* 1.3 61.5 + - - +
194A GLY 6.1 0.4 - - - +
195A SER 3.9 3.6 - - - -
196A THR* 3.2 25.8 - - + +
243A LYS* 4.4 28.5 + - + +
355A ASP* 2.7 37.9 + - - +
356A ARG* 3.4 8.1 - - + +
357A PRO* 2.9 26.5 - - - +
----------------------------------------------------------
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