Contacts of the strand formed by residues 200 - 205 (chain H) in PDB entry 2VDK
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 THR 200 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160H TRP* 3.6 11.1 - - - -
161H ASN* 2.9 36.7 + - - -
198H SER* 3.9 10.0 + - - -
199H ILE* 1.3 75.3 - - - +
201H CYS* 1.3 71.3 + - - +
202H ASN* 3.8 12.0 - - - +
213H ASP* 3.9 10.5 - - + -
214H LYS 3.5 24.2 - - - +
215H LYS* 3.6 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 201 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127H VAL* 4.4 1.2 - - - +
146H CYS* 2.0 53.4 - - + -
158H LEU* 4.1 10.1 - - - -
159H THR 4.0 3.1 - - - -
160H TRP* 4.0 15.1 - - + -
200H THR* 1.3 69.2 - - - +
202H ASN* 1.3 69.6 + - - +
203H VAL* 4.0 14.1 - - - -
212H VAL 3.6 0.9 - - - +
213H ASP* 3.2 3.1 - - - -
214H LYS* 2.7 44.5 + - + +
216H ILE* 4.9 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 202 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157H THR 3.4 2.3 - - - +
158H LEU* 3.2 6.9 - - - -
159H THR* 2.9 45.0 + - - +
161H ASN* 3.4 7.8 + - - +
162H SER* 2.5 44.0 + - - +
200H THR* 3.8 13.0 + - - +
201H CYS* 1.3 80.3 + - - +
203H VAL* 1.3 61.3 + - - +
212H VAL 3.6 3.8 - - - -
213H ASP* 2.8 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 203 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H PRO* 4.2 12.6 - - + -
127H VAL* 3.8 36.8 - - + -
148H VAL* 3.6 38.8 - - + -
156H VAL* 4.4 9.0 - - + -
157H THR 3.6 2.9 - - - +
158H LEU* 3.9 14.6 - - + -
201H CYS* 4.0 3.6 - - - -
202H ASN* 1.3 77.1 - - - +
204H ALA* 1.3 67.8 + - - +
205H HIS 4.5 0.2 + - - -
210H THR 4.1 0.5 - - - +
211H LYS* 3.4 2.6 - - - +
212H VAL* 2.9 38.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 204 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156H VAL* 3.2 9.7 - - - +
157H THR* 3.0 47.4 + - - +
203H VAL* 1.3 75.5 - - - +
205H HIS* 1.3 59.2 + - - +
206H PRO* 3.7 7.6 - - + +
210H THR 3.4 4.5 - - - +
211H LYS* 4.0 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 205 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122H THR* 4.4 0.2 - - + -
123H THR 3.7 11.4 - - - -
125H PRO* 3.7 20.4 - - + +
151H TYR* 3.9 6.4 - + - -
152H PHE 3.3 23.1 + - - -
153H PRO 2.8 24.3 + - - -
155H PRO 3.5 19.5 - - - -
156H VAL* 3.7 12.1 - - + -
204H ALA* 1.3 73.6 - - - +
206H PRO* 1.4 66.8 - - - +
207H ALA* 3.0 20.9 + - + +
208H SER* 2.6 36.5 + - - -
209H SER 3.2 8.7 + - - -
210H THR* 3.0 25.9 + - - +
----------------------------------------------------------
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