Contacts of the strand formed by residues 234 - 239 (chain I) in PDB entry 3VD1
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 GLN 234 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178I MET* 3.8 4.3 - - - +
179I PRO* 3.7 23.6 - - - +
190I VAL* 4.5 4.9 - - + +
191I VAL 4.9 7.8 + - - +
192I LYS* 4.0 21.0 - - + +
212I SER* 2.7 39.2 + - - +
213I HIS* 3.2 37.8 + - + +
214I LEU 5.8 0.4 - - - +
226I VAL 3.3 4.0 - - - -
227I ASP* 2.5 30.7 + - - +
232I GLY 3.7 12.5 + - - +
233I ARG* 1.3 71.9 - - - +
235I SER* 1.3 60.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 235 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176I ARG* 3.8 39.4 + - - -
177I ALA 4.0 8.5 - - - -
178I MET* 4.3 11.8 - - - +
213I HIS* 3.4 6.3 - - - -
215I ILE 5.6 0.2 - - - -
225I TYR* 3.0 5.9 - - - -
226I VAL* 2.6 47.2 + - - +
233I ARG 4.1 4.5 + - - -
234I GLN* 1.3 76.1 - - - +
236I VAL* 1.3 60.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 236 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175I ILE 3.7 1.0 - - - +
176I ARG* 3.0 1.0 - - - -
177I ALA* 2.8 57.6 + - + +
215I ILE* 3.5 23.3 - - + +
217I VAL* 3.4 25.6 - - + -
223I SER* 4.6 1.1 - - - -
224I GLN 3.1 8.5 - - - +
225I TYR* 3.4 36.1 - - + -
235I SER* 1.3 75.2 - - - +
237I VAL* 1.3 65.2 + - - +
238I VAL* 5.2 0.8 - - + +
254I TYR* 4.4 6.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 237 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174I ALA* 3.3 31.0 - - + -
175I ILE 3.3 14.4 - - - +
176I ARG* 3.1 40.6 - - + +
222I LEU 4.1 0.9 - - - +
223I SER* 3.2 2.1 - - - -
224I GLN* 2.8 45.3 + - + +
226I VAL* 4.4 13.2 - - + -
236I VAL* 1.3 74.6 - - - +
238I VAL* 1.3 84.1 + - - +
278I GLU* 5.0 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 238 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174I ALA* 3.5 0.8 - - - -
175I ILE* 2.9 38.0 + - + +
217I VAL* 4.0 18.8 - - + -
220I ASN* 3.5 20.2 - - - +
222I LEU 4.4 0.2 - - - -
223I SER* 3.5 22.0 - - - -
236I VAL* 5.2 0.2 - - + -
237I VAL* 1.3 92.5 - - - +
239I PRO* 1.3 74.1 - - - +
240I TYR 3.3 0.2 + - - -
252I ILE* 3.8 31.2 - - + -
254I TYR* 5.2 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 239 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173I THR 3.8 8.7 - - - +
174I ALA* 4.4 3.1 - - + -
220I ASN* 4.2 2.8 + - - +
222I LEU* 3.5 53.8 - - + +
238I VAL* 1.3 92.3 - - + +
240I TYR* 1.3 64.6 + - - +
241I GLU* 3.4 17.2 + - + +
----------------------------------------------------------
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